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Supplementary Materials and Methods
Histology and electron microscopy
Left ventricular heart tissue from P0 pup was minced and fixed in 2%
paraformaldehyde, 2.5% glutaraldehyde, and 0.1M cacodylate buffer. For
electron microscopy on heart tissue of 7-week old mice, animals were perfused
with a 4% paraformaldehyde, 1% gluteraldehyde, and 0.1M cacodylate buffer,
followed by isolation and mincing of left ventricular heart tissue. Electron
microscopy was performed at the UT Southwestern Electron Microscopy Core
Facility using a FEI Tecnai G2 Spirit 120 Biotwin TEM.
Differential gene expression analysis
We performed RNA-seq using the Next Generation Sequencing Core at the
University of Texas Southwestern Medical Center. Three micrograms of DNAse-
treated RNA per replicate were prepared using the TruSeq Stranded LT Kit from
Illumina. Samples were then PCR amplified and purified with Ampure XP beads
before sequencing on a HiSeq 2500 instrument (Illumina, Inc., San Diego, CA).
All procedures were carried out according to manufacturer protocols.
Quality assessment of the RNA-seq data was done using NGS-QC-Toolkit
(Patel and Jain, 2012). Reads with mean phred quality scores of less than 20
were removed from further analysis. Quality filtered reads were then aligned to
the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0 )
aligner (Kim et al., 2013) using default setting. Differential gene expression
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analysis was done using the R package DESeq (v 1.10.1) (Anders and Huber,
2010) following the protocols outlined in (Anders et al., 2013). Read counts were
normalized by taking the median of each gene count across samples and
dividing each sample gene count by the relative ratio of library sizes between the
calculated median and sample size. The averaged normalized expression values
of the triplicate samples were used to calculate fold change and p-values. Cutoff
values of fold change greater than 1.5 and p-value less than 0.01 were then used
to select for differentially expressed genes between sample group comparisons.
Pathway enrichment analysis
Significant pathway enrichment analysis was performed using Ingenuity
Pathways Analysis (Ingenuity® Systems). Differentially expressed genes from
the RNA expression data are associated with a biological function supported by
at least one publication in the Ingenuity Pathways Knowledge Base. Fisher’s
exact test was used to calculate the p-value and determine the probability that
each biological function was enriched in the dataset due to chance alone.
Statistically significant biological pathways were then identified by selection for
pathways with p-values less than 0.05. DAVID gene functional annotation and
classification tool (Huang et al., 2007) was used to annotate the list of
differentially expressed genes with respective Gene Ontology terms and perform
GO enrichment analysis for molecular and biological functional categories.
Functional Gene Ontology groups were selected for significance by using a p-
value cutoff of 1%.
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CArG-box scan
Known mouse CArG-box sequences were previously reported (Sun et al., 2006).
The genomic sequences around the transcription start site (TSS) (-5 kb/+5 kb) of
each differential expressed transcript were retrieved from the Ensembl bioMart
server. In-house script was used to search each TSS flanking sequences for
exact match of any known CArG-box sequences. Euarchontoglaire subset of
basewise conservation scores (phyloP) for mouse genome (mm10) was
downloaded from UCSC genome browser (Kent et al., 2002). Genomic locations
of CArG-box sequences in TSS flanking regions were kept if: (1) the average
phyloP of the motif is positive and no less than 80% of the nucleotides have
positive phyloP and (2) the flanking (-50 bp/+50 bp) region of the motif has a
positive average phyloP.
Transthoracic echocardiography
Measurements of interventricular septum, left ventricular posterior wall thickness
and the diameter of the LV at the end-diastole and end-systole were obtained.
Images were digitally recorded and analyzed using the Visual Sonic software
Vevo 770 (Version 2.30). Left ventricular fractional shortening (FS) was
calculated based on the left ventricular internal dimension-diastole (LVIDd) and
the left ventricular internal dimension in systole (LVIDs) according to the
following formula: FS (%) = [(LVIDd – LVIDs)/LVIDd] × 100.
