Loci-specific histone acetylation profiles associated with transcriptional coactivator p300 during early myoblast differentiation

References

• Creyghton MP, Cheng AW, Welstead GG, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci. 2010;107:21931–21936.
   PubMed Web of Science ®Google Scholar
• Rada-Iglesias A, Bajpai R, Swigut T, et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011;470:279–283.
   PubMed Web of Science ®Google Scholar
• Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, et al. Chromatin state dynamics during blood formation. Science. 2014;345(80):943-9.
   PubMedGoogle Scholar
• Asp P, Blum R, Vethantham V, et al. Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A. 2011;108:E149–58.
   PubMed Web of Science ®Google Scholar
• Lee DY, Hayes JJ, Pruss D, et al. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell. 1993;72:73–84.
   PubMed Web of Science ®Google Scholar
• Roh T-Y, Cuddapah S, Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 2005;19:542–552.
   PubMed Web of Science ®Google Scholar
• Eberharter A, Becker PB. Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep. 2002;3:224–229.
   PubMed Web of Science ®Google Scholar
• Wang Z, Zang C, Rosenfeld JA, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008;40:897–903.
   PubMed Web of Science ®Google Scholar
• Halsall J, Gupta V, O’Neill LP, et al. Genes are often sheltered from the global histone hyperacetylation induced by HDAC inhibitors. Cotterill S, Editor. PLoS One. 2012;7:e33453.
   PubMed Web of Science ®Google Scholar
• Karmodiya K, Krebs AR, Oulad-Abdelghani M, et al. H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics. 2012;13:424.
   PubMed Web of Science ®Google Scholar
• Azuara V, Perry P, Sauer S, et al. Chromatin signatures of pluripotent cell lines. Nat Cell Biol. 2006;8:532–538.
   PubMed Web of Science ®Google Scholar
• Heintzman ND, Hon GC, Hawkins RD, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature. 2009;459:108–112.
   PubMed Web of Science ®Google Scholar
• Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 2011;21:1273–1283.
   PubMed Web of Science ®Google Scholar
• Hamed M, Khilji S, Dixon K, et al. Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation. Nucleic Acids Res. 2017 ;45:11236-11248.
   PubMed Web of Science ®Google Scholar
• Moncaut N, Rigby PWJ, Carvajal JJ. Dial M(RF) for myogenesis. FEBS J. 2013;280:3980–3990.
   PubMed Web of Science ®Google Scholar
• Blum R, Vethantham V, Bowman C, et al. Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. Genes Dev. 2012;26:2763–2779.
   PubMed Web of Science ®Google Scholar
• Fong AP, Yao Z, Zhong JW, et al. Genetic and epigenetic determinants of neurogenesis and myogenesis. Dev Cell. 2012;22:721–735.
   PubMed Web of Science ®Google Scholar
• Chakravarti D, LaMorte VJ, Nelson MC, et al. Role of CBP/P300 in nuclear receptor signalling. Nature. 1996;383:99–103.
   PubMed Web of Science ®Google Scholar
• Goodman RH, Smolik S. CBP/p300 in cell growth, transformation, and development. Genes Dev. 2000;14:1553–1577.
   PubMed Web of Science ®Google Scholar
• Chen J, Li Q. Life and death of transcriptional co-activator p300. Epigenetics. 2011;6:957–961.
   PubMed Web of Science ®Google Scholar
• Arany Z, Sellers WR, Livingston DM, et al. E1A-associated p300 and CREB-associated CBP belong to a conserved family of coactivators. Cell. 1994;77:799–800.
   PubMed Web of Science ®Google Scholar
• Polesskaya A, Naguibneva I, Fritsch L, et al. CBP/p300 and muscle differentiation: no HAT, no muscle. EMBO J. 2001;20:6816–6825.
   PubMed Web of Science ®Google Scholar
• Roth J-F, Shikama N, Henzen C, et al. Differential role of p300 and CBP acetyltransferase during myogenesis: p300 acts upstream of MyoD and Myf5. EMBO J. 2003;22:5186–5196.
   PubMed Web of Science ®Google Scholar
• Jin Q, Yu L-R, Wang L, et al. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J. 2011;30:249–262.
   PubMed Web of Science ®Google Scholar
• Bricambert J, Miranda J, Benhamed F, et al. Salt-inducible kinase 2 links transcriptional coactivator p300 phosphorylation to the prevention of ChREBP-dependent hepatic steatosis in mice. J Clin Invest. 2010;120:4316–4331.
   PubMed Web of Science ®Google Scholar
• Heintzman ND, Stuart RK, Hon G, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39:311–318.
   PubMed Web of Science ®Google Scholar
• Blow MJ, McCulley DJ, Li Z, et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010;42:806–810.
   PubMed Web of Science ®Google Scholar
• Visel A, Blow MJ, Li Z, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009;457:854–858.
   PubMed Web of Science ®Google Scholar
• May D, Blow MJ, Kaplan T, et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2011;44:89–93.
   PubMed Web of Science ®Google Scholar
• Shen Y, Yue F, McCleary DF, et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012;488:116–120.
   PubMed Web of Science ®Google Scholar
• Schwaiger M, Schönauer A, Rendeiro AF, et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 2014;24:639–650.
   PubMed Web of Science ®Google Scholar
• Nègre N, Brown CD, Ma L, et al. A cis-regulatory map of the drosophila genome. Nature. 2011;471:527–531.
