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

@article{citeulike:1388715, 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. 10.1101/gr.5704207}, author = {Koch, Christoph M. and Andrews, Robert M. and Flicek, Paul and Dillon, Shane C. and Karaoz, Ulas and Clelland, Gayle K. and Wilcox, Sarah and Beare, David M. and Fowler, Joanna C. and Couttet, Phillippe and James, Keith D. and Lefebvre, Gregory C. and Bruce, Alexander W. and Dovey, Oliver M. and Ellis, Peter D. and Dhami, Pawandeep and Langford, Cordelia F. and Weng, Zhiping and Birney, Ewan and Carter, Nigel P. and Vetrie, David and Dunham, Ian }, citeulike-article-id = {1388715}, doi = {10.1101/gr.5704207}, journal = {Genome Res.}, keywords = {encode, epigenetics, histone}, month = {June}, number = {6}, pages = {691--707}, posted-at = {2008-05-15 17:47:56}, priority = {2}, title = {The landscape of histone modifications across 1\% of the human genome in five human cell lines}, url = {http://dx.doi.org/10.1101/gr.5704207}, volume = {17}, year = {2007} }

TY - JOUR ID - citeulike:1388715 L3 - citeulike-article-id:1388715 TI - The landscape of histone modifications across 1% of the human genome in five human cell lines JF - Genome Res. VL - 17 IS - 6 SP - 691 EP - 707 N2 - 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. 10.1101/gr.5704207 KW - encode KW - epigenetics KW - histone AU - Koch, Christoph AU - Andrews, Robert AU - Flicek, Paul AU - Dillon, Shane AU - Karaoz, Ulas AU - Clelland, Gayle AU - Wilcox, Sarah AU - Beare, David AU - Fowler, Joanna AU - Couttet, Phillippe AU - James, Keith AU - Lefebvre, Gregory AU - Bruce, Alexander AU - Dovey, Oliver AU - Ellis, Peter AU - Dhami, Pawandeep AU - Langford, Cordelia AU - Weng, Zhiping AU - Birney, Ewan AU - Carter, Nigel AU - Vetrie, David AU - Dunham, Ian PY - 2007/06/01/ UR - http://dx.doi.org/10.1101/gr.5704207 ER -