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Supplemental References
Anders, S., Huber, W., 2010. Differential expression analysis for sequence count data. Genome Biol. 11, R106. doi:10.1186/gb-2010-11-10-r106
Anders, S., McCarthy, D.J., Chen, Y., Okoniewski, M., Smyth, G.K., Huber, W., Robinson, M.D., 2013. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc 8, 1765–1786. doi:10.1038/nprot.2013.099
Huang, D.W., Sherman, B.T., Tan, Q., Kir, J., Liu, D., Bryant, D., Guo, Y., Stephens, R., Baseler, M.W., Lane, H.C., Lempicki, R.A., 2007. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35, W169–75. doi:10.1093/nar/gkm415
Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., Haussler, D., 2002. The human genome browser at UCSC. Genome Res. 12, 996–1006. doi:10.1101/gr.229102
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36. doi:10.1186/gb-2013-14-4-r36
Patel, R.K., Jain, M., 2012. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7, e30619. doi:10.1371/journal.pone.0030619
Sun, Q., Chen, G., Streb, J.W., Long, X., Yang, Y., Stoeckert, C.J., Miano, J.M., 2006. Defining the mammalian CArGome. Genome Res. 16, 197–207. doi:10.1101/gr.4108706
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Supplementary Figures
Figure S1. Generating and analyzing MRTFcdKO animals. (A) Breeding strategy used to generate MRTF cardiac double knockout (MRTFcdKO) mice. Global MRTF-A knockout mice and conditional cardiac MRTF-B knockout mice were used to generate MRTF-A-/-; MRTF-Bfl/fl;αMHC-Cre (MRTFcdKO) mice. (B) qRT-PCR confirmed deletion of MRTF-A and MRTF-B in MRTFcdKO hearts at P0. MRTF-A was undetectable in MRTFcdKO hearts. Residual MRTF-B levels represent MRTF-B expression in non-cardiomyocytes. Shown also is the down-regulation of SRF following MRTF deletion. (C) H&E staining of MRTFcdKO hearts at 10 days and 3 weeks of age revealed left ventricle dilation, indicative of heart failure. Scale Bar: 2mm. (D) Representative echocardiography images from control (top panel) and MRTFcdKO animals (bottom panel) at 7-8 weeks of age.
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Figure S2. Gene ontology analysis of differentially expressed genes in
MRTFcdKO hearts.
(A) GO analysis identified multiple enriched terms in MRTFcdKO hearts at P0. (B)
Genes relating to apoptosis and cell death were significantly altered by GO
analysis in MRTFcdKO hearts at P0 compared to control mice.
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Figure S3. Validation of RNA-seq analysis by RT-qPCR.
qPCR for genes relating to apoptosis and the cytoskeleton confirmed changes in
expression similar to those observed by RNA-seq.
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Table S1. The top 50 most differentially expressed genes in MRTFcdKO mice.
