METHIONINE ADENOSYLTRANSFERASE 4 mediates DNA and … · 31 which encodes methionine adenosyltransferase 4 (MAT4)/S-adenosyl-methionine 32 synthetase 3 that catalyzes the synthesis

1

METHIONINE ADENOSYLTRANSFERASE 4 mediates DNA and histone 1

methylation 2

Jingjing Meng#, Lishuan Wang#, Jingyi Wang, Xiaowen Zhao, Jinkui Cheng, 3

Wenxiang Yu, Dan Jin, Qing Li, and Zhizhong Gong* 4

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological 5

Sciences, China Agricultural University, Beijing 100193, China. 6

#These authors contribute equally to this work. 7

*Corresponding author: 8

Zhizhong Gong 9

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological 10

Sciences, China Agricultural University, Beijing 100193, China. 11

Email: [email protected]; Tel: 86-10-62733733 12

Key words: DNA methylation, histone methylation, gene silencing, Arabidopsis, 13

SAM 14

Author Contributions 15

Z. G conceived the original research plans; J. M. performed most of the experiments; 16

L.W. performed the mutant screening and gene cloning; J. C. provided bioinformatics 17

analysis; X. Z, J. W, D. J, W. Y and Q. L. assisted with some experiments. J. M. and Z. 18

G designed the project and wrote the article with contributions from all the authors. 19

Running title: MAT4 mediates DNA and histone methylation 20

One sentence summary: MAT4 is an essential gene in Arabidopsis that plays key 21

roles in regulating DNA and histone modifications as well as plant growth and 22

development. 23

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Plant Physiology Preview. Published on March 23, 2018, as DOI:10.1104/pp.18.00183

Copyright 2018 by the American Society of Plant Biologists

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2

Abstract 25

DNA and histone methylation co-regulate heterochromatin formation and gene 26

silencing in animals and plants. To identify factors involved in maintaining gene 27

silencing, we conducted a forward genetic screen for mutants that release the silenced 28

transgene Pro35S::NEOMYCIN PHOSPHOTRANSFERASE II in the transgenic 29

Arabidopsis thaliana line L119. We identified MAT4/SAMS3/MTO3/AT3G17390, 30

which encodes methionine adenosyltransferase 4 (MAT4)/S-adenosyl-methionine 31

synthetase 3 that catalyzes the synthesis of S-adenosyl-methionine (SAM) in the 32

one-carbon metabolism cycle. mat4 mostly decreases CHG and CHH DNA 33

methylation and histone H3K9me2 and reactivates certain silenced transposons. The 34

exogenous addition of SAM partially rescues the epigenetic defects of mat4. SAM 35

content and DNA methylation were reduced more in mat4 than in three other mat 36

mutants. MAT4 knock-out mutations generated by CRISPR/Cas9 were lethal, 37

indicating that MAT4 is an essential gene in Arabidopsis. MAT1, 2, and 4 proteins 38

exhibited nearly equal activity in an in vitro assay, whereas MAT3 exhibited higher 39

activity. The native MAT4 promoter driving MAT1, 2 and 3 cDNA complemented the 40

mat4 mutant. However, most mat4 transgenic lines carrying native MAT1, 2, and 3 41

promoters driving MAT4 cDNA did not complement the mat4 mutant, because of 42

their lower expression in seedlings. Genetic analyses indicated that the mat1mat4 43

double mutant is dwarfed and the mat2mat4 double mutant was non-viable, while 44

mat1mat2 showed normal growth and fertility. These results indicate that MAT4 45

plays a predominant role in SAM production, plant growth and development. Our 46

findings provide direct evidence of the cooperative actions between metabolism and 47

epigenetic regulation. 48

49



3

INTRODUCTION 50

DNA and histone methylation are important epigenetic modifications that regulate 51

gene expression and genome stability, and can be inherited (Law and Jacobsen, 2010). 52

Compared with animals, which largely display CG methylation, plants present 53

symmetric CG and CHG methylation and asymmetric CHH methylation. In 54

Arabidopsis (Arabidopsis thaliana), DNA methylation is mediated by the 55

RNA-directed DNA methylation pathway (RdDM) and dicer-independent RdDM 56

(Matzke et al., 2015; Yang et al., 2016; Ye et al., 2016); CG methylation is maintained 57

by DNA METHYLTRANSFERASE1 (MET1, a functional equivalent protein of DNA 58

methyltransferase 1 in mammals); CHH methylation is maintained by DOMAINS 59

REARRANGED METHYLASE 2 (DRM2) and CHROMOMETHYLASE2 (CMT2) 60

(Cao and Jacobsen, 2002, 2002; Du et al., 2014); and CHG methylation is maintained 61

by CMT3. CHG methylation is recognized by the SET and RING Associated (SRA) 62

domain histone methyltransferase KRYPTONITE/(SU(VAR) homolog (SUVH)4 63

(KYP/SUVH4), and its homologs SUVH5 and SUVH6 to establish the dimethylation 64

of histone H3 at lysine 9 (H3K9me2) (Jackson et al., 2002; Ebbs et al., 2005; Ebbs 65

and Bender, 2006). H3K9me2 is bound by CMT3 through its H3 tails (Johnson et al., 66

2007; Bernatavichute et al., 2008; Law and Jacobsen, 2010; Du et al., 2012), which 67

form a reinforcing feedback loop that maintains CHG methylation and H3K9me2. 68

The one-carbon metabolism pathway plays an important role in epigenetic 69

regulation because it provides methyl groups for most methylation reactions (Fig. 1). 70

The initial methyl group donor is polyglutamate-5-methyl-tetrahydrofolate 71

(5-CH3-THF-Glun), which is the most common form of folate and has a high affinity 72

for folate-dependent methionine synthase as the methyl-group donor. 73

Folate-dependent methionine synthase catalyzes the methylation of homocysteine to 74

methionine using 5-CH3-THF-Glun as the methyl-group donor (Friso et al., 2002; 75

Ravanel et al., 2004; Mehrshahi et al., 2010). S-adenosyl-methionine (SAM), one of 76

the most abundant co-factors in plant metabolism, is synthesized by methionine 77

adenosyltransferase (MAT) (also known as S-adenosyl-methionine synthetase, SAMS) 78



4

using methionine and ATP as substrates. After transferring a methyl group to DNA, 79

RNA, proteins or other metabolites by SAM-dependent methyltransferases (Sauter et 80

al., 2013), SAM is changed into S-adenosyl-homocysteine (SAH), which competes 81

with SAM and is an inhibitor for many Methionine Synthetases (MTs) (Molloy, 2012). 82

SAH is then converted to adenosine and homocysteine by SAH hydrolase encoded by 83

the HOMOLOGY-DEPENDENT GENE SILENCING1 (HOG1) in Arabidopsis, thus 84

finishing a single cycle of one-carbon metabolism. The T-DNA (hog1-5) or 85

transposon (hog1-4) insertion mutants are zygotic embryo lethal, whereas its weak 86

mutation can cause delayed germination, poor growth, reduced seed viability, and 87

reduced whole-genome DNA and histone methylation (Rocha et al., 2005; Mull et al., 88

2006; Baubec et al., 2010; Ouyang et al., 2012). A mutation of folylpolyglutamate 89

synthetase 1 (FPGS1) that converts 5-CH3-THF-Glu1 to 5-CH3-THF-Glun in 90

Arabidopsis can slow germination and reduce levels of whole-genome DNA 91

methylation and H3K9me2 (Zhou et al., 2013). Treatment with sulfamethazine (SMZ), 92



5

which is a structural analog and competitor of p-aminobenzoic acid (PABA), the 93

precursor of folate, causes the release of endogenous transposons and repeat elements 94

and the reduction of DNA methylation levels and H3K9me2 (Zhang et al., 2012). A 95

mutation in the cytoplasmic bifunctional methylenetetrahydrofolate 96

dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1) leads to 97

decreased levels of oxidized tetrahydrofolates, DNA hypomethylation, loss of 98

H3K9me and transposon reactivation (Groth et al., 2016). 99

The Arabidopsis genome has 4 MAT genes with different nomenclatures 100

(MAT1/SAM1/AT1G02500, MAT2/SAM2/AT4G01850, MAT3/AT2G36880, 101

MAT4/MTO3/SAMS3/AT3G17390) in different publications (Peleman et al., 1989; 102

Peleman et al., 1989; Goto et al., 2002; Mao et al., 2015; Chen et al., 2016). A 103

previous study indicates that SAMS RNAi transgenic rice (Oryza sativa) lines with 104

down-regulation of OsSAMS1, 2 and 3 show reduced histone H3K4me3 and DNA 105

methylation (Li et al., 2011). In Arabidopsis, the pollen expressed MAT3 is required 106

for maintaining histone and tRNA methylation in pollen, and pollen germination and 107

pollen tube growth (Chen et al., 2016). However, the biological roles of other MAT 108

proteins in Arabidopsis epigenetic regulation are still unknown. 109

In this study, we screened a mutagenized population from the transgenic line 110

L119, which harbors two silenced transgenes, Pro35S::NPTII (NEOMYCIN 111

PHOSPHOTRANSFERASE II) and ProRD29A (RESPONSE TO DESSICATION 29A, 112

a stress-inducible promoter)::LUC, and identified the mat4/sams3/mto3 (methionine 113

over-accumulation) mutant (Shen et al., 2002; Jin et al., 2017) that releases the 114

silencing of both genes. We found that the mat4 mutant, harboring a missense point 115

mutation, dramatically decreases SAM content and CHG and CHH methylation and 116

H3K9me2, leading to the activation of some transposable elements. Exogenous 117

additions of SAM to the medium partially restored histone methylation levels in mat4. 118

The mat1, 2 or 3 mutants reduced SAM content and DNA methylation to a lesser 119

extent than did mat4, indicating a predominant role of MAT4 among MATs. MAT3 120

showed the highest activity among the four MAT proteins in an in vitro assay. The 121



6

expression of MAT4 in seedlings was much higher than MAT1, MAT2 and MAT3. 122

The MAT4 promoter driving MAT1, MAT2 or MAT3 cDNA could complement the 123

mat4 mutant, while most transgenic lines carrying the MAT1, MAT2, or MAT3 124

promoters driving MAT4 cDNA could not complement the mat4 mutant. The MAT4 125

loss-of-function mutation generated using the CRISPR/Cas9 technique was lethal. We 126

also found that the MAT proteins in Arabidopsis interacted with each other and 127

themselves both in vitro and in vivo, indicating that they may form homologous or 128

heterogeneous oligomers in Arabidopsis. 129

130



7

RESULTS 131

Identification and characterization of mat4 132

To further study the mechanisms regulating transcriptional gene silencing (TGS), we 133

obtained the transgenic line L119 carrying ProRD29A::LUC and Pro35S::NPTII in 134

the Columbia gl1 background. In L119, the transgene loci consist of at least two 135

T-DNA insertions, each with two repeats (Supplemental Fig. 1A-F). ProRD29A is a 136

stress inducible promoter that is induced by ABA, low temperatures and high NaCl 137

concentrations (Yamaguchishinozaki and Shinozaki, 1994). The L119 plants were 138

very sensitive to kanamycin (Kan) and showed little luciferase activity; they grew 139

poorly on media containing 25 mg/L Kan (Fig. 2A) and did not emit any fluorescence 140

after NaCl treatment (Fig. 2D), indicating that both ProRD29A::LUC and 141

Pro35S::NPTII are silenced in L119. However, after introducing the defective in 142

meristem silencing 3 (dms3-1) mutation in the RdDM pathway (Kanno et al., 2008) 143

into L119, ProRD29A::LUC, but not Pro35S::NPTII, was reactivated (Supplemental 144

Fig. 1G-J), suggesting that similar to the C24/RD29A::LUC line (He et al., 2009), 145