   PubMed Web of Science ®Google Scholar
• Vo N, Goodman RH. CREB-binding protein and p300 in transcriptional regulation. J Biol Chem. 2001;276:13505–13508.
   PubMed Web of Science ®Google Scholar
• Chan HM, La Thangue NB. p300/CBP proteins: hATs for transcriptional bridges and scaffolds. J Cell Sci. 2001;114:2363–2373.
   PubMed Web of Science ®Google Scholar
• Blais A, Tsikitis M, Acosta-Alvear D, et al. An initial blueprint for myogenic differentiation. Genes Dev. 2005;19:553–569.
   PubMed Web of Science ®Google Scholar
• Chen J, Wang Y, Hamed M, et al. Molecular Basis for the Regulation of Transcriptional Coactivator p300 in Myogenic Differentiation. Sci Rep. 2015;5:13727.
   PubMed Web of Science ®Google Scholar
• Laclef C, Hamard G, Demignon J, et al. Altered myogenesis in Six1-deficient mice. Development. 2003;130:2239–2252.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Babin J, Feldhaus AL, et al. HTF4: a new human helix-loop-helix protein. Nucleic Acids Res. 1991;19:4555.
   PubMed Web of Science ®Google Scholar
• Hu JS, Olson EN, Kingston RE. HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. Mol Cell Biol. 1992;12:1031–1042.
   PubMed Web of Science ®Google Scholar
• Yue F, Cheng Y, Breschi A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515:355–364.
   PubMed Web of Science ®Google Scholar
• Bergstrom DA, Penn BH, Strand A, et al. Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression. Mol Cell. 2002;9:587–600.
   PubMed Web of Science ®Google Scholar
• Tapscott SJ. The circuitry of a master switch: MyoD and the regulation of skeletal muscle gene transcription. Development. 2005;132:2685–2695.
   PubMed Web of Science ®Google Scholar
• Xu J, Watts JA, Pope SD, et al. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 2009;23:2824–2838.
   PubMed Web of Science ®Google Scholar
• Puri PL, Sartorelli V, Yang XJ, et al. Differential roles of p300 and PCAF acetyltransferases in muscle differentiation. Mol Cell. 1997;1:35–45.
   PubMed Web of Science ®Google Scholar
• Sartorelli V, Huang J, Hamamori Y, et al. Molecular mechanisms of myogenic coactivation by p300: direct interaction with the activation domain of MyoD and with the MADS box of MEF2C. Mol Cell Biol. 1997;17:1010–1026.
   PubMed Web of Science ®Google Scholar
• Wang Z, Zang C, Cui K, et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 2009;138:1019–1031.
   PubMed Web of Science ®Google Scholar
• Gan Q, Yoshida T, McDonald OG, et al. Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells. Stem Cells. 2007;25:2–9.
   PubMed Web of Science ®Google Scholar
• Delgado I, Huang X, Jones S, et al. Dynamic gene expression during the onset of myoblast differentiation in vitro. Genomics. 2003;82:109–121.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511–515.
   PubMed Web of Science ®Google Scholar
• Doynova MD, Markworth JF, Cameron-Smith D, et al. Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. Skelet Muscle. 2017;7:5.
   PubMed Web of Science ®Google Scholar
• Cao Y, Yao Z, Sarkar D, et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010;18:662–674.
   PubMed Web of Science ®Google Scholar
• Cui H, Bansal V, Grunert M, et al. Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation. Mantovani R, editor. PLoS One. 2017;12:e0179464.
   PubMed Web of Science ®Google Scholar
• Chen J, St-Germain JR, Li Q. B56 Regulatory subunit of protein phosphatase 2A mediates valproic acid-induced p300 degradation B56 regulatory subunit of protein phosphatase 2A mediates valproic acid-induced p300 degradation. Mol Cell Biol. 2005;25:525–532.
   PubMed Web of Science ®Google Scholar
• Le May M, Mach H, Lacroix N, et al. Contribution of retinoid X receptor signaling to the specification of skeletal muscle lineage. J Biol Chem. 2011;286:26806–26812.
   PubMed Web of Science ®Google Scholar
• Hamed M, Khilji S, Chen J, et al. Stepwise acetyltransferase association and histone acetylation at the Myod1 locus during myogenic differentiation. Sci Rep. 2013;3:2390.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
   PubMed Web of Science ®Google Scholar
• Heinz S, Benner C, Spann N, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–589.
   PubMed Web of Science ®Google Scholar
• McLean CY, Bristor D, Hiller M, et al. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28:495–501.
   PubMed Web of Science ®Google Scholar
• Shen L, Shao N, Liu X, et al. ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284.
   PubMed Web of Science ®Google Scholar
• Di Padova M, Caretti G, Zhao P, et al. MyoD acetylation influences temporal patterns of skeletal muscle gene expression. J Biol Chem. 2007;282:37650–37659.
   PubMed Web of Science ®Google Scholar
• Usardi A, Iyer K, Sigoillot SM, et al. The immunoglobulin-like superfamily member IGSF3 is a developmentally regulated protein that controls neuronal morphogenesis. Dev Neurobiol. 2017;77:75–92.
   PubMed Web of Science ®Google Scholar
• D’Angelo MA, Gomez-Cavazos JS, Mei A, et al. A change in nuclear pore complex composition regulates cell differentiation. Dev Cell. 2012;22:446–458.
   PubMed Web of Science ®Google Scholar