ID Fold Change Log2FoldChange P-‐Value GM28438 0.006991375 -‐6.913357102 8.66E-‐77 2610507I01RIK 0.024794668 -‐5.197798958 4.62E-‐32 LYNX1 0.027393684 -‐5.168201061 2.23E-‐12 GM3650 48.6092862 4.860981491 6.93E-‐15 ACTA1 0.047721728 -‐4.377932644 0.000992976 GM8210 0.051578972 -‐3.978989328 6.60E-‐08 UNC13C 16.59667462 3.967248271 4.77E-‐28 GM5860 0.060054144 -‐3.935039121 2.66E-‐21 GM11469 0.066478934 -‐3.796788214 3.08E-‐20 UNC5A 0.059165642 -‐3.61240345 4.32E-‐07 EIF3J1 0.083257466 -‐3.51892299 3.94E-‐22 GM14267 0.083466882 -‐3.513042584 3.48E-‐22 TRPV3 0.057750553 -‐3.488026787 2.90E-‐05 MUC5B 0.067284126 -‐3.39322234 1.93E-‐06 GM9522 11.34369589 3.357454595 2.34E-‐08 GM12247 12.2692679 3.291540761 1.77E-‐07 DDX4 0.087372346 -‐3.156585105 8.96E-‐06 1700119I11RIK 0.089300824 -‐3.052548135 0.003527209 RP23-‐172B15.2 0.09806965 -‐2.98359562 3.05E-‐05 KLHDC9 9.366912286 2.836143723 0.005455509 MOGAT2 0.092112142 -‐2.774327258 0.001905934 PCSK1 0.089317443 -‐2.688478302 0.008775964 GM15848 10.04943971 2.663034354 0.008423659 ZFP429 0.151458396 -‐2.655658924 2.37E-‐07 NEK5 7.490095467 2.539384444 0.000956468 MYL9 0.174558299 -‐2.518023512 2.09E-‐05 2510016G02RIK 0.146303782 -‐2.487030755 0.002497563 G530011O06RIK 7.021882749 2.480727966 0.001107203 GM1966 0.141353602 -‐2.403275937 0.00951382 GM13841 5.82283645 2.397705576 0.000257269 4932418E24RIK 0.155926692 -‐2.392875205 0.003945343 TRIM5 0.163355153 -‐2.320831509 0.004483675 ACTN3 5.749525499 2.311248472 0.005789967 SERPINA3H 5.619168988 2.303683426 0.000559737 4930556M19RIK 5.765472303 2.297798561 0.00085532 PLA2G4B 0.18976905 -‐2.271402081 0.00010793 HBB-‐BT 0.207084867 -‐2.264965171 0.000159347 ANGPTL3 0.190215162 -‐2.259072117 0.000307181 SERTM1 0.196793464 -‐2.244957912 2.61E-‐05 TRIM30D 0.175402082 -‐2.236070712 0.002857508
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BANF2OS 0.203176088 -‐2.223357451 0.000122305 RHBDL2 0.177829033 -‐2.196002688 0.006149259 GM11627 0.210179365 -‐2.188972706 0.000211178 GM28515 4.806953603 2.188306636 2.88E-‐06 GM14018 0.200150263 -‐2.166925754 0.001705125 4930458D05RIK 0.220096867 -‐2.146118008 6.18E-‐10 GM26782 0.221579179 -‐2.136064944 2.25E-‐08 GM10435 0.228238604 -‐2.127967789 5.94E-‐13 SEMA5B 0.214816333 -‐2.082665987 0.000669866 8430419K02RIK 4.393285413 2.027666993 0.000241323
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Table S2. The 21 genes with altered expression in MRTFcdKO mice in the top 5
Canonical Pathways by Ingenuity Pathway Analysis.
ID Fold Change Log2FoldChange P-‐Value ACTA1 0.047721728 -‐4.389209894 0.000992976 MYL9 0.174558299 -‐2.518219151 2.09E-‐05 CDH6 0.314165124 -‐1.670405063 0.008952751 RHOJ 0.417505323 -‐1.260133503 7.88E-‐05 ACTC1 0.42738002 -‐1.22640863 0.000473576 NME1 0.444463448 -‐1.169863317 2.44E-‐05 EPN3 0.454044278 -‐1.1390951 0.005201225 TUBA4A 0.470514507 -‐1.087688889 0.000363999 PAK6 0.471730137 -‐1.083966324 5.07E-‐05 TUBB4A 0.477602957 -‐1.066116326 0.00959656 ITGA2 0.551414173 -‐0.858791745 0.003510127 TUBB2A 0.573225532 -‐0.802825224 0.002759575 TUBG1 0.581554405 -‐0.78201393 0.002377598 ACTG1 0.592564452 -‐0.754956013 0.004970196 TUBB6 0.651918472 -‐0.61723654 0.004347837 ACTB 0.656546268 -‐0.607031412 0.002607208 PIP4K2C 1.539197091 0.622177977 0.005479088 RHOU 1.639862995 0.713575287 0.003396742 GNAO1 1.858589575 0.894208221 0.00056425 MYL1 2.120180046 1.084186784 0.000388454 MYH14 2.31729352 1.212440795 0.000241154
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Table S3. The 37 differentially expressed genes in MRTFcdKO mice that were
associated with cell death and survival by DAVID Gene Ontology Analysis.