ProRD29A::LUC is regulated by the RdDM pathway while Pro35S::NPTII is not. 146

The transgenic line L119 was mutagenized by ethyl-methanesulfonate, and the F2 147

population was screened for Kan-resistant mutants. A mutant, named mat4-3, was 148

isolated in this screen (hereafter referred to as mat4) (Fig. 2A). mat4 seeds germinated 149

later (Fig. 2A) and the seedlings were smaller compared with L119, although these 150

seedlings had relatively normal fertility (Supplemental Fig. S2A, S2B). Two alleles of 151

ddm1, ddm1-18 and ddm1-19, were also identified in this system. ddm1-18 [a G-to-A 152

change at position 2803 (counting from the first putative ATG in the coding frame), 153

which causes a stop codon with a TGG to TGA transition; hereafter referred to as 154

ddm1] and ddm1-19 (a G-to-A change at position 3125, which causes a stop codon 155

with a TGG to TGA transition) exhibited more resistance to kanamycin than mat4, 156

whereas L119 seedlings did not survive on the medium containing 25 mg/L Kan 157

(Supplemental Fig. S2C). DDM1 is a nucleosome-remodeling protein involved in 158

facilitating DNA methyltransferase access to heterochromatin to silence certain 159



8 transposable elements and repeats in cooperation with the RdDM pathway (Singer et 160



9

al., 2001; Zemach et al., 2013). Here, we used ddm1 as a positive control for reduced 161

DNA methylation. Greater increases of NPTII expression and its protein levels were 162

observed in mat4 than in L119, although the NPTII expression and protein levels were 163

less in mat4 than in ddm1 (Fig. 2B, 2C). Treatment with 300 mM NaCl reactivated the 164

expression of ProRD29A::LUC in mat4 (Fig. 2D). Two silenced transgenic loci were 165

reactivated in mat4, which was also observed in ddm1; thus, we detected 166

endogenously silenced genes, DNA repeats and transposable elements. SUPPRESSOR 167

OF DRM1 DRM2 CMT3 (SDC) is regulated by non-CG DNA methylation 168

(Henderson and Jacobsen, 2008); TSIs are endogenous transcriptionally silent 169

information sites regulated by the DNA replication and repair pathway and DNA 170

methylation independent of the RdDM pathway (Andrea Steimer, 2000; Xia et al., 171

2006); AtGP1 is a LTR-Gypsy transposon modulated by the RdDM pathway (He et al., 172

2009; He et al., 2009); 180-bp CEN are centromeric satellite repeats regulated by 173

DNA methylation independent of the RdDM pathway but not by the DNA replication 174

and repair pathway (Bruce P. May, 2005; Xia et al., 2006). The transcript levels of all 175

these loci were higher in mat4 than in L119 but lower than in ddm1 (Fig. 2C). 176

We then cloned the MAT4 gene by map-based cloning. We first crossed the mat4 177

mutant with the wild-type Ler. The 519 F2 plants that were Kan resistant were 178

isolated and used for mapping. We narrowed mat4 to a region between bacterial 179

artificial chromosome (BAC) clones K14A17 and MPK6 on chromosome 3. We 180

sequenced candidate genes in this region and observed that a G-to-A mutation in 181

AT3G17390 changed 246D to 246N (Fig. 2E, Supplemental Fig. 2D). This mutation 182

occurs in a conserved amino acid that is involved in binding methionine during the 183

reaction, according to the crystal structure of human (Homo sapiens) MAT2A, which 184

is different from the mto3 mutation in the ATP binding site (Shen et al., 2002). This 185

point mutation did not cause alteration in the transcript level (Supplemental Fig. S2E). 186

To confirm whether the mutation in MAT4 is responsible for the Kan resistance of 187

mat4, we transformed the full genomic length of MAT4, including the 2221-bp 188

promoter and the full genomic sequence fused with FLAG or a GFP tag into the mat4 189



10

mutant. A number of different transgenic lines were obtained and shown to be Kan 190

sensitive, which was also observed in L119. We selected one MAT4-FLAG line (line 1) 191

for further study (hereafter referred as MAT4-FLAG). Immunoblotting using 192

anti-FLAG antibodies indicated that MAT4-FLAG expressed the MAT4-FLAG protein 193

(Supplemental Fig. S2F). MAT4-FLAG was sensitive to Kan and had normal 194

germination (Fig. 2F), and the NPTII protein level was restored to the basal level 195

observed in L119 (Fig. 2G), suggesting that AT3G17390 could complement the mat4 196

mutant phenotype. Reverse transcription quantitative PCR (RT-qPCR) analyses 197

indicated that the expression of NPTII, and certain endogenous loci in the 198

MAT4-FLAG also returned to the basal level observed in L119 (Supplemental Fig. 199

S2G). We did not observe any enhanced severe phenotypes of the mat4 mutant after 200

several generations. We used the egg cell-specific CRISPR/Cas9 system in L119 201

(Wang et al., 2015) and created two MAT4 knock-out lines mat4-c19 and mat4-c32. 202

mat4-c19 has a fragment deletion from 76 to 180 bp (counting from the first putative 203

ATG) and mat4-c32 from 706 to 797 bp (Supplemental Fig. S2H). However, we were 204

unable to obtain homozygous mat4 mutants, indicating that MAT4 is an essential gene 205

in Arabidopsis. 206

The subcellular localization in transgenic L119 plants expressing 207

Pro35S::MAT4-GFP indicated that MAT4-GFP was localized in the nucleus and 208

cytosol (Fig. 2H a). A similar localization of MAT4-GFP was observed in a transient 209

transformation assay using Arabidopsis protoplasts and Nicotiana benthamiana leaves 210

(Fig. 2H b, c). To avoid the possibility that GFP translocates to the nucleus by itself, 211

we isolated the cytosol and nuclei from L119 and the MAT4-FLAG transgenic line and 212

performed an immunoblot assay. MAT4-FLAG protein was detected in both the 213

cytosol and the nucleus (Fig. 2I). Previous studies also indicate that SAM1/MAT1, 214

SAM2/MAT2 and MAT3 are all localized in both cytosol and nuclei (Mao et al., 2015; 215

Chen et al., 2016). These results suggest that MAT proteins may function in both the 216

cytosol and the nucleus in Arabidopsis. 217

DNA methylation of transgenic loci is reduced in mat4 218



11

MAT4 catalyzes the biosynthesis of SAM, which is a universal methyl group donor 219

for DNA and histone methylation; thus, mat4 may reactivate the silenced 220

Pro35S::NPTII and ProRD29A::LUC because of decreased DNA and/or histone 221

methylation. Bisulfite sequencing analyses indicated that CHG and CHH methylation 222

of transgenic and endogenous RD29A promoters largely decreased in mat4 compared 223

with that in L119 (Fig. 3B, 3C), which was consistent with the data from 224

whole-genome bisulfite sequencing (Fig. 3D). However, CHG and CHH methylation 225

decreased to a lesser extent at the 35S promoter in mat4 compared with that in L119 226

(Fig. 3A, 3D). However, only limited changes were observed in the CG methylation 227

with transgenic RD29A and 35S promoters in mat4. In contrast, ddm1 greatly reduced 228

CG methylation and only moderately affected CHG and CHH methylation, except for 229

the transgene RD29A promoter, in which ddm1 did not affect CHH methylation. In 230

addition, the DNA methylation of the MAT4-FLAG line was consistently restored to 231

the L119 level (Fig. 3A, 3B, 3C). These results indicate that mat4 reduces DNA 232

methylation in transgenes in L119. 233

mat4 reduces DNA methylation at the whole-genome level 234

We compared the DNA methylation level of mat4 with that of L119 at the 235

whole-genome level by bisulfite sequencing. We obtained nearly 5G raw data 236

including adapter and low-quality data for each sample, from which we obtained 4.2G 237

clean data for our subsequent analyses. The total reads were mapped to the genome of 238

TAIR 10. We then obtained the methylation level of CG, CHG, and CHH by 239

calculating the ratio of C to C+C/T using the tool of Bismark (Krueger and Andrews, 240

2011) (Fig. 4A). We also included the previously published data of ddm1 (Zemach et 241

al., 2013) for comparison. The methylation levels of CG (22.9%), CHG (4.2%), and 242

CHH (1.4%) in mat4 were lower than the levels of CG (25.2%), CHG (8.2%), and 243

CHH (2.4%) in L119 (Fig. 4A). CHG and CHH methylation in mat4 decreased by 244

nearly half, whereas CG methylation decreased approximately by 9.2%, suggesting 245

that mat4 has different effects on CG, CHG and CHH DNA methylation (Fig. 4B). 246

mat4 displayed a relatively smaller reduction of CG and CHG methylation and greater 247



12

reduction of CHH methylation compared with that observed in ddm1 (Fig. 4B). 248

Frequency distribution histograms of significant methylation differences between 249

L119 and mat4 in CG, CHG, and CHH also indicated that the CHG and CHH 250

methylation dramatically decreased in mat4 (Fig. 4C). 251

To determine the distribution of changes in the DNA methylation patterns in 252

detail, we calculated the DNA methylation 2 kb upstream and downstream of the 253

genes and transposable elements (TEs), respectively. In genes that exclude TEs or 254

repeats, CG methylation mainly occurred in the gene bodies. mat4 reduced the CG 255

methylation in the gene body regions by approximately 2.5% (Fig. 4D). However, 256

ddm1 showed greater reductions in CG methylation compared with mat4 in these 257

regions (Fig. 4D). CHG and CHH methylation did not show noticeable changes (Fig. 258

4D) because these regions exhibit limited CHG and CHH methylation. For TEs, we 259

focused on two TE types: TEs shorter than 0.5 kb (S-TEs, usually regulated by the 260



13

RdDM pathway) and TEs longer than 4 kb (L-TEs, usually regulated by the DDM1 261

pathway) (Teixeira et al., 2009; Zemach et al., 2013). Generally, mat4 displayed less 262

CG, CHG and CHH methylation than the L119 in both S-TEs and L-TEs (Fig. 4E, 4F). 263

Compared with ddm1, mat4 displayed more CG methylation in both short and long 264

TEs and more CHG methylation in long TEs. However, mat4 showed similar CHG 265

methylation in short TEs and CHH methylation in long TEs as ddm1 (Fig. 4E, 4F). 266

mat4 displayed less CHH methylation in short TEs than ddm1, which is consistent 267

with previous studies of DDM1 regulation of DNA methylation in long TEs, but not 268

short TEs that are mostly regulated by the RdDM pathway (Teixeira et al., 2009; 269



14

Zemach et al., 2013). These results suggest that mat4 mainly reduces CHG and CHH 270

methylation and, to a lesser extent, CG methylation. When mapping these 271

hypo-differentially methylated regions (hypo-DMRs) to the five chromosomes, we 272

found that the distribution of these hypo-DMRs were concentrated around the five 273

centromeres, which displayed a dramatic decrease of CHG and CHH methylation 274

(Supplemental Fig. S3, Supplemental data set S1-S3). These results indicate that mat4 275

reduces genomic-wide DNA methylation, especially CHG and CHH methylation at 276

pericentromeric heterochromatin regions. 277

mat4 decreases histone modifications in heterochromatin regions 278

Because DNA methylation, especially CHG and CHH methylation, is reduced 279

throughout the genome in mat4, we sought to determine whether mat4 has an effect 280

on histone methylation. We verified the histone modifications in H3K9me2, 281

H3K9me1, and H3K27me1 because these modifications usually accompany DNA 282

methylation in heterochromatin regions, and we also verified the modifications in 283

H3K4me3 because this modification accompanies high gene expression (Tariq et al., 284

2003; Jacob et al., 2009). Using immunoblotting assays, we found that the H3K9me2 285

levels in mat4 were comparable to those in ddm1, and greatly reduced compared with 286

that of L119. In addition, only a small decrease in H3K9me1 was exhibited in mat4, 287

whereas a dramatic decrease was observed in ddm1 compared with L119 (Fig. 5A, 288

5B). Both mat4 and ddm1 had a lower H3K27me1 level than L119. In the mat4 289

complementary line, both H3K9me2, H3K9me1 and H3K27me1 were restored to the 290

wild-type level, whereas in mat4, ddm1, L119 or MAT4-FLAG, H3K4me3 was not 291

changed (Supplemental Fig. S4A, S4B). 292

We then compared the heterochromatin status in nuclei using an 293

immunofluorescence assay with different antibodies. In the wild-type cells, more than 294

89% of the interphase nuclei showed H3K9me2, H3K9me1 and H3K27me1 295

immunofluorescence associated with the condensed pericentromeric heterochromatin 296

regions stained with 4',6-diamidino-2-phenylindole (DAPI). However, approximately 297

