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Supplementary Table and Figures
PcG complex Drosophila Human RING1A
Ring/Sex Combs Extra (Sce) RING1B CBX2 CBX4 CBX6 CBX7
Polycomb (Pc)
CBX8 PCGF1/NSPC1 PCGF2/MEL18
PCGF3 PCGF4/BMI1
PCGF5
Posterior Sex Combs (Psc)
PCGF6/MBLR PHC1
PRC1
Polyhomeotic (Ph) PHC2 EZH1
Enhancer of Zeste (E(z)) EZH2
Suppressor of Zeste 12 (Suz12) SUZ12 Extra Sex combs (Esc) EED variants
RBAP46
PRC2
Nucleosome remodeling factor 55 (p55) RBAP48 SFMBT1 SFMBT2 L3MBTL2
Scm with Four MBT Domains (Sfmbt)
MBTD1 PhoRC
Pleiohomeotic (Pho) YY1
Number of MBT domains Drosophila Human
SCMH1 2 Sex Comb on Midleg (Scm)
SCML2 L3MBTL1 L3MBTL3 3
lethal (3) malignant brain tumor (L(3)mbt)
L3MBTL4 SFMBT1 SFMBT2 L3MBTL2
4 Scm with Four MBT Domains (Sfmbt)
MBTD1
Table S1. PcG complexes (top) and MBT domain-containing proteins (bottom) in
flies and humans.
nor
mal
ized
den
sity
SFMBT1LSD1CoRESTINPUT
SFMBT1LSD1
CoRESTCTCF
H3K27ac
H3K27me3
POL IIH3K36me3
H3K4me1
H3K4me2
H3K4me3
H3K79me2
H3K9acH4K20me1
Scalechr1:
20 kb hg19149790000 149800000 149810000 149820000 149830000 149840000 149850000 149860000
HIST2H2BFHIST2H2BFHIST2H2BFHIST2H3D
HIST2H4AHIST2H4ABC019846
HIST2H3CHIST2H2AA3
HIST2H2BCHIST2H2AA3
HIST2H3C
BC019846
HIST2H4A
HIST2H4AHIST2H2BE
HIST2H2ACHIST2H2AB
40 -
0 40 -
0 40 -
0 40 -
0
INPUT
SFMBT1
LSD1
CoREST
A
Figure S1
-10 -8 -6 -4 -2 0 2 4 6 8 10
1
2
3
4
Distance from TSS (kbp)
B
C
Figure S1, related to Figure 2, ChIP-seq read density profiles and correlation with
histone PTMs.
A. SFMBT1 (blue), LSD1 (orange), CoREST (violet) and input (grey) ChIP-seq read
distribution on ± 10kb from TSSs. The x axis represents the distance from the TSS (kbp)
and the y axis indicates the normalized read density.
B. High-density map of all the SFMBT1 ERs that are also bound by LSD1 or
CoREST. Each horizontal line represents a separate TSS (± 5kb region), with the
position of the TSS marked by the vertical green midline. The position of ERs for the
indicated protein is represented by horizontal segments.
C. Read density profile for input, SFMBT1, LSD1, and CoREST at the HIST2
cluster. The x axis corresponds to the genomic location and the y axis corresponds to the
normalized ChIP-seq signal density. Location of the histone genes are represented at the
bottom.
unsynch
ronized
early S
late SG2/M
G1
synchronized
SFMBT1
LSD1
CoREST
Cyclin E2
p-H3S10
ß-tubulin0 200400
600 8001000PI
unsynchronized
early S
late S
G2/M
G1
−600 −400 −200 0 200 400 600
−20
020
4060
SFMBT1
bp from TSS
Ant
ibod
y −
inpu
t (R
P10
M) G1
S
−600 −400 −200 0 200 400 600
050
100
150
200 LSD1
bp from TSS
Ant
ibod
y −
inpu
t (R
P10
M) G1
S
−600 −400 −200 0 200 400 600
−20
020
4060
CoREST
bp from TSS
Ant
ibod
y −
inpu
t (R
P10
M) G1
S
−600 −400 −200 0 200 400 600
−20
020
4060
IgG
bp from TSS
Ant
ibod
y −
inpu
t (R
P10
M) G1
S
Scalechr5:
1 kb hg19
PWWP2A
6 -
-6 _10 -
-10 _10 -
-10 _6 -
-6 _10 -
-10 _10 -
-10 _
SFMBT1
LSD1
CoREST
SFMBT1
LSD1
CoREST
S phase
G1 phase
Figure S2
A B
C
D
Figure S2, related to Figure 5, Components of the SLC complex are enriched at the
replication-dependent histone loci during G1 phase but not S phase.
