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PMID: 17567990 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

The landscape of histone modifications across 1% of the human genome in five human cell lines.

Genome research ·Vol. 17 ·No. 6 ·2007-06-00 ·Pages 691-707

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I

Abstract

We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including the ENCODE Consortium common cell lines GM06990 (lymphoblastoid) and HeLa-S3, as well as K562, HFL-1, and MOLT4, we identified clear patterns of histone modification profiles with respect to genomic features. H3K4me3, H3K4me2, and H3ac modifications are tightly associated with the transcriptional start sites (TSSs) of genes, while H3K4me1 and H4ac have more widespread distributions. TSSs reveal characteristic patterns of both types of modification present and the position relative to TSSs. These patterns differ between active and inactive genes and in particular the state of H3K4me3 and H3ac modifications is highly predictive of gene activity. Away from TSSs, modification sites are enriched in H3K4me1 and relatively depleted in H3K4me3 and H3ac. Comparison between cell lines identified differences in the histone modification profiles associated with transcriptional differences between the cell lines. These results provide an overview of the functional relationship among histone modifications and gene expression in human cells.

MeSH Terms
Genome, Human/physiology HeLa Cells Histones/metabolism Humans K562 Cells Protein Processing, Post-Translational/physiology Transcription, Genetic/physiology
Chemicals
Histones
Authors & Affiliations
22 authors, click to expand affiliations / ORCID
Koch Christoph M
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SA, United Kingdom.
Andrews Robert M
Flicek Paul
Dillon Shane C
Karaöz Ulaş
Clelland Gayle K
Wilcox Sarah
Beare David M
Fowler Joanna C
Couttet Phillippe
James Keith D
Lefebvre Gregory C
Bruce Alexander W
Dovey Oliver M
Ellis Peter D
Dhami Pawandeep
Langford Cordelia F
Weng Zhiping
Birney Ewan
Carter Nigel P
Vetrie David
Dunham Ian
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.5704207
Published
2007-06-00
Pages
691-707
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1891331
Subset
IM
Grants
NHGRI NIH HHS · R01 HG003110 · United States
NHGRI NIH HHS · U01 HG003168 · United States
NHGRI NIH HHS · R01HG03110 · United States
NHGRI NIH HHS · U01HG003168 · United States
External Links
PubMed source DOI: 10.1101/gr.5704207 PMC Full Text View journal details
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