ID Fold Change Log2FoldChange P-‐Value ACTC1 0.42738002 -‐1.226403272 0.000473576 ADAMTSL4 1.617712492 0.692130131 0.004393991 AEN 0.630454695 -‐0.664412906 0.009034744 APOE 1.727525341 0.788491093 9.52E-‐05 BCL2L11 1.56601491 0.646696821 0.001865514 BMF 2.157140936 1.107524977 1.22E-‐06 BNIP3L 1.603804386 0.68109972 0.001246198 BRCA1 0.595314607 -‐0.746112436 0.002705932 BTG1 1.51929204 0.603160188 0.005733564 CD24A 1.831528173 0.872129683 4.34E-‐05 CD28 2.070189386 1.032001254 0.005147117 CDKN1B 1.563887858 0.644964303 0.002473 CIAPIN1 0.582696652 -‐0.778373251 0.000236447 CLU 1.696087711 0.761973833 0.000144536 CYFIP2 0.279645662 -‐1.833096629 5.77E-‐14 DAP 0.568491801 -‐0.813128752 0.001086605 DHCR24 0.580551317 -‐0.782838132 0.003277917 DNAJA3 0.625828004 -‐0.675894475 0.001838312 DRAM1 1.756618864 0.808589516 0.004050185 EYA1 2.499402622 1.297129794 0.001190505 GM10053 0.624017963 -‐0.68010448 0.000946801 IFI204 2.318606706 1.190849174 0.001765931 LIG4 0.647190911 -‐0.626332888 0.009444837 MKL1 0.276763636 -‐1.837787283 7.90E-‐09 NMNAT3 1.786468276 0.833711075 0.006846066 NTF3 1.947184431 0.948194331 0.006238083 PDCD4 1.910788959 0.933211369 1.22E-‐05 PEG10 0.420515546 -‐1.246505817 3.70E-‐07 PEG3 1.505389899 0.590072905 0.003992632 PGP 0.630298741 -‐0.664364141 0.006545294 SERINC3 1.735154225 0.794996449 0.003539044 SOD2 0.615487811 -‐0.700068608 0.000620067 TNFRSF10B 0.538229818 -‐0.888572672 0.002276175 TRP53INP1 2.436747562 1.284350206 5.13E-‐08 UNC5A 0.059165642 -‐3.61240345 4.32E-‐07 XAF1 2.894341231 1.528310499 2.73E-‐10 YPEL3 2.179018158 1.121093471 3.63E-‐06
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Table S4. The 212 MRTF-regulated genes identified as having a conserved
CArG box within 5kb of the Transcriptional Start Site.
ID Fold Change Log2FoldChange P-‐Value 1190007I07RIK 0.35733476 -‐1.460220054 0.000166275 2210404O09RIK 1.755826455 0.808368442 0.002749905 2810408A11RIK 2.12523291 1.075681187 0.000962172 4930556M19RIK 5.765472303 2.297798561 0.00085532 ACTA1 0.047721728 -‐4.377932644 0.000992976 ACTB 0.656546268 -‐0.606985671 0.002607208 ACTC1 0.42738002 -‐1.226403272 0.000473576 ACTG1 0.592564452 -‐0.752301125 0.004970196 ACTN3 5.749525499 2.311248472 0.005789967 ADAMTSL1 0.450486758 -‐1.140148538 0.00033726 ALAS1 0.602436034 -‐0.730915264 0.000268256 ALG8 0.602918962 -‐0.727392693 0.004227898 AMPD3 0.608333115 -‐0.716090282 0.000990776 ANKRA2 1.581814332 0.660783043 0.003089801 APPL2 1.521854804 0.60557871 0.004574438 AZIN2 2.133719546 1.080289378 0.005215069 B130055M24RIK 0.419959048 -‐1.23051908 0.001839326 B3GALT1 1.615515915 0.689357059 0.007343401 BANF2OS 0.203176088 -‐2.223357451 0.000122305 BC030867 0.487200878 -‐1.021155822 0.006220687 BCAS3 1.899821144 0.924231518 0.000986544 BCL2L11 1.56601491 0.646696821 