78% of mat4 and 87% of ddm1 nuclei showed chromocenter decondensation and 298



15

reduced H3K9me2 immunofluorescence. ddm1 showed strongly reduced H3K9me1 299

immunofluorescence, which was not observed in mat4, whereas ddm1 and mat4 300

mutants showed substantially reduced H3K27me1 immunofluorescence (Fig. 5C-E). 301



16

In MAT4-FLAG, H3K9me2 immunofluorescence was restored to the L119 level 302

(Supplemental Fig. S4C, S4D). However, we did not detect a difference in H3K4me3 303

immunofluorescence in L119, mat4 and MAT4-FLAG (Supplemental Fig. 4E, 4F). We 304

confirmed the decrease of H3K9me2 at certain loci using chromatin 305

immunoprecipitation (ChIP)-PCR (Fig. 5F). These results suggest that mat4 reduces 306

the histone methylation in heterochromatin regions, especially H3K9me2 and 307

H3K27me1. 308

mat4 reactivates silenced TEs 309

To determine how mat4 modulates gene expression, we performed RNA sequencing 310

(RNA-seq). Total RNA was extracted from 15-day-old seedlings and then subjected to 311

RNA-Seq with two biological replicates. We obtained 3G clean data with each 312

replicate, mapped all of the obtained reads to TAIR 10, and then compared the 313

transcript levels between mat4 and L119 using edgeR (Robinson et al., 2010). We 314

obtained 1284 protein coding genes and 364 TEs with transcript level changes of at 315

least two-fold and P<0.0001. Among these protein-coding genes, 66% (842) were 316

up-regulated and 34% (442) were down-regulated (Fig. 6A, 6B, Supplemental data set 317

S4-7). After mapping these genes on the five chromosomes, we found that they were 318

evenly distributed along the chromosomes arms and rarely localized at the centromere 319

regions (Fig. 6C). Approximately 92% (334) of the differentially-expressed TEs were 320

up-regulated and concentrated around the centromeres (Fig. 6C). The expression of 321

certain genes and TEs was confirmed by RT-qPCR in L119, mat4 and MAT4-FLAG 322

(Supplemental Fig. S5A, S5B). Compared with previously published data in ddm1 323

and fpgs1, we found that 127 up-regulated TEs in mat4 were also up-regulated in 324

ddm1 and fpgs1 with reduced DNA methylation and H3K9me2 (Fig. 6D) (Zemach et 325

al., 2013; Zhou et al., 2013). After dividing the up-regulated TEs according to their 326

characteristics, two categories of TEs, long terminal repeat (LTR) /Gypsy and 327

Enhancer/Suppressor Mutator (En/Spm)-like transposons (Fig. 6E), accounted for 328

nearly 50% of all of the up-regulated TEs in mat4. Alterations to DNA methylation 329

were not associated with the expression of protein coding genes, however, reduced 330



17

DNA methylation in mat4 was closely associated with increased TE expression 331

(Supplemental Fig. S5C). When comparing the CHG hypo-DMRs and up-regulated 332

TEs in mat4 with the published data in suvh4/5/6 and cmt3 (Stroud et al., 2013), we 333

found that these mutants had higher overlap than that by chance as viewed in VENNY 334

diagram (Fig. S5D), indicating that MAT4 affects a large number of targets shared 335

with those methyltransferases. In conclusion, mat4 led to the activation of the silenced 336

transposons as a result of the reduction in DNA methylation and histone methylation. 337

Application of SAM partially rescues the phenotype of mat4 338

To test whether the decreases of DNA and histone methylation were caused by the 339



18

alteration of SAM content in mat4, we measured SAM contents in mat4, L119 and 340

MAT4-FLAG by liquid chromatography-mass spectrometry (LC-MS). The SAM 341

content in mat4 was decreased by nearly 35% compared to that in L119 (Fig. 7A). 342

Interestingly, the content of SAH, which is a strong inhibitor of SAM-dependent 343



19

methyltransferases, was significantly increased in mat4, leading to a large decrease in 344

the ratio of SAM/SAH, which is an important index influencing the methylation status 345

(Fig. 7B). Meanwhile, the contents of SAM and SAH in MAT4-FLAG were restored 346

to L119 level (Fig. 7A, 7B). Therefore, we sought to determine whether the exogenous 347

application of SAM could rescue the phenotype of mat4. After adding 400 mg/L SAM 348

to the medium, the Kan susceptibility of mat4 was partially rescued (Fig. 7C, 7D). An 349

analysis of the transcript levels of transgenic and endogenous genes indicated that the 350

application of SAM inhibited the high expression of these genes in mat4 (Fig. 7E). An 351

immunofluorescence assay indicated that H3K9me2 levels were restored by the 352

application of SAM (Fig. 7F, 7G). These results suggest that the decreased SAM in 353

mat4 leads to the release of the silencing of these tested genes. 354

MAT4 plays a predominant role in SAM production and DNA methylation 355

among different MAT homologs 356

In Arabidopsis, four MAT homologs present near 90% identity between each other in 357

their amino acid sequences (Shen et al., 2002; Lindermayr et al., 2006). Because mat4 358

reduces SAM content and DNA methylation, we sought to determine whether other 359

MAT mutants have similar roles. We obtained three T-DNA lines: SALK_059210 360

carrying a T-DNA insertion in the C-terminus of AT1G02500 (mat1); SALK_052006 361

carrying a T-DNA insertion in the N-terminus of AT4G01850 (mat2), and 362

SALK_019375 carrying a T-DNA insertion after the putative stop codon of 363

AT2G36880 (mat3), which was used in the previous study (Chen et al., 2016). All 364

three T-DNA insertion lines greatly reduced the expression of each targeted gene 365

(Supplemental Fig. S6A). We measured the contents of SAM in these mutants, and 366

found that SAM content in mat1 and mat2 decreased only about 6% compared to that 367

in L119, but no clear change was observed in mat3 (Supplementary Fig. S6B), which 368

is consistent with its main expression in pollen (Chen et al., 2016). We further 369

measured the DNA methylation level in these mutants at the whole genomic level by 370

bisulfite sequencing, and found that the DNA methylation in CG, CHG and CHH 371

slightly decreased in these mutants (Supplementary Fig. S7A), among which mat3 372



20

CHG and CHH methylation was reduced to a lesser extent than mat1 or 2 in Long and 373

Short-TEs (Supplementary Fig. S7B, S7C), which was consistent with the SAM 374

contents in these mutants. These results indicate that MAT1, 2 and 3 have less of an 375

effect on DNA methylation than MAT4 in seedlings. However, MAT3 may play a 376

major role in pollens (Chen et al., 2016). 377

In order to clarify the effect of these MAT proteins on expression of 378

Pro35S::NPTII in L119, we created loss of function mutants of MAT1, 2, 3 genes 379

using the egg cell-specific CRISPR/Cas9 system in the L119 background 380

(Supplementary Fig. S8A) (Wang et al., 2015). mat1-c3 was a single base insertion 381

mutant, in which an A insertion after 421 bp (counting from the first putative ATG), 382

led to a frame-shift mutation; mat1-c19 had a fragment deletion from 222 bp to 450 383

bp; mat2-c6 was a single base deletion mutant at 488 bp, leading to a frame-shift 384

mutation; mat2-c13 had a fragment deletion from 490 bp to 569 bp; mat3-c8 had a 385

fragment deletion from 366 bp to 420 bp. The expression of each target gene was 386

greatly reduced compared to the wild type (Supplemental Figure S8A). All these 387

mutants were sensitive to Kan (Supplementary Fig. S8B) and the transcriptional levels 388

of NPTII did not differ with that in L119 (Supplementary Fig. S8C), indicating that 389

the mutations in MAT 1, 2 and 3 do not release the silencing of Pro35S::NPTII, which 390

was consistent with the results of a smaller reduction in DNA methylation in their 391

T-DNA lines. The mat3-c8 mutant produced 1–2 seeds per silique, which is similar 392

with previous results (Chen et al., 2016). 393

The expression pattern of MAT4 determines its predominant biological roles in 394

Arabidopsis 395

Although the amino acid sequences of the four MATs shared a high percentage of 396

identity, these proteins did not compensate for each other in plants. Whether their 397

expression patterns or protein activities determined their specificity is not known. To 398

address this question, firstly, we compared the catalytic activities of those four 399

proteins in vitro. The MAT proteins were expressed in and purified from Escherichia 400

coli. MAT1, MAT2 and MAT4 exhibited similar activity, while MAT3 had higher 401



21

activity than other three (Fig. 8A). The amount of SAM produced increased with 402

increasing MAT4 protein concentration as well (Fig. 8B). However, we could not 403

detect any activity for the MAT4D246N mutant protein (Fig. 8B), indicating that the 404

mutant protein largely loses its activity in vitro. 405

We used the MAT4 promoter driving MAT1, MAT2 or MAT3 cDNA to evaluate 406



22

whether these cDNAs could complement mat4. Here we fused MAT cDNA with GFP 407

to observe its expression. We obtained 12 mat4 transgenic lines carrying 408

ProMAT4::MAT1-GFP, 8 carrying ProMAT4::MAT2-GFP, and 19 carrying 409

ProMAT4::MAT3-GFP. These transgenic plants had high GFP fluorescence. All these 410

transgenic plants had high expression of transgenes and complemented mat4 mutant 411

phenotypes (Fig. 8C-E). These results indicated that MAT proteins have comparable 412

biological functions in plants. 413

A previous study indicates that transforming Pro35S::MAT2 into mto3-1 (the 414

mat4 allele) failed to complement the mto3 phenotype (Shen et al., 2002). Given that 415

MAT1 and MAT2 are expressed in most plant tissues (Peleman et al., 1989; Mao et al., 416

2015) and MAT3 is mainly expressed in pollens (Chen et al., 2016), we used MAT1, 2, 417

or 3 promoters driving MAT4 cDNA to examine whether they could complement mat4. 418

We obtained 27 mat4 transgenic lines carrying ProMAT1::MAT4-GFP, 5 carrying 419

ProMAT2::MAT4-GFP and 6 carrying ProMAT3::MAT4-GFP. We found that all 420

ProMAT2::MAT4-GFP or ProMAT3::MAT4-GFP and most ProMAT1::MAT4-GFP 421

transgenic plants did not complement the mat4 Kan resistant phenotype because they 422

had lower GFP levels, as indicated by fluorescence imaging and immunoblotting 423

using GFP antibodies (Figure 9A-D). In contrast, ProMAT4::MAT2-GFP transgenic 424

lines had higher GFP levels (Figure 9A-D). In 27 ProMAT1::MAT4-GFP transgenic 425

lines, 7 lines showed different Kan sensitive phenotypes. We selected three lines and 426

compared their Kan sensitivity with other lines. These three lines showed more Kan 427

sensitivity than other lines (Supplemental Fig. 9A), indicating that they complemented 428

or partially complemented the mat4 mutant. GFP protein levels were higher in these 429

complemented lines than in non-complemented lines as indicated by GFP 430

fluorescence and protein immunoblotting (Supplementary Fig. S9B-D). The 431

expression levels of transgenes were also higher in these complemented lines than 432

others (Supplementary Fig. S9E). The higher expression of ProMAT1::MAT4-GFP 433

may be caused by the different genomic site in which the T-DNA was inserted. These 434

results indicate that the expression level of MAT genes determined their biological 435



23

roles in Arabidopsis. 436

We performed further genetic analyses among these mutants. mat1mat2 double 437

mutants did not show any growth or developmental differences from the wild-type 438

plants (Supplementary Fig. S10A). mat1-c19 mat4 double mutant seedlings were 439

much smaller than the wild type, and did not produce any seeds (Fig. 9E). We could 440

not obtain mat2-c13 mat4 homozygous double mutants because the double mutants 441

had embryonic defects (Fig. 9F, 9G, Supplementary Fig. S10B). These results indicate 442



24

that the expression pattern of MAT4 gene determines its predominant biological roles 443

in Arabidopsis. 444

MATs form homologous or heterologous oligomers in cells 445

To explore the functions of MAT4, we tried to identify the MAT4-interacting proteins 446

by immunoprecipitation followed by mass spectrometry analysis using the 447

complementary transgenic line MAT4-FLAG. We precipitated MAT4-FLAG with 448

anti-FLAG beads, and used the L119 lines as negative controls. We identified MAT1, 449

