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 R. R., Drabløs, Finn and The FANTOM consortium (2014) Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics, 15 120: 1-21. doi:10.1186/1471-2164-15-120

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Author Rye, Morten
Sandve, Geir Kjetil
Daub, Carsten O.
Kawaji, Hideya
Carninci, Piero
Forrest, Alistair R. R.
Drabløs, Finn
The FANTOM consortium
Title Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2014-03-26
Sub-type Article (original research)
DOI 10.1186/1471-2164-15-120
Open Access Status DOI
Volume 15
Issue 120
Start page 1
End page 21
Total pages 21
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
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.
Keyword Fantom
Encode
Cage
Transcription start sites
Chromatin states
Gene expression
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
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Created: Fri, 27 Jun 2014, 01:18:52 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology