title: Quantitative analysis reveals increased histone modifications and a broad nucleosome-free region bound by histone acetylases in highly expressed genes in human CD4+ T cells.
abstract: Genome-wide mapping of nucleosomes and histone modifications revealed meaningful patterns. Despite advances in resolving the associations between chromatin and transcription, quantitative chromatin dynamics have not been well defined. We quantitatively determined differences in histone modifications, nucleosome positions, DNA methylation, and transcription factor binding in highly expressed and repressed genes in human CD4(+) T cells. We showed that the first (-1) nucleosome upstream of the transcription start site (TSS) is shifted to the 5' direction, thus forming a broad nucleosome-free region (NFR) near the TSS in highly expressed genes in CD4(+) T cells. Moreover, the transcription factor YY1 and histone acetyltransferases bind the NFR with high affinity. Most of histone acetylations drastically increase in transcription activation (>5 folds). We also suggested that single nucleotide polymorphisms (SNPs) occur at a much lower frequency in highly expressed genes than in repressed genes. Our analysis quantitatively revealed details of chromatin dynamics.
authors.affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: liuhongde@seu.edu.cn.
authors.forename: Hongde
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Neurosurgery, Xinjiang Evidence-based Medicine Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Luo
authors.affiliation: State Key Laboratory Incubation Base of Xinjiang Major Diseases Research, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Wen
authors.affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Ma
authors.affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Jianming
authors.initials: J
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
mesh_terms: D015496:CD4-Positive T-Lymphocytes / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D051548:Histone Acetyltransferases / Q000378:metabolism*; D006657:Histones / Q000378:metabolism*; D006801:Humans; D009707:Nucleosomes; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D024363:Transcription Initiation Site; D050986:YY1 Transcription Factor / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D050986:YY1 Transcription Factor; C494698:YY1 protein, human; D051548:Histone Acetyltransferases