MAT2 and MAT3, each with unique peptides from MAT4-FLAG 450

co-immunoprecipitation (co-IP) proteins (Supplemental table S1). Then, we 451

confirmed their interactions in vivo using co-immunoprecipitation assays in 452

Arabidopsis protoplasts transiently expressing different proteins (Fig. 10A). In E. coli, 453

when co-expressing MAT4-His with GST-MAT1, GST-MAT2, GST-MAT3, 454

GST-MAT4 or only GST (as the negative control), respectively, we found that each of 455

them, but not GST, could be purified together with MAT4-His (Fig. 10B), suggesting 456

that MAT4 can interact with MAT1, MAT2, MAT3 and itself in vitro. We further 457

confirmed that MAT1, MAT2 and MAT3 were able to interact with each other and 458

themselves in both in vivo and in vitro assays (Supplementary Fig. S11, S12). Next, 459

we carried out gel filtration using the proteins isolated from the MAT4-FLAG 460

transgenic complementary line. We observed three peaks from the eluted fractions 461

(Fig. 10C). LC-MS analyses of each peak authenticated four MAT proteins (Fig. 10D), 462

indicating that these MATs can form different sizes of homologous or heterologous 463

oligomer complexes in vivo, which merits further examination. 464

465



25

DISCUSSION 466

SAM provides methyl groups for numerous methyltransferases in transmethylation 467

reactions, including DNA and histone methylations in all living cells. In this study, we 468

identified MAT4 because its mutation reactivates the silenced Pro35S::NPTII and 469

ProRD29A::LUC in L119. MAT is well conserved during evolution, and it usually has 470

three domains: the N-terminal domain, the C-terminal domain and the central 471

M-domain (Fusao Takusagawa, 1996). In Arabidopsis, there are four homologs of 472

MAT, MAT1-4; these homologs share nearly 90% amino acid sequence identity 473

(Peleman et al., 1989; Peleman et al., 1989; Shen et al., 2002). mto3, an allele of mat4, 474

was isolated in a screen based on ethionine (a toxic analog of methionine) sensitivity. 475



26

The level of methionine is increased more than 200-fold and the concentration of 476

SAM is decreased by 35% compared with the wide type (Shen et al., 2002). In this 477

study, we found that both DNA and histone methylation were largely reduced as a 478

result of the decrease of SAM content in mat4. Our study provides direct evidence for 479

the importance of SAM in providing methyl donors and modulating epigenetic status. 480

In theory, SAM is a general methyl group donor and the reduction of SAM 481

should have an unbiased effect on DNA and histone methylations. However, we 482

found that the reduction of DNA and histone methylation was uneven, with mat4 483

showing large decreases in CHG and CHH methylation as well as H3K9me2 and 484

H3K27me1 (Fig. 4, 5). Changes in H3K4me3 were not observed and CG methylation 485

decreased to a lesser extent. In animals, the supplementation of methionine, an 486

essential amino acid, can modulate the SAM/SAH ratio and impact H3K4me3 487

(Mentch et al., 2015). Threonine, another essential amino acid, is the major fuel 488

source for glycine, acetyl-CoA and SAM. Restricted applications of threonine can 489

reduce H3K4me3 levels, which results in slower growth and increased differentiation 490

in mouse embryonic stem cells (Shyh-Chang et al., 2013). In addition, in SAMS RNAi 491

rice, H3K4me3 is significantly reduced (Li et al., 2011). These results suggest that 492

SAM limitation can result in different changes in DNA and histone modifications in 493

different species. These differences can be explained by several factors. First, 494

different methyltransferases might have different SAM concentration thresholds. In 495

addition, MET1 and H3K4 methyltransferases might efficiently use low 496

concentrations of SAM to complete the reactions in mat4, whereas the histone 497

methyltransferases for H3K9me2 and DNA methyltransferases for CHG and CHH 498

might have lower activity at such concentrations. Second, the reinforcing loop 499

between CHG methylation and H3K9me2 cannot be maintained and is even disrupted 500

in mat4, which would lead to a serious reduction in methylation for both. Third, the 501

increased SAH in mat4 would compete with SAM and decrease SAM accessibility to 502

methyltransferases, which mostly reduced the CHG and CHH methylation and 503

H3K9me. Similar results have been observed in both fpgs1 and mthfd1 mutants (Zhou 504



27

et al., 2013; Groth et al., 2016). Both fpgs1 and mthfd1 mutants accumulate relatively 505

more SAH, which leads to a decreased ratio of SAM/SAH (Zhou et al., 2013; Groth et 506

al., 2016). SAH is a strong inhibitor that competes with SAM for SAM-dependent 507

transmethylation (De La Haba and Cantoni, 1959). These studies suggest that the 508

CMT3 or the CMT2 pathway has a positive feedback circuit with SUVH4 509

(KRYPTONITE)/5/6 to maintain CHG or CHH methylation and H3K9me (Zhou et al., 510

2013; Stroud et al., 2014; Groth et al., 2016). Consistent with the reduced DNA 511

methylation, our RNA-seq data indicated that a large number of TEs were activated in 512

the mat4 mutant. These up-regulated TEs were enriched around the heterochromatin 513

regions of the centromeres, which are largely shared with those found in ddm1 and 514

fpgs1 mutants. Given that reduced DNA methylation is found only at certain sequence 515

contexts, it is also possible that the inefficient histone methylation might indirectly 516

affect DNA methylation. For example, the CHG DNA methylation in the 517

Pro35S-NPTII transgene was only moderately reduced, while a more significant 518

reduction in H3K9me2 was found in the 35S promoter of the mat4 mutant. However, 519

this hypothesis is hard to test as SAM is a common substrate for both DNA and 520

histone methylation. Reduced SAM must more or less affect both DNA and histone 521

methylation. 522

In humans, three MAT genes encode MATα1, MATα2 and MATβ. MATα1 and 523

MATα2 can form homo- dimers or tetramers that have different affinity for substrates, 524

and MATα2 can interact with MATβ to strengthen the activity of (MATβ)4 (Murray et 525

al., 2014). In Saccharomyces cerevisiae, when two MATs that share 92% identity in 526

amino acid sequence are disrupted, the mutants display opposite phenotypes to the 527

excess ethionine added in the growth medium (Thomas and Surdin-Kerjan, 1987; 528

Thomas et al., 1988; Thomas and Surdin-Kerjan, 1991), indicating that different MAT 529

isoforms act on their own rhythms. There are four close MAT homologs in 530

Arabidopsis. However, we found that in the in vitro assays MAT3 has the highest 531

activity, while MAT1, MAT2 and MAT4 have comparable but lower activities. Among 532

them, MAT4 is predominant as its missense mutation reduces SAM and DNA 533



28

methylation to greater extent than MAT1 and MAT2 loss-of-function mutations, and 534

can release the silencing of Pro35S::NPTII, while other mutations cannot. We used 535

the CRISPR/Cas9 technique, but failed to get the loss-of-function homozygous 536

mutant of MAT4. These results indicate that MAT4 is an essential gene for plant 537

growth and development in Arabidopsis. We found that the MAT4 promoter driving 538

different MAT cDNAs can complement mat4 mutants. However, only a few mat4 539

mutants can be complemented by the MAT1 promoter driving MAT4 cDNA, which 540

might be caused by high expression of ProMAT1::MAT4-GFP in these transgenic 541

lines, likely because the T-DNAs were inserted in environment-friendly sites in the 542

genomic region. Nevertheless, mat4 mutants were not complemented in several 543

ProMAT2::MAT4-GFP and ProMAT3::MAT4-GFP transgenic lines. These results 544

indicate the expression pattern of MAT4, but not MAT4 protein itself, is important for 545

its predominant biological roles in Arabidopsis. Using pull-down assays and co-IP 546

assays, we found that MATs interacted with each other both in vitro and in vivo, 547

suggesting that MATs can also form homo-, and/or hetero- oligomers of different sizes 548

in Arabidopsis. However, more attempts or even crystallographic structural analyses 549

should be carried out to obtain more information about their precise composition in 550

Arabidopsis. 551

Materials and Methods 552

Plant Growth Conditions, Mutant Screening and Identification 553

Arabidopsis (Arabidopsis thaliana) seeds were sterilized with 0.5% NaClO and then 554

sown into Murashige and Skoog (MS) medium, which contained 2% (weight/volume) 555

sucrose and 0.8% (w/v) agar. After 3 days at 4°C, the plates were transferred to 556

growth chambers with long-day conditions (23 h of light / 1 h of dark) at 22°C. 557

Generally, 10-day seedlings were transferred to soil and cultured in a greenhouse with 558

long-day conditions (16 h of light / 8 h of dark) at 20°C. 559

We used L119, which harbors two transgenes, ProRD29A::LUC and 560

Pro35S::NPTII, as the wild-type line. The mutants were selected from an 561



29

ethyl-methanesulfonate mutagenized population of L119 for resistance to 25 mg/L 562

Kan, whereas the L119 lines are typically sensitive under this condition. Map-based 563

cloning was conducted to identify the mutation. We crossed our mutants with Ler and 564

obtained the F2 population, from which we selected Kan-resistant lines (519 total) for 565

mapping. 566

For mutant complementation, the full genomic length of MAT4, including the 2221 bp 567

promoter and the overall genomic sequence, was cloned into pCAMBIA1307. The 568

construct in Agrobacterium tumefaciens strain GV3101 was transformed into mat4 by 569

the floral dip method (Clough and Bent, 1998). The homozygous transgenic lines 570

were selected on MS medium supplemented with 30 mg/L hygromycin from the next 571

T2 generation. All of the primers used in this study are listed in the Supplemental 572

Table S2. 573

RNA Analysis 574

For real-time reverse transcription quantitative PCR (RT-qPCR), total RNA was 575

isolated using TRIzol reagent (Invitrogen) from 15-day seedlings, and 4 µg RNA was 576

reverse-transcribed into cDNA using the GOSCRIPT reverse transcription system 577

(Promega A5001). Then, 2 µL of diluted (10X) cDNA mixture was used as the 578

template for a PCR assay using 20 µL of SYBR Green Master Mix (TaKaRa) 579

performed on a Step One Plus system (Applied Biosystems). The experiments were 580

performed in three independent biological replicates with technical triplicate. All of 581

the primers used in the real-time PCR assay are listed in Supplemental Table S2. 582

Subcellular Localization 583

The full-length cDNA of MAT4 fused with a GFP tag under the control of the super 584

promoter was constructed in the pCAMBIA 1300 vector and the full genomic length 585

of MAT4, including the 2221 bp promoter and the overall genomic sequence, was 586

cloned into pCAMBIA1300. The plasmids were extracted and purified with the 587

Plasmid Maxprep Kit (VIGOROUS N001). Then, we introduced the plasmids into 588

Arabidopsis protoplasts as previously described (Kong et al., 2015). After 14-16 h of 589



30

incubation in light, the protoplasts were viewed using a confocal microscope (Zeiss 590

LSM 510 META), and the GFP signal was detected with 488 nm excitation. Empty 591

GFP plasmids were used as a control. A. tumefaciens strain GV3101 carrying the 592

same constructs were also injected into N. benthamiana leaves. After 48-72 hours of 593

incubation, a section of the injected leaves was examined using the confocal 594

microscope, and the GFP signal was detected using 488 nm excitation. An empty GFP 595

construct was used as a control. We also obtained transgenic lines by transforming 596

this construct into L119 using A. tumefaciens strain GV3101. The 7-day growth of the 597

T2 homozygous transgenic plants was used to detect fluorescence signals using a 598

confocal microscope (Zeiss LSM 510 META) with 488 nm excitation. 599

Cellular Distribution of MAT4-FLAG 600

Next, 0.1 g of 15-day seedlings was ground into powder in liquid nitrogen and 601

suspended with 200 µL isolation buffer (0.4 M sucrose, 10 mM Tris∙HCl (pH=8.0), 10 602

mM MgCl2, 5 mM β-Mercaptoethanol, 1 mM PMSF), then filtered through 603

microcloth (Calbiochem: 475855-1R), and the flow-through was centrifuged at 2800 g 604

for 10 minutes at 4°C. The supernatant was used for the cytosol, while the precipitate 605

was used for the nuclei after four washes with isolation buffer. Then immunoblotting 606

using antibodies (H3: Millipore, 07-690; FLAG: Sigma-Aldrich, F3165; PEPC: 607

Agrisera, AS09458) was carried out. Here, phosphoenolpyruvate carboxylase (PEPC) 608

was used as the cytosol marker, while H3 was used as the nucleus marker. 609

Bisulfite Sequencing 610

Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN 69104) 611

from 15-day seedlings. The EZ Methylation-Gold Kit (Zymo Research D5005) was 612

used to analyze DNA methylation. Five hundred nanograms of DNA was added to the 613

reaction, and all steps followed the protocol supplied in the kit. Nearly 50 ng treated 614

