Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding Export

@article{citeulike:3482487, abstract = {10.1101/gr.078519.108 We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined \^{a}ˆ¼270,000 and \^{a}ˆ¼301,000 H3K4me1-enriched regions, and \^{a}ˆ¼54,500 and \^{a}ˆ¼76,100 H3K4me3-enriched regions. In mouse adult liver, we determined \^{a}ˆ¼227,000 and \^{a}ˆ¼34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the \^{a}ˆ¼70,300 STAT1 binding sites in stimulated HeLa cells and 87\% of the \^{a}ˆ¼11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, \^{a}ˆ¼83\% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96\% of marked distal sites. After filtering against predicted transcription start sites, 50\% of \^{a}ˆ¼26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95\% of \^{a}ˆ¼5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25\% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding.}, author = {Robertson, A. Gordon and Bilenky, Mikhail and Tam, Angela and Zhao, Yongjun and Zeng, Thomas and Thiessen, Nina and Cezard, Timothee and Fejes, Anthony P. and Wederell, Elizabeth D. and Cullum, Rebecca and Euskirchen, Ghia and Krzywinski, Martin and Birol, Inanc and Snyder, Michael and Hoodless, Pamela A. and Hirst, Martin and Marra, Marco A. and Jones, Steven J. M.}, citeulike-article-id = {3482487}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.078519.108}, citeulike-linkout-1 = {http://genome.cshlp.org/content/18/12/1906.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/18/12/1906.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18787082}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18787082}, day = {3}, doi = {10.1101/gr.078519.108}, issn = {1088-9051}, journal = {Genome Research}, keywords = {chip-seq, chromatin, human}, month = {December}, number = {12}, pages = {1906--1917}, posted-at = {2008-11-09 19:13:59}, priority = {0}, title = {Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding}, url = {http://dx.doi.org/10.1101/gr.078519.108}, volume = {18}, year = {2008} }

TY - JOUR ID - citeulike:3482487 L3 - citeulike-article-id:3482487 N2 - 10.1101/gr.078519.108 We characterized the relationship of H3K4me1 and H3K4me3 at distal and proximal regulatory elements by comparing ChIP-seq profiles for these histone modifications and for two functionally different transcription factors: STAT1 in the immortalized HeLa S3 cell line, with and without interferon-gamma (IFNG) stimulation; and FOXA2 in mouse adult liver tissue. In unstimulated and stimulated HeLa cells, respectively, we determined ∼270,000 and ∼301,000 H3K4me1-enriched regions, and ∼54,500 and ∼76,100 H3K4me3-enriched regions. In mouse adult liver, we determined ∼227,000 and ∼34,800 H3K4me1 and H3K4me3 regions. Seventy-five percent of the ∼70,300 STAT1 binding sites in stimulated HeLa cells and 87% of the ∼11,000 FOXA2 sites in mouse liver were distal to known gene TSS; in both cell types, ∼83% of these distal sites were associated with at least one of the two histone modifications, and H3K4me1 was associated with over 96% of marked distal sites. After filtering against predicted transcription start sites, 50% of ∼26,800 marked distal IFNG-stimulated STAT1 binding sites, but 95% of ∼5800 marked distal FOXA2 sites, were associated with H3K4me1 only. Results for HeLa cells generated additional insights into transcriptional regulation involving STAT1. STAT1 binding was associated with 25% of all H3K4me1 regions in stimulated HeLa cells, suggesting that a single transcription factor can interact with an unexpectedly large fraction of regulatory regions. Strikingly, for a large majority of the locations of stimulated STAT1 binding, the dominant H3K4me1/me3 combinations were established before activation, suggesting mechanisms independent of IFNG stimulation and high-affinity STAT1 binding. IS - 12 JF - Genome Research SN - 1088-9051 EP - 1917 TI - Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding VL - 18 SP - 1906 KW - chip-seq KW - chromatin KW - human AU - Robertson, Gordon AU - Bilenky, Mikhail AU - Tam, Angela AU - Zhao, Yongjun AU - Zeng, Thomas AU - Thiessen, Nina AU - Cezard, Timothee AU - Fejes, Anthony AU - Wederell, Elizabeth AU - Cullum, Rebecca AU - Euskirchen, Ghia AU - Krzywinski, Martin AU - Birol, Inanc AU - Snyder, Michael AU - Hoodless, Pamela AU - Hirst, Martin AU - Marra, Marco AU - Jones, Steven PY - 2008/12/03/ UR - http://dx.doi.org/10.1101/gr.078519.108 ER -