Supplementary Figure 1. Chromatin immunoprecipitation (ChIP) for Smad1, Zfx and E2f1 on histone gene promoters. From left to right: ChIP for Smad1 on H1 and H4 promoters, Zfx on H1 promoter, E2f1 on H1, H2a, H2b, H3 and H4 promoters. Next three bars and right-most bars show no enrichment for these factors on Serpin promoter and on an intergenic region, both of which were used as negative controls.
Supplementary Figure 2. Fold enrichment of E2f4 in different tissues. 1.7-fold in adipocyte (P = 1.3x10-3), 1.9-fold in liver (P = 1.8x10-4), 3.1-fold in Myoblast (P < 10-15 ), 3.9-fold in ESCs (P < 10-15 ), 5.4-fold in B-cell lymphoma (P < 10-15 ) and 7.5-fold in erythroleukemia (P < 10-15 ).
Supplementary Figure 3. Read density of p300 on chromosome 13 in ESC, forebrain, midbrain and limb bud.
Supplementary Figure 4. Histone genes are enriched with histone acetylation marks. Expected Vs. observed percentage of histones genes with modification.
Supplementary Figure 5. Percentage of histone genes bound by Tet1, within each subtype.
Supplementary Figure 6. Histone genes are enriched with Med1, Med12, Smc1, Smc3, Nipbl and Tet1. Read density of various TFs within locus chr13: 21866000-21877500.
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Supplementary Table 2 List of primer sequences used for ChIP Name Gene Sequence Smad1_H1 Hist1h1d F: TTTCCAATCCGGCTACACAAGGTG R: CTGATTGGTGCAACACCCATGACT Smad1_H4 Hist1h4i F: TGCCTACTGGAACTAAATGCGTGC R: GCATCCTCGTTCAGTCCATAATTGGG Zfx_H1 Hist1h1a F: CTTCGTCTTGGGTATAGCTGTTGT R: ACGCTTCGCCATGTCCGAGA E2f1_H1 Hist1h1b F: AACAGCCTTAGTGATGAGCTCGGA R: TCCCGCCAAGAAGAAGACAACGAA E2f1_H2A Hist1h2ae F: TGTTTGCCACGTCCAGACATTGAC R: CGAGTATAAGTAGCTTCTCGTCTGGC E2f1_H2B Hist1h2bk F: TACCCGTGGTGTTCCTATCTGCTT R: AGGCTCAGGCATGGCGTAGAAAT E2f1_H3 Hist1h3a F: CTAGAAAGCAAGCTGGTGAGCACT R: TCATCCAATCACTATCCTTTGCAT E2f1_H4 Hist1h4n F: TGCCACGACCAGACATGATGAAGA R: TCCGGTCCGCAAGTTCCCTATAA Genic Serpin F: GCTGGAAGCACTTACTTGTGTTTCTGAAGG R: AGATCTCAGGATCAGCCACACACA Intergenic F: TGCATGTATTACTTTGTGGAATTT R: CCTTTCTCACAAACTAGCTCATTAC
Supplementary Table 3 Smad2 knockout under TGF-β stimulated and non-stimulated conditions Fold change TGF-β (+)/TGF-β (-) Affymetrix ID Gene SMAD2 WT SMAD2 KO No TGF-β stimulation Fold change (KO/WT) TGF-β stimulated 1416101_a_at Hist1h1c 0.737873149 0.704235466 0.941517167 0.898595893 1418072_at Hist1h2bc 0.306910728 1.463938269 0.69935619 3.335869997 1418366_at Hist2h2aa2 0.801716407 1.066472735 0.890625778 1.184743261 1418367_x_at Hist2h2aa1, Hist2h2aa2 0.613544909 0.844744179 0.778291065 1.071570862 1422398_at Hist1h1e 0.551664714 0.751157158 0.962108204 1.310024814 1422948_s_at H4 0.595005417 0.625437887 0.758163593 0.796941041 1424854_at Hist1h4i 0.173612409 0.532563319 0.474188387 1.454592691 1427762_x_at Hist1h2bp 0.426113019 0.414640584 0.705561456 0.686565304 1427864_at Hist1h3d 0.475922568 0.792788554 0.637373684 1.061732717 1428014_at Hist1h4h 0.664402181 0.336298388 1.081139886 0.547237218 1431231_at Hist1h3f, Hist1h3e 0.361014693 0.847387956 0.718966313 1.687586143 1435865_at Hist3h2a 0.960636278 1.003775491 0.99863314 1.043478676 1435866_s_at Hist3h2a 0.755221818 1.475319366 1.151540319 2.24952417 1438009_at Hist1h2ao 0.671653959 0.84074474 1.072548892 1.342566104 1450608_at Hist1h1t 0.176773194 0.716825815 0.472517396 1.916086142 1452540_a_at H2b 0.486336272 0.580489283 0.850570106 1.015237519 1453573_at Hist1h3d 0.159931413 0.352559734 1.153273942 2.542327027 1460314_s_at H3 0.593952162 0.480641394 0.980307947 0.793290451
Supplementary Table 4 Smad2 activation/inhibition Affymetrix ID Gene Activation fold change Inhibition fold change Controlaverage Activationaverage Inhibitionaverage 1416101_a_at Hist1h1c 0.74676259 1.175539568 347.5 259.5 408.5 1418072_at Hist1h2bc 0.934640523 1.558823529 153 143 238.5 1418366_at Hist2h2aa2 1.169491525 1.293785311 88.5 103.5 114.5 1418367_x_at Hist2h2aa1, Hist2h2aa2 1.207317073 1.317073171 123 148.5 162 1422948_s_at H4 0.942602041 1.035714286 392 369.5 406 1431231_at Hist1h3f, Hist1h3e 1.047058824 1.2 85 89 102 1435865_at Hist3h2a 0.921015515 0.936530324 354.5 326.5 332 1436994_a_at Hist1h1c 0.752066116 1.425619835 121 91 172.5 1438009_at Hist1h2ao 0.90289542 0.882508555 20601.5 18601 18181 1449482_at Hist3h2ba 0.827272727 0.909090909 55 45.5 50 1452540_a_at H2b 0.976253298 1.270888303 568.5 555 722.5 1453573_at Hist1h3d 0.689655172 0.848275862 72.5 50 61.5 1460314_s_at H3 0.881147541 0.967213115 488 430 472