Causal role of histone acetylations in enhancer function

References

• Calo E, Wysocka J. Modification of enhancer chromatin: what, how, and why? Mol Cell 2013; 49:825-37; PMID:23473601; http://dx.doi.org/10.1016/j.molcel.2013.01.038
   PubMed Web of Science ®Google Scholar
• Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011; 21:381-95; PMID:21321607; http://dx.doi.org/10.1038/cr.2011.22
   PubMed Web of Science ®Google Scholar
• Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 2012; 8:e1002717; PMID:22615581; http://dx.doi.org/10.1371/journal.pgen.1002717
   PubMed Web of Science ®Google Scholar
• Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 2010; 327:996-1000; PMID:20133523; http://dx.doi.org/10.1126/science.1184208
   PubMed Web of Science ®Google Scholar
• Pradeepa MM, Grimes GR, Taylor GC, Sutherland HG, Bickmore WA. Psip1/Ledgf p75 restrains Hox gene expression by recruiting both trithorax and polycomb group proteins. Nucleic Acids Res 2014; 42:9021-32; PMID:25056311; http://dx.doi.org/10.1093/nar/gku647
   PubMed Web of Science ®Google Scholar
• Daugaard M, Baude A, Fugger K, Povlsen LK, Beck H, Sørensen CS, Petersen NH, Sorensen PH, Lukas C, Bartek J et al. LEDGF (p75) promotes DNA-end resection and homologous recombination. Nat Struct Mol Biol 2012; 19:803-10; PMID:22773103; http://dx.doi.org/10.1038/nsmb.2314
   PubMed Web of Science ®Google Scholar
• Baker M. Mass spectrometry for chromatin biology. Nat Methods 2012; 9:649-52; http://dx.doi.org/10.1038/nature01096
   Web of Science ®Google Scholar
• Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 2006; 311:844-7; PMID:16469925; http://dx.doi.org/10.1126/science.1124000
   PubMed Web of Science ®Google Scholar
• Allahverdi A, Yang R, Korolev N, Fan Y, Davey CA, Liu CF, Nordenskiöld L. The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association. Nucleic Acids Res 2011; 39:1680-91; PMID:21047799; http://dx.doi.org/10.1093/nar/gkq900
   PubMed Web of Science ®Google Scholar
• Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K. The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol 2008; 15:1122-4; PMID:18794842; http://dx.doi.org/10.1038/nsmb.1489
   PubMed Web of Science ®Google Scholar
• Di Cerbo V, Mohn F, Ryan DP, Montellier E, Kacem S, Tropberger P, Kallis E, Holzner M, Hoerner L, Feldmann A et al. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. Elife 2014; 3:e01632; PMID: 24668167; http://dx.doi.org/10.7554/eLife.01632
   PubMed Web of Science ®Google Scholar
• Tropberger P, Pott S, Keller C, Kamieniarz-Gdula K, Caron M, Richter F, Li G, Mittler G, Liu ET, Bühler M et al. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 2013; 152:859-72; PMID:23415232; http://dx.doi.org/10.1016/j.cell.2013.01.032
   PubMed Web of Science ®Google Scholar
• Mersfelder EL, Parthun MR. The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure. Nucleic Acids Res 2006; 34:2653-62; PMID:16714444; http://dx.doi.org/10.1093/nar/gkl338
   PubMed Web of Science ®Google Scholar
• Kim TK, Shiekhattar R. Architectural and functional commonalities between enhancers and promoters. Cell 2015; 162:948-59; PMID:26317464; http://dx.doi.org/10.1016/j.cell.2015.08.008
   PubMed Web of Science ®Google Scholar
• Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 2010; 107:21931-6; PMID: 21106759; http://dx.doi.org/10.1073/pnas.1016071107
   PubMed Web of Science ®Google Scholar
• Taylor G, Eskeland R, Hekimoglu-Balkan B, Pradeepa M, Bickmore WA. H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res 2013; 23:2053-65; PMID:23990607; http://dx.doi.org/10.1101/gr.155028.113
   PubMed Web of Science ®Google Scholar
• Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470:279-83; PMID:21160473; http://dx.doi.org/10.1038/nature09692
   PubMed Web of Science ®Google Scholar
• Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009; 459:108-12; PMID:19295514; http://dx.doi.org/10.1038/nature07829
   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; 21:1273-83; PMID:21632746; http://dx.doi.org/10.1101/gr.122382.111
   PubMed Web of Science ®Google Scholar
• Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007; 39:311-8; http://dx.doi.org/10.1038/ng1966
   PubMed Web of Science ®Google Scholar
• Tropberger P, Schneider R. Scratching the (lateral) surface of chromatin regulation by histone modifications. Nat Struct Mol Biol 2013; 20:657-61; PMID:23739170; http://dx.doi.org/10.1038/nsmb.2581
