publication . Article . Other literature type . 2016

Histone H3 globular domain acetylation identifies a new class of enhancers

Madapura Pradeepa;
Open Access English
  • Published: 18 Apr 2016
  • Country: United Kingdom
Abstract
Histone acetylation is generally associated with active chromatin, but most studies have focused on the acetylation of histone tails. Various histone H3 and H4 tail acetylations mark the promoters of active genes. These modifications include acetylation of histone H3 at lysine 27 (H3K27ac), which blocks Polycomb-mediated trimethylation of H3K27 (H3K27me3). H3K27ac is also widely used to identify active enhancers, and the assumption has been that profiling H3K27ac is a comprehensive way of cataloguing the set of active enhancers in mammalian cell types. Here we show that acetylation of lysine residues in the globular domain of histone H3 (lysine 64 (H3K64ac) and ...
Subjects
free text keywords: Article, Histone acetylation, H3K122ac H3K64ac, Enhancers, Polycomb, Genetics
Funded by
EC| FUNCTIONALEDGE
Project
FUNCTIONALEDGE
Determining the roles of the nuclear periphery in mammalian genome function
  • Funder: European Commission (EC)
  • Project Code: 249956
  • Funding stream: FP7 | SP2 | ERC
46 references, page 1 of 4

Wang, Z. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008; 40: 897-903 [OpenAIRE] [PubMed]

Kim, TW. Ctbp2 Modulates NuRD-Mediated Deacetylation of H3K27 and Facilitates PRC2-Mediated H3K27me3 in Active ESC Genes During Exit From Pluripotency. Stem Cells. 2015; 33: 2442-55 [OpenAIRE] [PubMed]

Creyghton, MP. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010; 107: 21931-6 [OpenAIRE] [PubMed]

Rada-Iglesias, A. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011; 470: 279-83 [OpenAIRE] [PubMed]

Tropberger, P, Schneider, R. Scratching the (lateral) surface of chromatin regulation by histone modifications. Nat Struct Mol Biol. 2013; 20: 657-61 [OpenAIRE] [PubMed]

Neumann, H. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol Cell. 2009; 36: 153-63 [OpenAIRE] [PubMed]

Di Cerbo, V. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. Elife. 2014: 1-23 [OpenAIRE] [DOI]

Daujat, S. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nat Struct Mol Biol. 2009; 16: 777-81 [PubMed]

Tropberger, P. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell. 2013; 152: 859-72 [OpenAIRE] [PubMed]

Simon, M. Histone fold modifications control nucleosome unwrapping and disassembly. Proc Natl Acad Sci U S A. 2011; 108: 12711-12716 [OpenAIRE] [PubMed]

Heintzman, ND. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39: 311-8 [OpenAIRE] [PubMed]

Ernst, J. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473: 43-9 [OpenAIRE] [PubMed]

Bogu, GK. Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse. Mol Cell Biol. 2015 [OpenAIRE] [DOI]

Halley, JE, Kaplan, T, Wang, AY, Kobor, MS, Rine, J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol. 2010; 8: e1000401 [OpenAIRE] [PubMed]

Tie, F. Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing. Development. 2014; 141: 1129-39 [OpenAIRE] [PubMed]

46 references, page 1 of 4
Abstract
Histone acetylation is generally associated with active chromatin, but most studies have focused on the acetylation of histone tails. Various histone H3 and H4 tail acetylations mark the promoters of active genes. These modifications include acetylation of histone H3 at lysine 27 (H3K27ac), which blocks Polycomb-mediated trimethylation of H3K27 (H3K27me3). H3K27ac is also widely used to identify active enhancers, and the assumption has been that profiling H3K27ac is a comprehensive way of cataloguing the set of active enhancers in mammalian cell types. Here we show that acetylation of lysine residues in the globular domain of histone H3 (lysine 64 (H3K64ac) and ...
Subjects
free text keywords: Article, Histone acetylation, H3K122ac H3K64ac, Enhancers, Polycomb, Genetics
Funded by
EC| FUNCTIONALEDGE
Project
FUNCTIONALEDGE
Determining the roles of the nuclear periphery in mammalian genome function
  • Funder: European Commission (EC)
  • Project Code: 249956
  • Funding stream: FP7 | SP2 | ERC
46 references, page 1 of 4

Wang, Z. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008; 40: 897-903 [OpenAIRE] [PubMed]

Kim, TW. Ctbp2 Modulates NuRD-Mediated Deacetylation of H3K27 and Facilitates PRC2-Mediated H3K27me3 in Active ESC Genes During Exit From Pluripotency. Stem Cells. 2015; 33: 2442-55 [OpenAIRE] [PubMed]

Creyghton, MP. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010; 107: 21931-6 [OpenAIRE] [PubMed]

Rada-Iglesias, A. A unique chromatin signature uncovers early developmental enhancers in humans. Nature. 2011; 470: 279-83 [OpenAIRE] [PubMed]

Tropberger, P, Schneider, R. Scratching the (lateral) surface of chromatin regulation by histone modifications. Nat Struct Mol Biol. 2013; 20: 657-61 [OpenAIRE] [PubMed]

Neumann, H. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol Cell. 2009; 36: 153-63 [OpenAIRE] [PubMed]

Di Cerbo, V. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. Elife. 2014: 1-23 [OpenAIRE] [DOI]

Daujat, S. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nat Struct Mol Biol. 2009; 16: 777-81 [PubMed]

Tropberger, P. Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell. 2013; 152: 859-72 [OpenAIRE] [PubMed]

Simon, M. Histone fold modifications control nucleosome unwrapping and disassembly. Proc Natl Acad Sci U S A. 2011; 108: 12711-12716 [OpenAIRE] [PubMed]

Heintzman, ND. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39: 311-8 [OpenAIRE] [PubMed]

Ernst, J. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011; 473: 43-9 [OpenAIRE] [PubMed]

Bogu, GK. Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse. Mol Cell Biol. 2015 [OpenAIRE] [DOI]

Halley, JE, Kaplan, T, Wang, AY, Kobor, MS, Rine, J. Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory. PLoS Biol. 2010; 8: e1000401 [OpenAIRE] [PubMed]

Tie, F. Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing. Development. 2014; 141: 1129-39 [OpenAIRE] [PubMed]

46 references, page 1 of 4
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