Cargando…
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
BACKGROUND: Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status and processes is an important task for improving our understanding of human cellular biology. The FANTOM5 and ENCODE projects represent two independent large scale eff...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986914/ https://www.ncbi.nlm.nih.gov/pubmed/24669905 http://dx.doi.org/10.1186/1471-2164-15-120 |
_version_ | 1782311792076128256 |
---|---|
author | Rye, Morten Sandve, Geir Kjetil Daub, Carsten O Kawaji, Hideya Carninci, Piero Forrest, Alistair RR Drabløs, Finn |
author_facet | Rye, Morten Sandve, Geir Kjetil Daub, Carsten O Kawaji, Hideya Carninci, Piero Forrest, Alistair RR Drabløs, Finn |
author_sort | Rye, Morten |
collection | PubMed |
description | BACKGROUND: Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status and processes is an important task for improving our understanding of human cellular biology. The FANTOM5 and ENCODE projects represent two independent large scale efforts to map regulatory and transcriptional features to the human genome. Here we investigate chromatin features around a comprehensive set of transcription start sites in four cell lines by integrating data from these two projects. RESULTS: Transcription start sites can be distinguished by chromatin states defined by specific combinations of both chromatin mark enrichment and the profile shapes of these chromatin marks. The observed patterns can be associated with cellular functions and processes, and they also show association with expression level, location relative to nearby genes, and CpG content. In particular we find a substantial number of repressed inter- and intra-genic transcription start sites enriched for active chromatin marks and Pol II, and these sites are strongly associated with immediate-early response processes and cell signaling. Associations between start sites with similar chromatin patterns are validated by significant correlations in their global expression profiles. CONCLUSIONS: The results confirm the link between chromatin state and cellular function for expressed transcripts, and also indicate that active chromatin states at repressed transcripts may poise transcripts for rapid activation during immune response. |
format | Online Article Text |
id | pubmed-3986914 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-39869142014-04-16 Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines Rye, Morten Sandve, Geir Kjetil Daub, Carsten O Kawaji, Hideya Carninci, Piero Forrest, Alistair RR Drabløs, Finn BMC Genomics Research Article BACKGROUND: Deciphering the most common modes by which chromatin regulates transcription, and how this is related to cellular status and processes is an important task for improving our understanding of human cellular biology. The FANTOM5 and ENCODE projects represent two independent large scale efforts to map regulatory and transcriptional features to the human genome. Here we investigate chromatin features around a comprehensive set of transcription start sites in four cell lines by integrating data from these two projects. RESULTS: Transcription start sites can be distinguished by chromatin states defined by specific combinations of both chromatin mark enrichment and the profile shapes of these chromatin marks. The observed patterns can be associated with cellular functions and processes, and they also show association with expression level, location relative to nearby genes, and CpG content. In particular we find a substantial number of repressed inter- and intra-genic transcription start sites enriched for active chromatin marks and Pol II, and these sites are strongly associated with immediate-early response processes and cell signaling. Associations between start sites with similar chromatin patterns are validated by significant correlations in their global expression profiles. CONCLUSIONS: The results confirm the link between chromatin state and cellular function for expressed transcripts, and also indicate that active chromatin states at repressed transcripts may poise transcripts for rapid activation during immune response. BioMed Central 2014-03-26 /pmc/articles/PMC3986914/ /pubmed/24669905 http://dx.doi.org/10.1186/1471-2164-15-120 Text en Copyright © 2014 Rye et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Research Article Rye, Morten Sandve, Geir Kjetil Daub, Carsten O Kawaji, Hideya Carninci, Piero Forrest, Alistair RR Drabløs, Finn Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title | Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title_full | Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title_fullStr | Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title_full_unstemmed | Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title_short | Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
title_sort | chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986914/ https://www.ncbi.nlm.nih.gov/pubmed/24669905 http://dx.doi.org/10.1186/1471-2164-15-120 |
work_keys_str_mv | AT ryemorten chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT sandvegeirkjetil chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT daubcarsteno chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT kawajihideya chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT carnincipiero chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT forrestalistairrr chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines AT drabløsfinn chromatinstatesrevealfunctionalassociationsforgloballydefinedtranscriptionstartsitesinfourhumancelllines |