0.001865514 BCS1L 0.581952134 -‐0.779199153 0.001098062 BRCA1 0.595314607 -‐0.746112436 0.002705932 CALCOCO1 1.883146102 0.912928973 0.000137461 CAMK1G 1.600889387 0.675531713 0.007096875 CAPN6 1.966318775 0.975103131 4.00E-‐06 CAR3 0.250799149 -‐1.943992102 0.001435992 CCNG2 2.320097561 1.213399029 3.14E-‐08 CD28 2.070189386 1.032001254 0.005147117 CD59A 0.529242388 -‐0.915881326 0.000217994 CDC14B 1.850379087 0.887090046 0.00063515 CDO1 1.973914276 0.975133151 0.001271475 CECR2 1.602555862 0.678065285 0.007868531 CHCHD5 1.985208125 0.98474214 0.000165034 CHP2 2.966013801 1.545064309 8.59E-‐06 CHRM2 2.6296554 1.394525033 0.000173965 CKM 0.572760783 -‐0.803973096 4.57E-‐05
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CLEC4G 0.288746686 -‐1.7136804 0.004176137 CLSPN 0.634028494 -‐0.655848124 0.008172442 CNN1 0.355695003 -‐1.488867983 1.98E-‐06 CNN2 0.556641652 -‐0.844743185 0.006413844 CPEB1 2.090011609 1.051636639 0.001435961 CPXM1 1.645658475 0.714744387 0.005351331 CTSF 1.537670056 0.619760582 0.004799016 CYP2U1 0.512643885 -‐0.95611667 0.001142236 DAP 0.568491801 -‐0.813128752 0.001086605 DIXDC1 2.59772605 1.376270352 3.18E-‐10 DLAT 0.632822313 -‐0.660046003 0.00137105 DMPK 0.608053243 -‐0.71743095 0.002084121 DNAJC11 0.619838775 -‐0.689752402 0.007473582 DOK7 0.59177742 -‐0.754959908 0.00142638 DRAM1 1.756618864 0.808589516 0.004050185 DUOX2 4.114136065 1.997259797 5.10E-‐07 DUSP18 0.492845418 -‐1.019301008 5.57E-‐06 DYNLL2 0.621246407 -‐0.686573546 0.001909034 E2F8 0.611843574 -‐0.705697281 0.00995787 EYA1 2.499402622 1.297129794 0.001190505 EZH1 2.085826149 1.059562294 0.001792111 FAM161B 0.578628504 -‐0.787246489 0.002852108 FAM19A3 0.475337176 -‐1.067183223 0.008367932 FAM213B 0.359676788 -‐1.466075226 8.15E-‐07 FAM73B 0.624219853 -‐0.679416126 0.004992484 FAM81A 0.326081777 -‐1.614519915 1.31E-‐06 FANCA 0.555287979 -‐0.843069425 0.00374417 FBLIM1 0.633546885 -‐0.658056673 0.005268296 FBXL22 0.395269496 -‐1.338272995 0.009130366 FCGR2B 2.429937247 1.254143352 0.002714214 FGF11 0.515319775 -‐0.950633398 0.001700989 FRMD5 0.426037017 -‐1.230616901 4.69E-‐05 G530011O06RIK 7.021882749 2.480727966 0.001107203 GAP43 0.511877848 -‐0.956900299 0.003160424 GARNL3 1.620503121 0.694183567 0.002639159 GAS5 1.743804779 0.801167782 0.000618593 GBP6 2.103712575 1.056985301 0.005074501 GCNT1 1.760385519 0.814449032 0.00623247 GM10451 0.307890436 -‐1.651783961 0.00077112 GM11627 0.210179365 -‐2.188972706 0.000211178 GM12409 2.568682813 1.314504618 0.007002268 GM12522 2.614363723 1.347942314 0.002336385 GM12691 2.312181566 1.193114571 0.008727584