DNA was added to the PCR reaction using the specific primers listed in Supplemental 615

Table 2. The PCR products were introduced into the pMD18-T simple vector (Takara 616

6011), and at least 15 clones were sequenced for each sample. 617



31

Histone Extraction and Immunoblotting 618

Histone proteins were extracted from 15-day seedlings following the protocol as 619

previously described (Li et al., 2012). The antibodies used in immunoblotting were 620

H3 (Millipore: 07-690), H3K9me1 (Millipore: 17-680), H3K9me2 (Abcam: ab1220), 621

H3K27me1 (Millipore: 07-448), and H3K4me3 (Millipore: 07-473). H3 was used as 622

the loading control. The experiments were performed in three independent biological 623

replicates. 624

Histone Immunofluorescence Staining Assay 625

The assay mainly followed a previously described process (Soppe et al., 2002) with 626

subtle modifications. The nuclei were isolated from 15-day seedlings. After 627

resuspending with sorting buffer, the nuclei were dropped on the slides to air dry. The 628

nuclei were then post-fixed using 4% paraformaldehyde in PBS for 20 minutes, 629

washed four times with PBS, and closed with signal enhancer (Cell Signalling: 11932) 630

for 30 minutes at room temperature. After washing four times, the plates were 631

incubated with primary antibody for 2 hours at 37°C or overnight at 4°C covered with 632

parafilm. Then, the plates were washed four times in vats filled with PBST (PBS 633

added with 0.1% TWEEN20), each for five minutes, and incubated with secondary 634

antibody in dark for 1.5 hours at room temperature. Then, the plates were washed four 635

times in vats filled with PBST. Eight microliters of 4',6-diamidino-2-phenylindole 636

(DAPI) (1 µg/mL) was added onto the slides to counterstain the nuclei. The slides 637

were covered with cover glasses. The signal was observed with a confocal microscope 638

(Leica sp5) and collected under the emission wave-length of 405 nm and 561 nm for 639

DAPI and Rhodamine. 640

The primary antibodies used in this assay were H3K9me1 (Millipore: 17-680, 641

1:50, Rabbit), H3K9me2 (Abcam: ab1220, 1:100, Mouse), H3K27me1 (Millipore: 642

07-448, 1:100, Rabbit), H3K4me3 (Millipore: 07-473, 1:100, Rabbit). Secondary 643

antibodies used in this assay were Rhodamine Red conjugate-Goat anti-mouse 644

(Invitrogen R6393) and Rhodamine Red conjugate-Goat anti-rabbit (Invitrogen 645



32

R6394). 646

Whole-genome Bisulfite Sequencing and Analyses 647

Genomic DNA was extracted from 15-day seedlings using DNeasy Plant Mini Kit 648

(QIAGEN 69104). Two micrograms DNA was used for bisulfite treatment and library 649

construction, and MethylC-seq was carried out using HiSeq 2000 (Illumina). 650

Raw data were obtained from the whole-genome bisulfite sequencing using the 651

Illumina HiSeq platform. Clean data were generated by trimming adaptor bases and 652

removing low quality reads. For data analysis, paired-end clean reads were mapped to 653

the reference genome sequence of the Arabidopsis genome (TAIR10) with Bismark 654

(Krueger and Andrews, 2011). The DMRs (differentially-methylated regions) were 655

determined and identified as previously published (Zhao et al., 2014). 656

For investigation of DMR enrichment, we followed the previously described 657

analysis with some modifications (Zhao et al., 2014). The DNA methylation level in 658

genes without transposable elements (TEs), short TEs (shorter than 0.5 kb) and long 659

TEs (longer than 4 kb) were calculated. 660

RNA Sequencing and Analysis 661

Total RNA was extracted from 15-day-old seedlings using the RNeasy Plant Mini Kit 662

(QIAGEN 74904). Two µg RNA was used for library construction, each sample with 663

two replicates. The transcriptome data set used in this study was obtained using the 664

Illumina HiSeq platform, and 125 bp trimmed paired-end reads with high quality were 665

generated. The trimmed reads were mapped to the reference genome sequence of the 666

Arabidopsis genome (TAIR10) using bowtie2 667

(http://computing.bio.cam.ac.uk/local/doc/bowtie2.html) with default settings 668

(Langmead et al., 2009). Differential gene expression analyses were performed using 669

edgeR (http://bioinf.wehi.edu.au/edgeR/) (Robinson et al., 2010). We selected genes 670

with fold change >2 and P <0.0001 compared to wild type as differential expression 671

genes and TEs. The distribution of differentially-expressed genes and TEs in the 672

chromosomes was plotted by circos (Krzywinski et al., 2009). The categories of 673



33

up-regulated TEs were divided as previously described (Wang et al., 2015). 674

Chromatin Immunoprecipitation (ChIP) Assays 675

Nuclei were isolated from 15-day seedlings and fixed with 1% formaldehyde, 676

following the protocol as described previously (Saleh et al., 2008). The pure nuclei 677

were resuspended with 300 µL of cold nuclei lysis buffer, then the genomic DNA was 678

sonicated into 250-500 bp fragments, and the supernatant was diluted with ChIP 679

dilution buffer. Twenty microliters of protein A/G Magnetic beads (Millipore: 16-663) 680

was added for 90 minutes at 4°C to decrease nonspecific combination with gentle 681

rotation. All steps that needed to collect beads were carried out on a Magnetic rack on 682

ice. The antibody H3K9me2 (Abcam: ab1220) was added with gentle rotation over 683

night at 4°C to allow combination. The Magnetic beads were washed five times: one 684

time with low salt wash buffer, one time with high salt wash buffer, one time with 685

LiCl wash buffer and two times with TE buffer. Each wash was 5 minutes at 4°C with 686

gentle rotation. The protein and DNA complex were eluted by elution buffer at 65°C 687

and then incubated at 65°C for at least 6 h or overnight to reverse cross-linking. Next, 688

the RNAs were digested using RNase A at 37°C for 2 hours, and then the proteinase K 689

was added to digest the protein at 65°C at least for 6 hours. The QIAquick PCR 690

Purification Kit (QIAGEN: 28106) was used to obtain high quality DNA, then the 691

concentrations of the DNA measured with Qubit Fluorometer 3.0 (Invitrogen: Q33216) 692

were adjusted to 50 pg/µL. Lastly, 1 µL DNA was used as the template in 20 µL of 693

SYBR Green Master mix (TaKaRa) on a Step One Plus machine (Applied 694

Biosystems). The experiments were performed in three independent biological 695

replicates. 696

Measurement of SAM Contents by liquid chromatography-mass spectrometry 697

(LC-MS) 698

Sixteen-day-old seedlings were used for the subsequent measurements. The extraction 699

and determination methods were followed as previously described with some 700

modifications to extraction (Nikiforova et al., 2005). We added 300 µL methanol 701



34

(volume/volume: 80% and precooled at -20°C) and 100 µL precooled methanol with 702

15 mg/mL DTT to 100 mg plant samples that had been ground into powder in liquid 703

nitrogen, vortexed for 1 minute, extracted for 30 minutes on ice and then centrifuged 704

at 4 °C for 10 minutes at 12000 g. We added 300 µL precooled isopropanol and 100 705

µL precooled methanol with 15 mg/mL DTT to re-suspend the precipitation, extracted 706

for 30 minutes on ice and then centrifuged at 4°C for 10 minutes at 12000 g. The two 707

supernatants were combined, filtered, and then analyzed via LC-MS. The experiments 708

were performed in three independent biological replicates with technical triplicate. 709

Acquisition of Knockout Mutants using the CRISPR/Cas9 Assay 710

The targets were selected according to the website of 711

http://www.crisprscan.org/?page=sequence. Two targets were chosen for each gene, 712

and primers were designed. Fragments were amplified by PCR using pCBC-DT1T2 713

as a template (Wang et al., 2015). After PCR products were purified, they were 714

digested using the restriction enzyme BsaI and ligated using T4 ligase in one system 715

for 5 hours at 37°C, 5 minutes at 50°C and 10 minutes at 80°C. Then transformed 716

them into the competent cell of JM109. After incubation, the correct clone was 717

identified. The construct in A. tumefaciens strain GV3101 was transformed into L119 718

by the floral dip method (Clough and Bent, 1998). The transgenic lines were selected 719

on MS medium supplemented with 30 mg/L hygromycin from the T1 generation and 720

sequenced to obtain knockout lines. 721

Determination of the Activities of MATs 722

The activities of MATs were determined by measuring the production amount of SAM 723

after reactions. The purified proteins of MAT1-His, MAT2-His, MAT3-His, 724

MAT4-His and MAT4 (D246N)-His in Escherichia coli were desalted using a 10-kD 725

Centrifugal Filter Unit (Millipore UFC501096). The reaction was carried out in a 200 726

µl mixture that included 40 µg MAT, 10 mM ATP, 5 mM methionine, 0.1 M Tris-HCl 727

(pH=8.0), 0.02 M MgCl2 and 0.2 M KCl at 37°C for 20 minutes, and then the reaction 728

was terminated by adding 800 µl of 75% acetonitrile and 1.2% formic acid. The 729



35

reaction solution was transferred to a 10-kD Centrifugal Filter Unit and centrifuged at 730

full speed in 4°C for 10 minutes. The solution was used for LC-MS analysis. The 731

experiments were performed in three independent biological replicates with technical 732

triplicate. 733

Pull-Down Assays 734

The full-length cDNA of MAT1, MAT2, MAT3 and MAT4 fused with His and GST 735

tags were constructed in PET30a and pGEX-4T-1. The relevant plasmids were 736

co-transformed into the Rosetta (DE3) strain of E. coli. The Glutathione-Sepharose 737

beads were used to purify the proteins. Then the proteins were eluted from the 738

Glutathione-Sepharose beads using 10 mM reduced GSH in 50 mM Tris∙HCl. The cell 739

lysates before addition of Glutathione-Sepharose beads were used as input to detect 740

whether two proteins were both expressed. Then products were detected by 741

immunoblot using the antibodies of His and GST. 742

Co-immunoprecipitation (co-IP) Assays in Arabidopsis protoplasts 743

The full-length cDNAs of MAT1, MAT2, MAT3 and MAT4 fused with FLAG and GFP 744

tags under the control of the super promoter were constructed in the pCAMBIA 1300 745

vector. The plasmids were extracted and purified with the Plasmid Maxprep Kit 746

(VIGOROUS N001). Then, the two relevant plasmids were co-introduced into 747

Arabidopsis protoplasts as previously described (Kong et al., 2015). After 14-16 h of 748

incubation in light, the protoplasts were collected and total protein was extracted 749

using the immunoprecipitation buffer (50 mM Tris-HCl, pH 7.6, 5 mM MgCl2, 150 750

mM NaCl, 10% glycerol, 0.5% NP-40, 1 mM DTT, 1 mM PMSF, and protease 751

inhibitor cocktail, 1:100, 1 plate per mL, Roche) for 30 minutes on ice. The protein 752

solution was centrifuged at 12000 g for 15 minutes at 4 °C. Ten microliter 753

GFP-Trap_A (Chromotek: gta-20) was added to the supernatant, then gently rotated 754

for 2.5 hours at 4°C to allow combination. The GFP-Trap_A was washed five times 755

using the immunoprecipitation buffer, then the immunoprecipitated products were 756

detected by immunoblot using the antibodies of GFP and FLAG. 757



36

Gel Filtration Assay 758

MAT4-FLAG was used to prepare the protein for gel filtration. More than 20 g of 759

