{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T00:16:37Z","timestamp":1759191397108},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1293,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Histone modifications regulate chromatin structure and gene expression. Although nucleosome formation is known to be affected by primary DNA sequence composition, no sequence signature has been identified for histone modifications. It is known that dense H3K4me3 nucleosome sites are accompanied by a low density of other nucleosomes and are associated with gene activation. This observation suggests a different sequence composition of H3K4me3 from other nucleosomes.<\/jats:p>\n               <jats:p>Approach: To understand the relationship between genome sequence and chromatin structure, we studied DNA sequences at histone modification sites in various human cell types. We found sequence specificity for H3K4me3, but not for other histone modifications. Using the sequence specificities of H3 and H3K4me3 nucleosomes, we developed a model that computes the probability of H3K4me3 occupation at each base pair from the genome sequence context.<\/jats:p>\n               <jats:p>Results: A comparison of our predictions with experimental data suggests a high performance of our method, revealing a strong association between H3K4me3 and specific genomic DNA context. The high probability of H3K4me3 occupation occurs at transcription start and termination sites, exon boundaries and binding sites of transcription regulators involved in chromatin modification activities, including histone acetylases and enhancer- and insulator-associated factors. Thus, the human genome sequence contains signatures for chromatin modifications essential for gene regulation and development. Our method may be applied to find new sequence elements functioning by chromatin modulation.<\/jats:p>\n               <jats:p>Availability: Software and supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0misook.ha@samsung.com or wli@uchicago.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt126","type":"journal-article","created":{"date-parts":[[2013,3,20]],"date-time":"2013-03-20T01:40:36Z","timestamp":1363743636000},"page":"1199-1205","source":"Crossref","is-referenced-by-count":5,"title":["Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context"],"prefix":"10.1093","volume":"29","author":[{"given":"Misook","family":"Ha","sequence":"first","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA, 2Future IT Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Yongin-City, Gyeonggi 446-712, 3Systems Engineering Team, Samsung Display Corporation, Asan-City, Chungnam 336-741, South Korea and 4Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan"},{"name":"1 Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA, 2Future IT Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Yongin-City, Gyeonggi 446-712, 3Systems Engineering Team, Samsung Display Corporation, Asan-City, Chungnam 336-741, South Korea and 4Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soondo","family":"Hong","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA, 2Future IT Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Yongin-City, Gyeonggi 446-712, 3Systems Engineering Team, Samsung Display Corporation, Asan-City, Chungnam 336-741, South Korea and 4Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen-Hsiung","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA, 2Future IT Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Yongin-City, Gyeonggi 446-712, 3Systems Engineering Team, Samsung Display Corporation, Asan-City, Chungnam 336-741, South Korea and 4Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,3,19]]},"reference":[{"key":"2023012810380200800_btt126-B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2023012810380200800_btt126-B2","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1126\/science.1183439","article-title":"PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice","volume":"327","author":"Baudat","year":"2010","journal-title":"Science"},{"key":"2023012810380200800_btt126-B3","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nature05915","article-title":"The complex language of chromatin regulation during transcription","volume":"447","author":"Berger","year":"2007","journal-title":"Nature"},{"key":"2023012810380200800_btt126-B4","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","article-title":"Core transcriptional regulatory circuitry in human embryonic stem cells","volume":"122","author":"Boyer","year":"2005","journal-title":"Cell"},{"key":"2023012810380200800_btt126-B5","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.stem.2008.11.011","article-title":"Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation","volume":"4","author":"Cui","year":"2009","journal-title":"Cell Stem Cell"},{"key":"2023012810380200800_btt126-B6","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/0022-2836(85)90396-1","article-title":"DNA bending and its relation to nucleosome positioning","volume":"186","author":"Drew","year":"1985","journal-title":"J. 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