   PubMed Web of Science ®Google Scholar
• Neumann H, Hancock SM, Buning R, Routh A, Chapman L, Somers J, Owen-Hughes T, van Noort J, Rhodes D, Chin JW. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol Cell 2009; 36:153-63; PMID:19818718; http://dx.doi.org/10.1016/j.molcel.2009.07.027
   PubMed Web of Science ®Google Scholar
• Das C, Lucia MS, Hansen KC, Tyler JK. CBP/p300-mediated acetylation of histone H3 on lysine 56. Nature 2009; 459:113-7; PMID:19270680; http://dx.doi.org/10.1038/nature07861
   PubMed Web of Science ®Google Scholar
• Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT et al. Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Mol Cell 2009; 33:417-27; PMID:19250903; http://dx.doi.org/10.1016/j.molcel.2009.02.004
   PubMed Web of Science ®Google Scholar
• Lawrence M, Daujat S, Schneider R. Lateral thinking: how histone modifications regulate gene expression. Trends Genet 2016; 32:42-56; PMID:26704082; http://dx.doi.org/10.1016/j.tig.2015.10.007
   PubMed Web of Science ®Google Scholar
• Simon M, North JA, Shimko JC, Forties RA, Ferdinand MB, Manohar M, Zhang M, Fishel R, Ottesen JJ, Poirier MG. Histone fold modifications control nucleosome unwrapping and disassembly. Proc Natl Acad Sci U S A 2011; 108:12711-6; PMID:21768347; http://dx.doi.org/10.1073/pnas.1106264108
   PubMed Web of Science ®Google Scholar
• Pradeepa MM, Grimes GR, Kumar Y, Olley G, Taylor GC, Schneider R, Bickmore WA. Histone H3 globular domain acetylation identifies a new class of enhancers. Nat Genet 2016; 48:681-6; PMID:27089178; http://dx.doi.org/10.1038/ng.3550
   PubMed Web of Science ®Google Scholar
• Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA. H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 2008; 135:649-61; PMID:18992931; http://dx.doi.org/10.1016/j.cell.2008.09.056
   PubMed Web of Science ®Google Scholar
• Illingworth RS, Botting CH, Grimes GR, Bickmore WA, Eskeland R. Prc1 and prc2 are not required for targeting of h2a.z to developmental genes in embryonic stem cells. PLoS One 2012; 7:1-13; http://dx.doi.org/10.1371/journal.pone.0034848
   Web of Science ®Google Scholar
• Devaiah BN, Case-Borden C, Gegonne A, Hsu CH, Chen Q, Meerzaman D, Dey A, Ozato K, Singer DS. BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin. Nat Struct Mol Biol 2016; 23:1-12; PMID:26733217; http://dx.doi.org/10.1038/nsmb.3228
   PubMed Web of Science ®Google Scholar
• Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L. 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; PMID:22920947; http://dx.doi.org/10.1186/1471-2164-13-424
   PubMed Web of Science ®Google Scholar
• Chelmicki T, Dündar F, Turley MJ, Khanam T, Aktas T, Ramírez F, Gendrel AV, Wright PR, Videm P, Backofen R et al. MOF-associated complexes ensure stem cell identity and Xist repression. Elife 2014; 3:e02024; PMID:24842875; http://dx.doi.org/10.7554/eLife.02024
   PubMedGoogle Scholar
• Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell 2011; 44:410-23; PMID:22055187; http://dx.doi.org/10.1016/j.molcel.2011.08.037
   PubMed Web of Science ®Google Scholar
• Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell 2013; 155:934-47; PMID:24119843; http://dx.doi.org/10.1016/j.cell.2013.09.053
   PubMed Web of Science ®Google Scholar
• Hah N, Benner C, Chong LW, Yu RT, Downes M, Evans RM. Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs. Proc Natl Acad Sci U S A 2015; 112:E297-302; PMID:25564661; http://dx.doi.org/10.1073/pnas.1424028112
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13:484-92; http://dx.doi.org/10.1038/nrg3230
   PubMed Web of Science ®Google Scholar
• Charlet J, Duymich CE, Lay FD, Mundbjerg K, Dalsgaard Sørensen K, Liang G, Jones PA. Bivalent regions of cytosine methylation and H3K27 acetylation suggest an active role for DNA methylation at enhancers. Mol Cell 2016; 62:422-31; PMID:27153539; http://dx.doi.org/10.1016/j.molcel.2016.03.033
   PubMed Web of Science ®Google Scholar
• Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond AS, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol 2016; 17:146; PMID:27381023; http://dx.doi.org/10.1186/s13059-016-1013-1
   PubMed Web of Science ®Google Scholar