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GM14267 0.083466882 -‐3.513042584 3.48E-‐22 GM17029 0.43510604 -‐1.190274972 0.000206294 GM28438 0.006991375 -‐6.913357102 8.66E-‐77 GM5499 0.605707857 -‐0.721639279 0.004513125 GM5860 0.060054144 -‐3.935039121 2.66E-‐21 GM6969 2.481174215 1.309247556 0.002815898 GM8210 0.051578972 -‐3.978989328 6.60E-‐08 GM8730 1.999561646 0.999157831 1.12E-‐06 GM9755 0.644497774 -‐0.633455061 0.002289689 GPR157 0.594932239 -‐0.74826847 0.000801552 GRAP2 3.084516205 1.575175215 0.000400381 GSPT2 1.885105946 0.905642744 0.003719586 GSTA3 3.539547505 1.72020055 0.004244988 HEATR5B 0.620083549 -‐0.689011823 0.001772654 HEBP1 1.888130611 0.914226473 0.002941431 HIST1H1C 1.66217713 0.732615806 0.000332387 HMGN3 1.701127666 0.763720833 0.001961087 HSPB6 0.381180447 -‐1.390635237 1.55E-‐06 HYDIN 3.309227742 1.618132557 0.008873111 IDE 2.134416682 1.093730273 7.44E-‐08 INPP5K 1.854582634 0.89043111 3.12E-‐05 KCNJ3 2.602541461 1.378800469 2.44E-‐07 KCNMB1 0.405570548 -‐1.274910279 0.001717594 KIF5C 0.394119556 -‐1.329097071 0.00010323 KLHL32 0.237626406 -‐2.016878646 0.000164738 LAMA3 1.801374397 0.844235413 0.003969264 LGALS4 0.440841434 -‐1.176732142 0.00096699 LIG4 0.647190911 -‐0.626332888 0.009444837 LMNB2 0.533202606 -‐0.905292101 0.0003583 LRPPRC 0.596990083 -‐0.744080501 0.000802412 LRTM1 0.254569847 -‐1.969925924 3.33E-‐16 MBP 1.626184353 0.697646867 0.008744114 MCM8 0.549620549 -‐0.858473967 0.002957034 MMACHC 0.63777839 -‐0.648312644 0.002876613 MORF4L1 1.933773301 0.948030371 0.000250541 MPI 0.638976806 -‐0.645775125 0.005053929 MRPL34 0.597233973 -‐0.742135237 0.001367958 MRPL42 0.648535447 -‐0.624430234 0.003891228 MRPS25 0.539004295 -‐0.8894007 0.000167034 MSMO1 0.582141904 -‐0.77956749 0.007848531 MTIF2 0.654229905 -‐0.611806443 0.006531523 MYH14 2.31729352 1.197688271 0.000241154 MYL1 2.120180046 1.08242375 0.000388454
15
MYL9 0.174558299 -‐2.518023512 2.09E-‐05 MYO19 0.607228069 -‐0.718062971 0.004138864 NAP1L5 2.146929152 1.087706884 0.001305404 NDUFAF1 0.518409365 -‐0.946859123 2.58E-‐05 NME1 0.444463448 -‐1.16358304 2.44E-‐05 NPPA 1.981809017 0.986687372 1.01E-‐06 NR5A2 0.506810955 -‐0.968589086 0.006604881 NRXN1 2.3145246 1.189743453 0.001147177 NUDT19 0.440788557 -‐1.180299377 1.08E-‐06 NXF3 3.967131057 1.89534454 0.002503031 OBSCN 0.662790825 -‐0.593330251 0.00528976 OCIAD2 2.183947378 1.123352458 0.003358055 OGDHL 0.312592701 -‐1.658709429 3.27E-‐06 OMA1 0.640685877 -‐0.640915637 0.00988875 OXCT1 0.649016174 -‐0.6236099 0.004215392 OXNAD1 0.62317947 -‐0.681842129 0.002102321 PAK6 0.471730137 -‐1.079832323 5.07E-‐05 PAM 1.55737667 0.639107706 0.001083628 PAPPA2 0.498733046 -‐0.982322274 0.009720914 PDE4A 0.613550578 -‐0.703093969 0.009825944 PI15 1.783840695 0.834051736 0.001437012 PIP4K2C 1.539197091 0.621436334 0.005479088 PKHD1L1 0.645475496 -‐0.630580827 0.004688553 PLEKHB2 0.607010295 -‐0.719860901 0.001094664 PM20D2 0.604319081 -‐0.723029633 0.006595691 POLA1 0.63112539 -‐0.662780271 0.007230553 POU6F1 1.719552639 