This Article OPEN ACCESS ARTICLE Full Text Full Text (PDF) Supplemental Reseach Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Koch, C. M. Articles by Dunham, I. Search for Related Content PubMed PubMed Citation Articles by Koch, C. M. Articles by Dunham, I. Social Bookmarking                   What's this?

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

Christoph M. Koch¹, Robert M. Andrews¹, Paul Flicek², Shane C. Dillon¹, Ula Karaöz³, Gayle K. Clelland¹, Sarah Wilcox¹, David M. Beare¹, Joanna C. Fowler¹, Phillippe Couttet¹, Keith D. James¹, Gregory C. Lefebvre¹, Alexander W. Bruce¹, Oliver M. Dovey¹, Peter D. Ellis¹, Pawandeep Dhami¹, Cordelia F. Langford¹, Zhiping Weng^3,4, Ewan Birney², Nigel P. Carter¹, David Vetrie¹, and Ian Dunham^1,5

¹ The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; ² European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; ³ Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; ⁴ Biomedical Engineering Department, Boston University, Boston, Massachusetts 02215, USA

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.

E-mail id1{at}sanger.ac.uk; fax 44 1223 494919.

[Supplemental material is available online at www.genome.org.]

Article is online at http://www.genome.org/cgi/doi/10.1101/gr.5704207

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				S. P. Atkinson, C. M. Koch, G. K. Clelland, S. Willcox, J. C. Fowler, R. Stewart, M. Lako, I. Dunham, and L. Armstrong Epigenetic Marking Prepares the Human HOXA Cluster for Activation During Differentiation of Pluripotent Cells Stem Cells, May 1, 2008; 26(5): 1174 - 1185. [Abstract] [Full Text] [PDF]

				J. D. Nelson, S. Flanagin, Y. Kawata, O. Denisenko, and K. Bomsztyk Transcription of laminin {gamma}1 chain gene in rat mesangial cells: constitutive and inducible RNA polymerase II recruitment and chromatin states Am J Physiol Renal Physiol, March 1, 2008; 294(3): F525 - F533. [Abstract] [Full Text] [PDF]

				S. Flanagin, J. D. Nelson, D. G. Castner, O. Denisenko, and K. Bomsztyk Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events Nucleic Acids Res., February 11, 2008; 36(3): e17 - e17. [Abstract] [Full Text] [PDF]

				S. Graf, F. G. G. Nielsen, S. Kurtz, M. A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek Optimized design and assessment of whole genome tiling arrays Bioinformatics, July 1, 2007; 23(13): i195 - i204. [Abstract] [Full Text] [PDF]

				G. M. Weinstock ENCODE: More genomic empowerment Genome Res., June 1, 2007; 17(6): 667 - 668. [Full Text] [PDF]

				J. M. Lin, P. J. Collins, N. D. Trinklein, Y. Fu, H. Xi, R. M. Myers, and Z. Weng Transcription factor binding and modified histones in human bidirectional promoters Genome Res., June 1, 2007; 17(6): 818 - 827. [Abstract] [Full Text] [PDF]

				R. E. Thurman, N. Day, W. S. Noble, and J. A. Stamatoyannopoulos Identification of higher-order functional domains in the human ENCODE regions Genome Res., June 1, 2007; 17(6): 917 - 927. [Abstract] [Full Text] [PDF]

				P. G. Giresi, J. Kim, R. M. McDaniell, V. R. Iyer, and J. D. Lieb FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin Genome Res., June 1, 2007; 17(6): 877 - 885. [Abstract] [Full Text] [PDF]