• Rinaldi L, Datta D, Serrat J, Morey L, Solanas G, Avgustinova A, Blanco E, Pons JI, Matallanas D, Von Kriegsheim A et al. Dnmt3a and Dnmt3b associate with enhancers to regulate human epidermal stem cell homeostasis. Cell Stem Cell 2016; 19:1-11; PMID:27476967; http://dx.doi.org/10.1016/j.stem.2016.06.020
   PubMed Web of Science ®Google Scholar
• Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 2014; 15:234-46; PMID:24614316; http://dx.doi.org/10.1038/nrg3663
   PubMed Web of Science ®Google Scholar
• Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010; 465:182-7; PMID:20393465; http://dx.doi.org/10.1038/nature09033
   PubMed Web of Science ®Google Scholar
• Arner E, Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (80-) 2015; 347:1010-5; http://dx.doi.org/10.1126/science.1259418
   PubMed Web of Science ®Google Scholar
• Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T et al. An atlas of active enhancers across human cell types and tissues. Nature 2014; 507:455-61; PMID:24670763; http://dx.doi.org/10.1038/nature12787
   PubMed Web of Science ®Google Scholar
• Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP et al. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 2015; 161:774-89; PMID:25957685; http://dx.doi.org/10.1016/j.cell.2015.04.034
   PubMed Web of Science ®Google Scholar
• Young RS, Kumar Y, Bickmore WA, Taylor MS. Bidirectional transcription marks accessible chromatin and is not specific to enhancers. BiorXiv 2016; http://dx.doi.org/http://dx.doi.org/10.1101/048629
   Google Scholar
• Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 2013; 49:524-35; PMID:23273978; http://dx.doi.org/10.1016/j.molcel.2012.11.021
   PubMed Web of Science ®Google Scholar
• Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel G a, Shiekhattar R. Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature 2013; 494:497-501; PMID:23417068; http://dx.doi.org/10.1038/nature11884
   PubMed Web of Science ®Google Scholar
• Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472:120-4; PMID:21423168; http://dx.doi.org/10.1038/nature09819
   PubMed Web of Science ®Google Scholar
• Pradeepa MM, Taylor GAG, Grimes GR, Wood A, Bickmore W. Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip. BiorXiv 2016; http://dx.doi.org/10.1101/061192
   Google Scholar
• Kanno T, Kanno Y, LeRoy G, Campos E, Sun H-W, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D et al. BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. Nat Struct Mol Biol 2014; 21:1047-57; PMID:25383670; http://dx.doi.org/10.1038/nsmb.2912
   PubMed Web of Science ®Google Scholar
• Xu F, Zhang K, Grunstein M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 2005; 121:375-85; PMID:15882620; http://dx.doi.org/10.1016/j.cell.2005.03.011
   PubMed Web of Science ®Google Scholar
• Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP et al. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 2015; 161:774-89; PMID:25957685; http://dx.doi.org/10.1016/j.cell.2015.04.034
   PubMed Web of Science ®Google Scholar
• Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. H3.3/H2A.Z double variant-containing nucleosomes mark “nucleosome-free regions” of active promoters and other regulatory regions. Nat Genet 2009; 41:941-5; PMID:19633671; http://dx.doi.org/10.1038/ng.409
   PubMed Web of Science ®Google Scholar
• Henikoff S. Labile H3.3+H2A.Z nucleosomes mark “nucleosome-free regions.” Nat Publ Gr 2009; 41:865-6; PMID: 19639024; http://dx.doi.org/10.1038/ng0809-865
   Web of Science ®Google Scholar
• Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R. Editing DNA methylation in the mammalian genome. Cell 2016; 167:233-47.e17; PMID:27662091; http://dx.doi.org/10.1016/j.cell.2016.08.056
   PubMed Web of Science ®Google Scholar
• Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol 2013; 31:1133-6; PMID:24013198; http://dx.doi.org/10.1038/nbt.2701
   PubMed Web of Science ®Google Scholar
• King AD, Huang K, Rubbi L, Liu S, Wang C-Y, Wang Y, Pellegrini M, Fan G. Reversible regulation of promoter and enhancer histone landscape by DNA methylation in mouse embryonic stem cells. Cell Rep 2016; 17:289-302; PMID:27681438; http://dx.doi.org/10.1016/j.celrep.2016.08.083
   PubMed Web of Science ®Google Scholar
• Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013; 152:1173-83; PMID:23452860; http://dx.doi.org/10.1016/j.cell.2013.02.022
   PubMed Web of Science ®Google Scholar