Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

BMC Genomics

Finn Drabløs¹  Alistair RR Forrest⁴  Piero Carninci⁴  Hideya Kawaji³  Carsten O Daub⁴  Geir Kjetil Sandve⁵  Morten Rye² 

[1] Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, P.O. Box 8905, NO-7491 Trondheim, Norway;St. Olavs Hospital, Postboks 3250, Sluppen 7006, Trondheim;RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan;RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan;Department of Informatics, University of Oslo, Oslo, Norway

关键词: Gene expression;    Chromatin states;    Transcription start sites;    Cage;    Encode;    Fantom;   

Others  :  1217632
DOI  :  10.1186/1471-2164-15-120

 received in 2013-05-21, accepted in 2013-12-07,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Rye et al.; licensee BioMed Central Ltd.

【 图 表 】

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