MAT4-FLAG seedlings grown on MS medium for 15 days were collected and then 760

ground to a powder in liquid nitrogen. The protein was extracted using IP buffer (10 761

mM HEPES, 1 mM EDTA (pH=8.0), 100 mM NaCl, 10% glycerol, 0.5%Triton X-100, 762

1 mM DTT, 1 mM PMSF, and protease inhibitor cocktail,1 plate per mL, Roche) for 763

30 minutes on ice. Then the protein solution was centrifuged at 12000 g for 15 764

minutes at 4 °C. The supernatant was added to the ANTI-FLAG M1 Agarose Affinity 765

Gel (Sigma-Aldrich: A4596), then gently rotated for 2.5 hours at 4°C to allow 766

combination. The FLAG Agarose was washed five times using the IP buffer, and the 767

protein was eluted using 0.5 µg/µL FLAG Peptide (Sigma-Aldrich: F3290). We 768

prepared 0.5 mg protein for gel filtration analysis. The effluent of the indicated peaks 769

were sent for LC-MS analysis. 770

Accession numbers 771

The gene accession numbers that were used in this study are as follows: AT3G17390 772

(MAT4/SAM3/MTO3), AT1G02500 (MAT1/SAM1), AT4G01850 (MAT2/SAM2), 773

AT2G36880 (MAT3), DDM1 (AT5G66750), AT3G18780 (ACTIN), AT5G52310 774

(RD29A), AT2G17690 (SDC), AT4G03650 (AtGP1), BD298459.1 (TSIs). 775

RNA-seq, and BS-seq data were deposited in the National Center for Biotechnology 776

Information GEO database under accession number GSE84014. 777

Supplemental Data 778

The following supplemental materials are available. 779

Supplemental Figure S1. T-DNA insertion positions in L119. 780

Supplemental Figure S2. Growth phenotypes of mat4 mutants and Kan-resistant 781

phenotypes of two ddm1 alleles. 782

Supplemental Figure S3. Effects of mat4 on DNA methylation throughout the five 783

chromosomes. 784

Supplemental Figure S4. Complementation of reduced histone modification in 785

mat4 by MAT4-FLAG. 786



37

Supplemental Figure S5. Confirmation of RNA-seq data by RT-qPCR and 787

association between DNA methylation and gene expression. 788

Supplemental Figure S6. T-DNA insertion positions, expression levels, and SAM 789

contents in mat1, mat2 and mat3. 790

Supplemental Figure S7. Whole genomic DNA methylation changes in mat1, 791

mat2 and mat3. 792

Supplemental Figure S8. Kanamycin sensitivity of mat1, mat2 and mat3 793

CRISPR/Cas9 mutants in L119. 794

Supplemental Figure S9. Complementation of mat4 by MAT4 driven by the 795

native MAT1 promoter. 796

Supplemental Figure S10. Growth and development phenotypes of mat1mat2 797

double mutants and embryogenic defects of mat2-c19mat4 double mutants. 798

Supplemental Figure S11. The interaction of MAT1, MAT2 and MAT3 with 799

different MATs as determined by co-immunoprecipitation assays. 800

Supplemental Figure S12. The interaction of MAT1, MAT2, MAT3 with different 801

MATs as determined by protein pull-down assays. 802

Supplemental Table 1. LC-MS/MS analyses of affinity co-purified proteins from 803

MAT4-FLAG seedlings. 804

Supplemental Table 2. Primers used in this study 805

Supplemental data set S1. Hypo- differentially methylated regions of CG in mat4. 806

Supplemental data set S2. Hypo- differentially methylated regions of CHG in 807

mat4. 808

Supplemental data set S3. Hypo- differentially methylated regions of CHH in 809

mat4. 810

Supplemental data set S4. Differentially-expressed genes up-regulated in mat4. 811

Supplemental data set S5. Differentially-expressed genes down-regulated in 812

mat4. 813



38

Supplemental data set S6. Differentially-expressed TEs up-regulated in mat4. 814

Supplemental data set S7. Differentially-expressed TEs down-regulated in mat4. 815

ACKNOWLEDGEMENTS 816

We thank Dr. Zhen Li and Dr. Zhongzhou Chen in China Agricultural University for 817

assistance in LC-MS analyses and gel filtration, respectively. This study was 818

supported by the Natural Science Foundation of China (31330041). 819

820



39

Figure Legends 821

Figure 1. Diagram of the methyl-group supply in one-carbon metabolism. 822

Enzymes involved in one-carbon metabolism: MAT/SAMS (methionine 823

adenosyltransferase/S-adenosyl-methionine synthetase); MT (methyltransferase); 824

SAHH1/HOG1 (S-adenosyl-homocysteine hydrolase/ homology-dependent gene 825

silencing1); MS (methionine synthase); FPGS (folylpolyglutamate synthetase). FPGS 826

catalyzes the synthesis of 5-CH3-THF-Glun, which provides active methyl group for 827

Hcy for Met synthesis by MS. MAT/SAMS uses Met and ATP as substrates to 828

synthesis SAM, which converts to SAH after methylation reaction of MT. 829

SAHH1/HOG1 can hydrolyze SAH to Hcy. 830

Figure 2. Identification and characterization of MAT4 831

A. Kan resistance of mat4 mutants. Seeds were germinated on Murashige and Skoog 832

(MS) medium or MS supplemented with 25 mg/L Kan. L119 was the transgenic line 833

harboring silenced Pro35S::NPTII and ProRD29A::LUC (proRD29A, an abiotic 834

stress-inducible promoter). ddm1-18 (indicated as ddm1) was selected in the same 835

genetic screening and reactivated both transgenic sites. 836

B. Protein levels of NPTII in L119, mat4 and ddm1 detected by immunoblot. ACTIN 837

was the loading control. 838

C. Transcript levels of transgenic and endogenous loci by real-time RT-qPCR analysis. 839

Transcript levels were normalized to ACTIN2 and relative to L119. Three independent 840

experiments were conducted with similar results. Data are from one experiment with 841

three technical replicates. Error bars are the means ± SD, asterisks indicate significant 842

differences determined by Student’s t-test (* indicates P< 0.05; ** indicates P< 0.01; 843

*** indicates P< 0.001). 844

D. Silenced ProRD29A::LUC reactivation in mat4 and ddm1. Seedlings of L119, mat4 845

and ddm1 were treated with 300 mM NaCl for three hours before detecting the 846

inflorescence signal with a CCD camera (Roper, 1300D). 847



40

E. Identification of MAT4 by map-based cloning. There was a G to A mutation, which 848

changed 246-Asp to 246-Asn in AT3G17390. 849

F. Complementation of Kan resistance and delayed-germination in mat4 by MAT4. 850

G. NPTII level restored to the basal level of L119 in MAT4-FLAG as determined by 851

immunoblot analyses using anti-NPTII antibodies. ACTIN was the loading control. 852

H. Subcellular localization of MAT4. a. Transgenic line carrying Pro35S::MAT4-GFP 853

in L119; b. Transient expression of ProMAT4::MAT4-GFP in a protoplast; c. 854

Transient expression of ProMAT4::MAT4-GFP in Nicotiana benthamiana leaf 855

epidermal cells. 856

I. Detection of the subcellular localization of MAT4-FLAG after isolating the cytosol 857

and nuclei. PEPC was a marker protein in the cytosol and H3 was a marker protein in 858

the nuclei. 859

Figure 3. DNA methylation of the transgenic and endogenous RD29A promoter 860

in mat4 861

A. DNA methylation of the 35S promoter region by bisulfite sequencing in L119, 862

mat4, ddm1, and MAT4-FLAG. 863

B. DNA methylation of the transgenic RD29A promoter region by bisulfite 864

sequencing in L119, mat4, ddm1, and MAT4-FLAG. 865

C. DNA methylation of the endogenous RD29A promoter region by bisulfite 866

sequencing in L119, mat4, ddm1, and MAT4-FLAG. 867

D. DNA methylation of the T-DNA insertion region in L119 and mat4 as determined 868

by whole-genome bisulfite sequencing as indicated by IGV software windows. 869

Figure 4. Whole-genome DNA methylation levels in mat4 870

A. Whole-genome DNA methylation levels of CG, CHG, and CHH in L119, ddm1 871

and mat4. Bisulfite sequencing data for L119 and mat4 were from this study. Data for 872

ddm1 were from a previously published study (Zemach et al., 2013). 873



41

B. Relative changes in the DNA methylation levels of CG, CHG, and CHH in L119, 874

ddm1 and mat4. 875

C. Frequency distribution histograms of significant methylation differences (P< 0.01) 876

between L119 and mat4 in CG, CHG, and CHH. The histograms were made with 877

100-bp analyzable windows over the genome-wide scale and the methylation levels of 878

L119 and mat4 in CG, CHG and CHH context were calculated separately. 879

D. CG, CHG and CHH methylation of L119, ddm1 and mat4 at genes that do not 880

contain TEs (including 2 kb upstream and downstream). TSS: transcription start site; 881

TTS: transcription termination site. 882

E. CG, CHG and CHH methylation of L119, ddm1 and mat4 at TEs that are shorter 883

than 0.5 kb (S-TE), including 2 kb upstream and downstream, and at TE body regions. 884

F. CG, CHG and CHH methylation of L119, ddm1 and mat4 at TEs that are longer 885

than 4 kb (L-TE), including 2 kb upstream and downstream, and at TE body regions. 886

Figure 5. Histone H3K9me2 and H3K27me1 levels in mat4 887

A. Immunoblot assays with antibodies against H3K9me1, H3K9me2, and H3K27me1 888

in L119, ddm1 and mat4. H3 was the loading control. 889

B. Statistical analyses of relative signal intensity in (A). We set the signal intensity of 890

L119 as 100 to calculate the relative signal intensity of other mutants. Error bars are 891

the means ± SD (n=3). Asterisks indicate significant differences determined by 892

Student’s t-test (* indicates P< 0.05; ** indicates P< 0.01). 893

C. Histone methylation patterns of H3K9me1 in the nuclei of L119, ddm1 and mat4 as 894

detected by immunofluorescence assay. 895

D. Histone methylation patterns of H3K9me2 in the nuclei of L119, ddm1 and mat4 as 896

detected by immunofluorescence assay. 897

E. Histone methylation patterns of H3K27me1 in the nuclei of L119, ddm1 and mat4 898

as detected by immunofluorescence assay. 899



42

From C-E. On the right, the graphs show the percentage of nuclei with condensed or 900

dispersed signal: gray represents a condensed and white represents a dispersed signal. 901

n = number of nuclei. 4',6-diamidino-2-phenylindole (DAPI) stains the 902

pericentromeric heterochromatin regions. 903

F. Detection of H3K9me2 in L119, ddm1 and mat4 at several selected loci by 904

chromatin immunoprecipitation (ChIP) combined with RT-qPCR. Three independent 905


three technical replicates. Error bars are the means ± SD (n=3). Asterisks indicate 907

significant differences determined by Student’s t-test (* indicates P < 0.05; ** 908

indicates P < 0.01). 909

Figure 6. Gene expression changes in mat4 by RNA sequencing 910

A. Differentially expressed genes in mat4 compared with L119. Transcript levels of 911

genes that changed more than two-fold and had P < 0.0001 were selected. Gene up: 912

up-regulated genes; Gene down: down-regulated genes. 913

B. Differentially expressed TEs in mat4 compared with L119. Transcript levels of TEs 914

that changed more than two-fold and had a P< 0.0001 were selected. TE up: 915

up-regulated TEs; TE down: down-regulated TEs 916

C. Distribution of the differentially expressed genes and TEs on the five chromosomes. 917

The purple circle represents the differentially expressed genes, the blue circle 918

represents the differentially expressed TEs, and the green circle represents the 919

differentially methylated regions in mat4. The outer bars indicate the up-regulated 920

genes, TEs and hyper-differentially methylated regions (DMRs), and the inner bars 921

indicate the down-regulated genes, TEs and hypo-DMRs; the length of the bars 922

represents the fold change of the genes, TEs and DMRs. The black dots indicate the 923

chromocenters. 924

D. Overlap of up-regulated TEs among mat4, ddm1 and fpgs1. The overlap number 925

was calculated using VENNY2.1. 926



43

E. Categories of up-regulated TEs in mat4. The diagram shows the percentage of 927

different TE types among the total up-regulated TEs. 928

Figure 7. Application of SAM to rescue the release of silencing in mat4 929

A. SAM content in mat4 compared with L119 as determined by LC-MS. Three 930

independent experiments were conducted with similar results. Data are from one 931

experiment with three technical replicates. Error bars are the means ± SD, n=3. 932