A. Cell cycle phases of HeLa S3 cells released after double thymidine
synchronization (Figure 5B-D) as confirmed by FACS analysis. The x axis represents the
propidium iodine (PI) reading. The cell population in different cell cycle stage is
represented by a histogram, with its correlated cell cycle phase indicated next to it.
B. SFMBT1, LSD1, and CoREST proteins are not differentially expressed during the
cell cycle. HeLa S3 cells were released after double thymidine synchronization and four
population of cells were collected: cells in early S, late S, G2/M, and G1 phase. Proteins
analyzed are marked on the right side of each panel.
C. Enrichment of SFMBT1, LSD1, CoREST, and IgG at all histone genes within
HIST1 and HIST2 loci. The x axis corresponds to number of base pair from TSS and the y
axis to read per 10 million reads (RP10M) after input subtraction.
D. Read density profile for SFMBT1, LSD1, and CoREST at the PWWP2A promoter
during two cell cycle stages: S and G1. The x axis corresponds to the genomic location
and the y axis to the normalized ChIP-seq signal density of each antibody after
subtraction of the IgG signal.
D10D12D14D16D18
D20D22D24D26six weeksmSFMBT1 mSFMBT2 mLSD1 mCoREST
mRN
A a
bund
ance
(rel
ativ
e to
β-a
cin)
15%
10%
5%
0%
SFMBT1
β-tubulin
D10 D14 D20 MiceMice PND Adult
RNA binding
RNA processing
ncRNA metabolic process
ncRNA processing
mRNA metabolic process
GO Molecular Function
GO Biological Process
1.0E-1 1.0E-5 1.0E-9 1.0E-13 1.0E-17 1.0E-21p-value
Figure S3
A B
C D
SFMBT1
LSD1
538 15965696
Figure S3. The SLC complex in mouse testes.
A. mRNA abundance of SFMBT1, SFMBT2, LSD1, and CoREST in mice testis.
The y axis represents the mRNA abundance (in percentages relative to β-actin). Bars
represent the protein expression levels in mouse testis every other day from postnatal day
10 (D10) to day 26 (D26) mice, and from six-week-old adult mice.
B. Western blot analysis of SFMBT1 protein levels in day 10/14/20 mice and in
adult mice. Equal loading was confirmed by blotting for β-actin.
C. Venn diagram showing the overlap of ERs for SFMBT1 (blue) and LSD1
(orange), as determined by ChIP-seq in pachytene stage spermatocytes.
D. GO molecular function and biological process analysis of the highly enriched
regions targeted by both SFMBT1 and LSD1 using GREAT. The x axis corresponds to
the binomial raw p-value (in logarithmic scale).
dSfmbt_MBT1
dSfmbt_MBT4dSfmbt_MBT3dSfmbt_MBT2
SFMBT2_MBT1
SFMBT2_MBT4SFMBT2_MBT3SFMBT2_MBT2
SFMBT1_MBT1
SFMBT1_MBT4SFMBT1_MBT3SFMBT1_MBT2
L3MBTL1_MBT1
L3MBTL1_MBT3L3MBTL1_MBT2
dSfmbt_MBT1
dSfmbt_MBT4dSfmbt_MBT3dSfmbt_MBT2
SFMBT2_MBT1
SFMBT2_MBT4SFMBT2_MBT3SFMBT2_MBT2
SFMBT1_MBT1
SFMBT1_MBT4SFMBT1_MBT3SFMBT1_MBT2
L3MBTL1_MBT1
L3MBTL1_MBT3L3MBTL1_MBT2
Figure S4
Figure S4, related to discussion and Figure 3. Amino acid sequence alignment of
MBT domains from dSfmbt, human L3MBTL1, SFMBT1, and SFMBT2.
The predicted secondary structure is represented at the bottom. Residues important for
binding, as determined byseveral structural studies, are indicated with red stars. Three
residues aligning the aromatic cage located at the loop region between β3 and β4 (as
identified in the fourth MBT domain of dSfmbt and the second MBT domain of
L3MBTL1) are highlighted in yellow. The four residues in the MBT domains of
SFMBT1 that are mutated in this study are highlighted in blue.