0.780183645 0.001088851 PPA1 0.590789716 -‐0.757866468 0.000966258 PPTC7 0.62536327 -‐0.676842973 0.000550215 PRDM16 0.647542696 -‐0.626039288 0.00733467 PRDM1 0.488027083 -‐1.02352385 0.004267062 PXYLP1 1.743225978 0.799539589 0.001076057 RAB3C 0.360760023 -‐1.440422959 0.000139775 RAD51 0.480417145 -‐1.052682614 0.004108274 RASD2 2.520037848 1.301641865 0.002816563 RHBDL2 0.177829033 -‐2.196002688 0.006149259 RHOJ 0.417505323 -‐1.258609754 7.88E-‐05 RNF167 1.582027924 0.660918738 0.00265968 RP23-‐172B15.2 0.09806965 -‐2.98359562 3.05E-‐05 RP23-‐330G24.3 1.818630316 0.855468674 0.00493082 RP23-‐82P18.3 3.102494642 1.557675167 0.004249188 RPS3A1 1.917583148 0.93718097 0.00013019 RPS3A3 0.390414188 -‐1.354905069 5.41E-‐06
16
RTN2 1.665467238 0.734688753 0.000686906 SEMA3C 0.589206414 -‐0.76195771 0.000781181 SFI1 1.584068706 0.661094723 0.008859806 SGTB 2.246418652 1.156022027 0.000581537 SH3BGRL2 1.767551275 0.819501919 0.000782512 SH3D21 1.994615242 0.985498964 0.004297125 SLC19A3 2.225123439 1.145153791 0.000203333 SLC24A4 2.572170968 1.34132013 0.000216107 SLC28A2 0.362158842 -‐1.458859724 2.34E-‐07 SLC46A3 1.810479091 0.847846921 0.009568978 SLC6A4 3.189730388 1.631923361 0.000126568 SMTN 0.591129301 -‐0.757972474 0.000559498 SOX5 1.825169802 0.861819282 0.006287993 SPATA13 0.577794423 -‐0.79069538 0.006172189 SPEG 0.566854312 -‐0.818649996 0.001848996 SPON1 1.704522159 0.769021581 0.000264427 SQLE 0.561877726 -‐0.830335234 0.000679576 TBC1D1 0.32342122 -‐1.627278636 0.000433226 TCP11L2 2.016820194 1.011578923 0.001132102 TGFA 2.141713324 1.092182206 6.54E-‐05 THRB 1.965956931 0.969292052 0.004082552 TLCD2 1.970431501 0.971592037 0.000596386 TLL1 1.989774993 0.986781723 0.000537508 TM6SF1 0.546624577 -‐0.869520577 0.000155201 TNFRSF19 1.698383063 0.762555036 0.006647234 TNIP1 1.70704759 0.770431073 0.000954218 TPM2 0.446130301 -‐1.163648775 0.001507463 TPM3 1.529984171 0.612872627 0.006216939 TRAFD1 1.53371511 0.616695294 0.004453647 TRIM5 0.163355153 -‐2.320831509 0.004483675 TRIM9 2.427628368 1.254373255 0.004776924 TRP53INP1 2.436747562 1.284350206 5.13E-‐08 TSFM 0.569154222 -‐0.810631909 0.001326032 TUBA4A 0.470514507 -‐1.086894619 0.000363999 TUBB4B-‐PS1 0.615488631 -‐0.697096976 0.003470427 TXNDC16 1.667972329 0.73745954 0.000950595 UBLCP1 0.395267543 -‐1.335242727 9.06E-‐08 UCHL1 0.659722953 -‐0.598224148 0.008746841 UNC13C 16.59667462 3.967248271 4.77E-‐28 WBSCR27 3.151480434 1.643578991 0.001009769 WNK2 0.518983353 -‐0.94192382 0.000999083 YPEL1 2.262632223 1.169513137 0.000661749 ZFP277 1.712236873 0.774763718 0.000710982
17
ZFP949 1.887901503 0.914533839 0.000277428 ZKSCAN2 2.405526056 1.250547415 0.003569223
18
Table S5. The 53 genes identified as both differentially expressed in MRTFcdKO
hearts at P0 and as a target for SRF binding.