Asterisks indicate significant differences determined by Student’s t-test (** indicates 933

P< 0.01). 934

B. SAH content in mat4 compared with L119 as determined by LC-MS. Three 935


experiment with three technical replicates. Error bars are the means ± SD, n=3. 937

Asterisks indicate significant differences determined by Student’s t-test (*** indicates 938

P< 0.001). 939

C. Kanamycin resistance of mat4 can be partially rescued by exogenously adding 400 940

mg/L SAM to medium supplemented with 25 mg/L Kan. 941

D. Statistical results show the survival rate of seedlings grown on the indicated 942

medium. Error bars are the means ± SD (n=15). Asterisks indicate significant 943

differences determined by Student’s t-test (* indicates P< 0.05; *** indicates P< 944

0.001). 945

E. Transcript levels of NTPII and endogenous loci by real-time RT-qPCR analysis 946

using the seedlings grown on medium supplemented with 400 mg/L SAM. Three 947


experiment with three technical replicates. Error bars are the means ± SD. Asterisks 949

indicate significant differences determined by Student’s t-test (* indicates P< 0.05; ** 950

indicates P< 0.01; *** indicates P < 0.001). 951

F. Histone methylation patterns of H3K9me2 in L119 and mat4 seedlings grown on 952

MS medium or MS medium supplemented with 400 mg/L SAM as determined by 953



44

immunofluorescence assays with anti-H3K9me2 antibodies. DAPI staining (blue) was 954

performed on the pericentromeric heterochromatin regions. 955

G. The percentage of nuclei that showed a condensed or dispersed signal. n = number 956

of nuclei. 957

Figure 8. The catalytic activities of MAT proteins 958

A. Comparison of the catalytic activities of MAT proteins. The same amount of MAT 959

proteins as indicated by Coomassie staining were added for individual reactions. The 960

reaction that had no protein added was used as a negative control. Three independent 961


three technical replicates. Error bars are the means ± SD (n=3). 963

B. SAM production with increasing concentrations of MAT4. Protein amounts were 964

indicated by Coomassie staining. The reaction that had no protein added was used as a 965

negative control. Three independent experiments were conducted with similar results. 966

Data are from one experiment with three technical replicates. Error bars are the means 967

± SD (n=3). 968

C, D. The GFP fluorescence of mat4 transgenic lines carrying the MAT4 promoter 969

driving MAT1, MAT2 or MAT3 cDNA. The seedlings were grown on MS for seven 970

days, and the GFP fluorescence in root tips (C) or the whole seedlings (D) was 971

visualized by a confocal microscope (Zeiss LSM 510 META) and a fluorescent 972

microscope (Olympus SEX16), respectively. 973

E. Kan resistance and delayed-germination in mat4 was complemented by MAT1, 974

MAT2 or MAT3 driven by the promoter of MAT4. 975

Figure 9. MAT4 plays a predominant role in plant growth and development 976

A. Kan resistance and delayed-germination in mat4 was not complemented by 977

ProMAT1::MAT4-GFP, ProMAT2:: MAT4-GFP or ProMAT3::MAT4-GFP, but was 978

complemented by ProMAT4::MAT2-GFP. 979

B. The GFP fluorescence in seedlings of transgenic lines carrying 980



45

ProMAT1::MAT4-GFP, ProMAT2::MAT4-GFP, ProMAT3::MAT4-GFP or 981

ProMAT4::MAT2-GFP grown on MS for seven days. 982

C. Statistical results of the fluorescence intensity of the transgenic lines in (B) in a 983

fixed area in cotyledons by ImageJ. Error bars are the mean ± SD (n=12). 984

D. Detection of MAT4-GFP in transgenic lines by immunoblotting using anti-GFP 985

antibodies. ACTIN was the loading control. 986

E. mat1-c19 mat4 double mutant seedlings compared to the wild type (L119) grown in 987

soil under long-day conditions. The mutant did not produce any seeds. 988

F. The siliques of WT and mat2-c13(-/-) mat4(+/-). Asterisks indicate the wizened 989

seeds of mat2-c13 mat4 homozygous double mutants. 990

G. Wizened seed percentages in siliques of mat2-c13(-/-) mat4(+/-) heterozygous 991

mutants compared to the WT. 992

Figure 10. MAT4 interacts with different MATs in plants 993

A. MAT4 interactions with MAT1, MAT2, MAT3 or MAT4 itself in a protein 994

co-immunoprecipitation (co-IP) assay. Total proteins were extracted from Arabidopsis 995

protoplasts transiently co-expressing the MAT4-FLAG with MAT1-, MAT2-, MAT3-, 996

MAT4-GFP or GFP (as a negative control) plasmids, and immunoprecipitated with 997

anti-GFP beads. The co-IP proteins were immunoblotted with anti-FLAG and 998

anti-GFP antibodies. 999

B. Protein pull-down assay for MAT4 interaction with MAT1, MAT2, MAT3 or 1000

MAT4 itself. Total proteins were isolated from E. coli co-expressing MAT4-His with 1001

GST-MAT1, -MAT2, -MAT3, -MAT4 or GST itself (as a negative control), and 1002

immunoprecipitated with Glutathione-Sepharose beads. The co-IP proteins were 1003

immunoblotted with anti-His and anti-GST antibodies. 1004

C. Gel filtration analyses. The 0.5 mg of total proteins extracted from approximately 1005

20 g of the 15-day seedlings of MAT4-FLAG were applied to an ANTI-FLAG M1 1006

Agarose Affinity Gel. The proteins were eluted using 0.5 µg/µL FLAG Peptide. The 1007



46

elution at the peaks was used for LC/MS analysis. 1008

D. LC-MS/MS analyses of the proteins of the three peaks in (C). Cov indicated the 1009

percentage of sequence coverage (%), Seq (sig) indicated number of significant 1010

sequences. 1011

1012

1013

1014



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http://www.ncbi.nlm.nih.gov/pubmed?term=Andrea Steimer PA%2C Karin Afsar%2CPaul Fransz%2COrtrun Mittelsten Scheid%2Cand Jerzy Paszkowskia %282000%29 Endogenous targets of transcriptional gene silencing in Arabidopsis%2Epdf%2E The Plant Cell 12%3A 1165�??1178&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Andrea Steimer PA, Karin Afsar,Paul Fransz,Ortrun Mittelsten Scheid,and Jerzy Paszkowskia (2000) Endogenous targets of transcriptional gene silencing in Arabidopsis.pdf. The Plant Cell 12: 1165?1178

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Andrea&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Endogenous targets of transcriptional gene silencing in Arabidopsis.pdf.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Endogenous targets of transcriptional gene silencing in Arabidopsis.pdf.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Andrea&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Baubec T%2C Dinh HQ%2C Pecinka A%2C Rakic B%2C Rozhon W%2C Wohlrab B%2C von Haeseler A%2C Mittelsten Scheid O %282010%29 Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis%2E Plant Cell 22%3A 34%2D47&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, Wohlrab B, von Haeseler A, Mittelsten Scheid O (2010) Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis. Plant Cell 22: 34-47

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Baubec&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic States in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Baubec&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bernatavichute YV%2C Zhang X%2C Cokus S%2C Pellegrini M%2C Jacobsen SE %282008%29 Genome%2Dwide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana%2E PLoS One 3%3A e3156&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3: e3156

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bernatavichute&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bernatavichute&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bruce P%2E May ZBL%2C Yuda Fang%2C David L%2E Spector%2C Robert A%2E Martienssen %282005%29 Differential Regulation of Strand%2DSpecific Transcripts from Arabidopsis Centromeric Satellite Repeats%2E PLoS Genetics 1&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bruce P. May ZBL, Yuda Fang, David L. Spector, Robert A. Martienssen (2005) Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats. PLoS Genetics 1

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bruce&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bruce&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Cao X%2C Jacobsen SE %282002%29 Locus%2Dspecific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes%2E Proceedings of the National Academy of Sciences 99%3A 16491%2D16498&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proceedings of the National Academy of Sciences 99: 16491-16498

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Cao&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Cao&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Cao X%2C Jacobsen SE %282002%29 Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing%2E Curr Biol 12%3A 1138%2D1144&dopt=abstract

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http://scholar.google.com/scholar?as_q=Mechanism of DNA methylation-directed histone methylation by KRYPTONITE&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Du&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Du J%2C Zhong X%2C Bernatavichute YV%2C Stroud H%2C Feng S%2C Caro E%2C Vashisht AA%2C Terragni J%2C Chin HG%2C Tu A%2C Hetzel J%2C Wohlschlegel JA%2C Pradhan S%2C Patel DJ%2C Jacobsen SE %282012%29 Dual binding of chromomethylase domains to H3K9me2%2Dcontaining nucleosomes directs DNA methylation in plants%2E Cell 151%3A 167%2D180&dopt=abstract

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Ebbs ML, Bender J (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell18: 1166-1176


Friso S, Choi SW, Girelli D, Mason JB, Dolnikowski GG, Bagley PJ, Olivieri O, Jacques PF, Rosenberg IH, Corrocher R, Selhub J (2002)A common mutation in the 5,10-methylenetetrahydrofolate reductase gene affects genomic DNA methylation through an interactionwith folate status. Proc Natl Acad Sci U S A 99: 5606-5611


Fusao Takusagawa SK, and George D. Markham (1996) Structure and Function of S-Adenosylmethionine Synthetase Crystal Structuresof S-Adenosylmethionine Synthetase with ADP, BrADP, and PPi at 2.8 Å Resolution.pdf. Biochemistry 35: 2586-2596


Goto DB, Ogi M, Kijima F, Kumagai T, van Werven F, Onouchi H, Naito S (2002) A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana. Genes & GeneticSystems 77: 89-95


Groth M, Moissiard G, Wirtz M, Wang H, Garcia-Salinas C, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J,Hale CJ, Long JA, Hell R, Diaz de la Garza RI, Jacobsen SE (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun 7:11640


He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK (2009) NRPD4, a protein related to the RPB4 subunit ofRNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev 23: 318-330


He XJ, Hsu YF, Pontes O, Zhu JH, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK (2009) NRPD4, a protein related to the RPB4 subunitof RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes &Development 23: 318-330


He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK (2009) An effector of RNA-directed DNAmethylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137: 498-508


Henderson IR, Jacobsen SE (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation andinitiate siRNA spreading. Genes Dev 22: 1597-1606


Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3methyltransferase. Nature 416: 556-560


Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD (2009)ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16:763-768


Jin Y, Ye N, Zhu F, Li H, Wang J, Jiang L, Zhang J (2017) Calcium-dependent protein kinase CPK28 targets the methionineadenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis.Plant J www.plantphysiol.orgon April 9, 2020 - Published by Downloaded from

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http://www.ncbi.nlm.nih.gov/pubmed?term=Ebbs ML%2C Bender J %282006%29 Locus%2Dspecific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase%2E Plant Cell 18%3A 1166%2D1176&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ebbs ML, Bender J (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18: 1166-1176

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ebbs&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ebbs&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Friso S%2C Choi SW%2C Girelli D%2C Mason JB%2C Dolnikowski GG%2C Bagley PJ%2C Olivieri O%2C Jacques PF%2C Rosenberg IH%2C Corrocher R%2C Selhub J %282002%29 A common mutation in the 5%2C10%2Dmethylenetetrahydrofolate reductase gene affects genomic DNA methylation through an interaction with folate status%2E Proc Natl Acad Sci U S A 99%3A 5606%2D5611&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Friso S, Choi SW, Girelli D, Mason JB, Dolnikowski GG, Bagley PJ, Olivieri O, Jacques PF, Rosenberg IH, Corrocher R, Selhub J (2002) A common mutation in the 5,10-methylenetetrahydrofolate reductase gene affects genomic DNA methylation through an interaction with folate status. Proc Natl Acad Sci U S A 99: 5606-5611

