title: Global mapping of the regulatory interactions of histone residues.
abstract: Histone residues can serve as platforms for specific regulatory function. Here we constructed a map of regulatory associations between histone residues and a wide spectrum of chromatin regulation factors based on gene expression changes by histone point mutations in Saccharomyces cerevisiae. Detailed analyses of this map revealed novel associations. Regarding the modulation of H3K4 and K36 methylation by Set1, Set2, or Jhd2, we proposed a role for H4K91 acetylation in early Pol II elongation, and for H4K16 deacetylation in late elongation and crosstalk with H3K4 demethylation for gene silencing. The association of H3K56 with nucleosome positioning suggested that this lysine residue and its acetylation might contribute to nucleosome mobility for transcription activation. Further insights into chromatin regulation are expected from this approach.
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.
authors.forename: Inkyung
authors.initials: I
authors.lastname: Jung
authors.affiliation: Research Institute of Bioinformatics, Omicsis, Inc., BVC, KRIBB, Daejeon 305-333, Republic of Korea.
authors.forename: Jungmin
authors.initials: J
authors.lastname: Seo
authors.affiliation: Research Institute of Bioinformatics, Omicsis, Inc., BVC, KRIBB, Daejeon 305-333, Republic of Korea.
authors.forename: Heun-Sik
authors.initials: HS
authors.lastname: Lee
authors.affiliation: Genome Institute of Singapore, Singapore 138672, Republic of Singapore.
authors.forename: Lawrence W
authors.initials: LW
authors.lastname: Stanton
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea.
authors.forename: Dongsup
authors.initials: D
authors.lastname: Kim
authors.affiliation: Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Republic of Korea; Genome Institute of Singapore, Singapore 138672, Republic of Singapore. Electronic address: jungkyoon@kaist.ac.kr.
authors.forename: Jung Kyoon
authors.initials: JK
authors.lastname: Choi
mesh_terms: D000107:Acetylation; D000123:Acetyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D056484:Jumonji Domain-Containing Histone Demethylases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D017354:Point Mutation; D025941:Protein Interaction Mapping; D011499:Protein Processing, Post-Translational; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000254:growth & development / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D006657:Histones; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; C519119:JHD2 protein, S cerevisiae; D056484:Jumonji Domain-Containing Histone Demethylases; D008780:Methyltransferases; C448996:Set2 protein, S cerevisiae; D011495:Histone-Lysine N-Methyltransferase; C411250:SET1 protein, S cerevisiae; D000123:Acetyltransferases; C475088:Sas4 protein, S cerevisiae; D008239:Lysine
keywords: Gene expression profile; Histone modification; Histone residue; Nucleosome positioning