ID Fold Change Log2FoldChange P-‐Value CYFIP2 0.279645662 -‐1.833096629 5.77E-‐14 RINL 0.421651597 -‐1.218305833 0.006466608 GDF15 0.248891136 -‐1.878144226 0.003651978 FANCA 0.555287979 -‐0.843069425 0.00374417 C1QBP 0.582267126 -‐0.779812193 0.000113259 SOD2 0.615487811 -‐0.700068608 0.000620067 DNAJC11 0.619838775 -‐0.689752402 0.007473582 ACTC1 0.42738002 -‐1.226403272 0.000473576 RSAD1 0.492701194 -‐1.018656005 2.58E-‐05 LDLR 0.526182016 -‐0.925077011 2.53E-‐05 ACBD4 1.656492048 0.725927862 0.004022942 APPL2 1.521854804 0.60557871 0.004574438 SFI1 1.584068706 0.661094723 0.008859806 RNMTL1 0.536831203 -‐0.894544115 0.000322837 SLC24A4 2.572170968 1.34132013 0.000216107 PARN 1.582149961 0.661184484 0.003687446 ACTB 0.656546268 -‐0.606985671 0.002607208 ANKRD6 1.680484141 0.746022074 0.006462825 ANKRD9 0.60079455 -‐0.730736377 0.008499818 MFN2 0.624031815 -‐0.680257971 0.00146577 SMTN 0.591129301 -‐0.757972474 0.000559498 CIRBP 1.621379661 0.696899857 0.001216818 DEF8 0.639310894 -‐0.64478498 0.005597044 RHOU 1.639862995 0.712248449 0.003396742 BOLA3 0.550968951 -‐0.857295732 0.000972265 MYL9 0.174558299 -‐2.518023512 2.09E-‐05 SPEG 0.566854312 -‐0.818649996 0.001848996 G530011O06RIK 7.021882749 2.480727966 0.001107203 OXCT1 0.649016174 -‐0.6236099 0.004215392 TPM2 0.446130301 -‐1.163648775 0.001507463 CYP1B1 2.823781654 1.493507639 6.43E-‐05 CNN1 0.355695003 -‐1.488867983 1.98E-‐06 CNN2 0.556641652 -‐0.844743185 0.006413844 CYP2U1 0.512643885 -‐0.95611667 0.001142236 CACNA1H 0.527077435 -‐0.922554824 0.000495267 ATPAF2 0.611207801 -‐0.708990679 0.002555179 NME1 0.444463448 -‐1.16358304 2.44E-‐05
19
PPP1R1B 0.457866507 -‐1.118535053 0.000284232 UNC13C 16.59667462 3.967248271 4.77E-‐28 MTL5 0.466576726 -‐1.085403063 0.00692577 ACTG1 0.592564452 -‐0.752301125 0.004970196 CDK5RAP1 1.660109692 0.729652785 0.001966415 NAMPT 1.706131089 0.77036227 0.002608782 LYRM7 0.349970402 -‐1.507068877 9.97E-‐06 MAP1LC3B 1.524187384 0.607743896 0.008754858 MORF4L1 1.933773301 0.948030371 0.000250541 PGP 0.630298741 -‐0.664364141 0.006545294 SEMA3C 0.589206414 -‐0.76195771 0.000781181 MRPL34 0.597233973 -‐0.742135237 0.001367958 PDE4A 0.613550578 -‐0.703093969 0.009825944 DSTN 0.633737283 -‐0.658016883 0.000960375 ACTA1 0.047721728 -‐4.377932644 0.000992976 EIF4B 1.568400066 0.649231352 0.002900104