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Friso&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Friso&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fusao Takusagawa SK%2C and George D%2E Markham %281996%29 Structure and Function of S%2DAdenosylmethionine Synthetase Crystal Structures of S%2DAdenosylmethionine Synthetase with ADP%2C BrADP%2C and PPi at 2%2E8 � Resolution%2Epdf%2E Biochemistry 35%3A 2586%2D2596&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fusao Takusagawa SK, and George D. Markham (1996) Structure and Function of S-Adenosylmethionine Synthetase Crystal Structures of S-Adenosylmethionine Synthetase with ADP, BrADP, and PPi at 2.8 � Resolution.pdf. Biochemistry 35: 2586-2596

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fusao&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Structure and Function of S-Adenosylmethionine Synthetase Crystal Structures of S-Adenosylmethionine Synthetase with ADP, BrADP, and PPi at 2&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Structure and Function of S-Adenosylmethionine Synthetase Crystal Structures of S-Adenosylmethionine Synthetase with ADP, BrADP, and PPi at 2&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fusao&as_ylo=1996&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Goto DB%2C Ogi M%2C Kijima F%2C Kumagai T%2C van Werven F%2C Onouchi H%2C Naito S %282002%29 A single%2Dnucleotide mutation in a gene encoding S%2Dadenosylmethionine synthetase is associated with methionine over%2Daccumulation phenotype in Arabidopsis thaliana%2E Genes %26 Genetic Systems 77%3A 89%2D95&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Goto DB, Ogi M, Kijima F, Kumagai T, van Werven F, Onouchi H, Naito S (2002) A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana. Genes & Genetic Systems 77: 89-95

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Goto&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Goto&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Groth M%2C Moissiard G%2C Wirtz M%2C Wang H%2C Garcia%2DSalinas C%2C Ramos%2DParra PA%2C Bischof S%2C Feng S%2C Cokus SJ%2C John A%2C Smith DC%2C Zhai J%2C Hale CJ%2C Long JA%2C Hell R%2C Diaz de la Garza RI%2C Jacobsen SE %282016%29 MTHFD1 controls DNA methylation in Arabidopsis%2E Nat Commun 7%3A 11640&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Groth M, Moissiard G, Wirtz M, Wang H, Garcia-Salinas C, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Diaz de la Garza RI, Jacobsen SE (2016) MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun 7: 11640

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http://scholar.google.com/scholar?as_q=MTHFD1 controls DNA methylation in Arabidopsis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Groth&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=He XJ%2C Hsu YF%2C Pontes O%2C Zhu J%2C Lu J%2C Bressan RA%2C Pikaard C%2C Wang CS%2C Zhu JK %282009%29 NRPD4%2C a protein related to the RPB4 subunit of RNA polymerase II%2C is a component of RNA polymerases IV and V and is required for RNA%2Ddirected DNA methylation%2E Genes Dev 23%3A 318%2D330&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK (2009) NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev 23: 318-330

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=He&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=He&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=He XJ%2C Hsu YF%2C Pontes O%2C Zhu JH%2C Lu J%2C Bressan RA%2C Pikaard C%2C Wang CS%2C Zhu JK %282009%29 NRPD4%2C a protein related to the RPB4 subunit of RNA polymerase II%2C is a component of RNA polymerases IV and V and is required for RNA%2Ddirected DNA methylation%2E Genes %26 Development 23%3A 318%2D330&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=He XJ, Hsu YF, Pontes O, Zhu JH, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK (2009) NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes & Development 23: 318-330



http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=He&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=He XJ%2C Hsu YF%2C Zhu S%2C Wierzbicki AT%2C Pontes O%2C Pikaard CS%2C Liu HL%2C Wang CS%2C Jin H%2C Zhu JK %282009%29 An effector of RNA%2Ddirected DNA methylation in arabidopsis is an ARGONAUTE 4%2D and RNA%2Dbinding protein%2E Cell 137%3A 498%2D508&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK (2009) An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137: 498-508


http://scholar.google.com/scholar?as_q=An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=He&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Henderson IR%2C Jacobsen SE %282008%29 Tandem repeats upstream of the Arabidopsis endogene SDC recruit non%2DCG DNA methylation and initiate siRNA spreading%2E Genes Dev 22%3A 1597%2D1606&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Henderson IR, Jacobsen SE (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev 22: 1597-1606

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Henderson&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Henderson&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jackson JP%2C Lindroth AM%2C Cao X%2C Jacobsen SE %282002%29 Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase%2E Nature 416%3A 556%2D560&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jackson&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

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http://www.ncbi.nlm.nih.gov/pubmed?term=Jacob Y%2C Feng S%2C LeBlanc CA%2C Bernatavichute YV%2C Stroud H%2C Cokus S%2C Johnson LM%2C Pellegrini M%2C Jacobsen SE%2C Michaels SD %282009%29 ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing%2E Nat Struct Mol Biol 16%3A 763%2D768&dopt=abstract

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Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE (2007) The SRA methyl-cytosine-binding domain linksDNA and histone methylation. Curr Biol 17: 379-384


Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJM (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nature Genetics 40: 670-675


Kong L, Cheng J, Zhu Y, Ding Y, Meng J, Chen Z, Xie Q, Guo Y, Li J, Yang S, Gong Z (2015) Degradation of the ABA co-receptor ABI1 byPUB12/13 U-box E3 ligases. Nat Commun 6: 8630


Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572


Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic forcomparative genomics. Genome Res 19: 1639-1645


Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the humangenome. Genome Biol 10: R25


Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204-220


Li W, Han Y, Tao F, Chong K (2011) Knockdown of SAMS genes encoding S-adenosyl-l-methionine synthetases causes methylationalterations of DNAs and histones and leads to late flowering in rice. J Plant Physiol 168: 1837-1843


Li X, Qian W, Zhao Y, Wang C, Shen J, Zhu JK, Gong Z (2012) Antisilencing role of the RNA-directed DNA methylation pathway and ahistone acetyltransferase in Arabidopsis. Proc Natl Acad Sci U S A 109: 11425-11430


Lindermayr C, Saalbach G, Bahnweg G, Durner J (2006) Differential inhibition of Arabidopsis methionine adenosyltransferases byprotein S-nitrosylation. J Biol Chem 281: 4285-4291


Mao D, Yu F, Li J, Van de Poel B, Tan D, Li J, Liu Y, Li X, Dong M, Chen L, Li D, Luan S (2015) FERONIA receptor kinase interacts withS-adenosylmethionine synthetase and suppresses S-adenosylmethionine production and ethylene biosynthesis in Arabidopsis. PlantCell Environ 38: 2566-2574


Mao DD, Yu F, Li J, Van de Poel B, Tan D, Li JL, Liu YQ, Li XS, Dong MQ, Chen LB, Li DP, Luan S (2015) FERONIA receptor kinaseinteracts with S-adenosylmethionine synthetase and suppresses S-adenosylmethionine production and ethylene biosynthesis inArabidopsis. Plant Cell and Environment 38: 2566-2574

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http://www.ncbi.nlm.nih.gov/pubmed?term=Jin Y%2C Ye N%2C Zhu F%2C Li H%2C Wang J%2C Jiang L%2C Zhang J %282017%29 Calcium%2Ddependent protein kinase CPK28 targets the methionine adenosyltransferases for degradation by the 26S proteasome and affects ethylene biosynthesis and lignin deposition in Arabidopsis%2E Plant J&dopt=abstract

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http://www.ncbi.nlm.nih.gov/pubmed?term=Mao DD%2C Yu F%2C Li J%2C Van de Poel B%2C Tan D%2C Li JL%2C Liu YQ%2C Li XS%2C Dong MQ%2C Chen LB%2C Li DP%2C Luan S %282015%29 FERONIA receptor kinase interacts with S%2Dadenosylmethionine synthetase and suppresses S%2Dadenosylmethionine production and ethylene biosynthesis in Arabidopsis%2E Plant Cell and Environment 38%3A 2566%2D2574&dopt=abstract


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http://www.ncbi.nlm.nih.gov/pubmed?term=Sauter M%2C Moffatt B%2C Saechao MC%2C Hell R%2C Wirtz M %282013%29 Methionine salvage and S%2Dadenosylmethionine%3A essential links between sulfur%2C ethylene and polyamine biosynthesis%2E Biochem J 451%3A 145%2D154&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Sauter M, Moffatt B, Saechao MC, Hell R, Wirtz M (2013) Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis. Biochem J 451: 145-154

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http://scholar.google.com/scholar?as_q=Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Methionine salvage and S-adenosylmethionine: essential links between sulfur, ethylene and polyamine biosynthesis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sauter&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Shen B%2C Li C%2C Tarczynski MC %282002%29 High free%2Dmethionine and decreased lignin content result from a mutation in the Arabidopsis S%2Dadenosyl%2DL%2Dmethionine synthetase 3 gene%2E Plant J 29%3A 371%2D380&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Shen B, Li C, Tarczynski MC (2002) High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene. Plant J 29: 371-380

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http://scholar.google.com/scholar?as_q=High free-methionine and decreased lignin content result from a mutation in the Arabidopsis S-adenosyl-L-methionine synthetase 3 gene&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

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Thomas D, Surdin-Kerjan Y (1987) SAM1, the structural gene for one of the S-adenosylmethionine synthetases in Saccharomycescerevisiae. Sequence and expression. J Biol Chem 262: 16704-16709


Thomas D, Surdin-Kerjan Y (1991) The synthesis of the two S-adenosyl-methionine synthetases is differently regulated inSaccharomyces cerevisiae. Mol Gen Genet 226: 224-232


Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z (2015) Methyl-CpG-binding domain protein MBD7 isrequired for active DNA demethylation in Arabidopsis. Plant Physiol 167: 905-914


Wang ZP, Xing HL, Dong L, Zhang HY, Han CY, Wang XC, Chen QJ (2015) Egg cell-specific promoter-controlled CRISPR/Cas9efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biology 16


Xia R, Wang J, Liu C, Wang Y, Wang Y, Zhai J, Liu J, Hong X, Cao X, Zhu JK, Gong Z (2006) ROR1/RPA2A, a putative replication proteinA2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 18: 85-103


Yamaguchishinozaki K, Shinozaki K (1994) A Novel Cis-Acting Element in an Arabidopsis Gene Is Involved in Responsiveness toDrought, Low-Temperature, or High-Salt Stress. Plant Cell 6: 251-264


Yang DL, Zhang G, Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK (2016) Dicer-independent RNA-directed DNA methylation inArabidopsis. Cell Res 26: 66-82


Ye R, Chen Z, Lian B, Rowley MJ, Xia N, Chai J, Li Y, He XJ, Wierzbicki AT, Qi Y (2016) A Dicer-Independent Route for Biogenesis ofsiRNAs that Direct DNA Methylation in Arabidopsis. Mol Cell 61: 222-235


Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer Stacey L, Zilberman D (2013) The ArabidopsisNucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin. Cell 153: 193-205


Zhang H, Deng X, Miki D, Cutler S, La H, Hou YJ, Oh J, Zhu JK (2012) Sulfamethazine suppresses epigenetic silencing in Arabidopsisby impairing folate synthesis. Plant Cell 24: 1230-1241


Zhao Y, Xie S, Li X, Wang C, Chen Z, Lai J, Gong Z (2014) REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat ShockProtein Family and Is Required for DNA Demethylation in Arabidopsis. Plant Cell 26: 2660-2675


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http://scholar.google.com/scholar?as_q=The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zemach&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhang H%2C Deng X%2C Miki D%2C Cutler S%2C La H%2C Hou YJ%2C Oh J%2C Zhu JK %282012%29 Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis%2E Plant Cell 24%3A 1230%2D1241&dopt=abstract

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http://scholar.google.com/scholar?as_q=Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhao Y%2C Xie S%2C Li X%2C Wang C%2C Chen Z%2C Lai J%2C Gong Z %282014%29 REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis%2E Plant Cell 26%3A 2660%2D2675&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhao Y, Xie S, Li X, Wang C, Chen Z, Lai J, Gong Z (2014) REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis. Plant Cell 26: 2660-2675

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhao&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhao&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhou HR%2C Zhang FF%2C Ma ZY%2C Huang HW%2C Jiang L%2C Cai T%2C Zhu JK%2C Zhang C%2C He XJ %282013%29 Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis%2E Plant Cell 25%3A 2545%2D2559&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhou HR, Zhang FF, Ma ZY, Huang HW, Jiang L, Cai T, Zhu JK, Zhang C, He XJ (2013) Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. Plant Cell 25: 2545-2559

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhou&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhou&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


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