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Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

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dc.contributor.author Vavouri, Tanya
dc.contributor.author Lehner, Ben, 1978-
dc.date.accessioned 2015-04-01T07:06:36Z
dc.date.available 2015-04-01T07:06:36Z
dc.date.issued 2012
dc.identifier.citation Vavouri T, Lehner B. Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biology. 2012; 13(11): R110. DOI 10.1186/gb-2012-13-11-r110
dc.identifier.issn 1465-6906
dc.identifier.uri http://hdl.handle.net/10230/23323
dc.description.abstract Background: More than 50% of human genes initiate transcription from CpG dinucleotide-rich regions referred to as CpG islands. These genes show differences in their patterns of transcription initiation, and have been reported to have higher levels of some activation-associated chromatin modifications. Results: Here we report that genes with CpG island promoters have a characteristic transcription-associated chromatin organization. This signature includes high levels of the transcription elongation-associated histone modifications H4K20me1, H2BK5me1 and H3K79me1/2/3 in the 5' end of the gene, depletion of the activation marks H2AK5ac, H3K14ac and H3K23ac immediately downstream of the transcription start site (TSS), and characteristic epigenetic asymmetries around the TSS. The chromosome organization factor CTCF may be bound upstream of RNA polymerase in most active CpG island promoters, and an unstable nucleosome at the TSS may be specifically marked by H4K20me3, the first example of such a modification. H3K36 monomethylation is only detected as enriched in the bodies of active genes that have CpG island promoters. Finally, as expression levels increase, peak modification levels of the histone methylations H3K9me1, H3K4me1, H3K4me2 and H3K27me1 shift further away from the TSS into the gene body. Conclusions: These results suggest that active genes with CpG island promoters have a distinct step-like series of modified nucleosomes after the TSS. The identity, positioning, shape and relative ordering of transcription-associated histone modifications differ between genes with and without CpG island promoters. This supports a model where chromatin organization reflects not only transcription activity but also the type of promoter in which transcription initiates.
dc.description.sponsorship TV is funded by MICINN grant BFU2011-30246, Ramon y Cajal grant RYC-2010-07114, European Commission Framework 7 European Re-integration grant PERG08-GA-2010-276741, and by the Institute of Predictive and Personalized Medicine of Cancer. BL is funded by an ERC Starting Grant, ERASysBio+ ERANET, MICINN grant BFU2008-00365, AGAUR, the EMBO Young Investigator Program, European Commission Framework 7 integrated project 4DCellFate, and by the EMBL-CRG Systems Biology Program
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Genome Biology. 2012; 13(11): R110
dc.rights © 2012 Vavouri and Lehner; licensee BioMed Central Ltd.
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.other Genètica
dc.subject.other Metabolisme
dc.subject.other RNA no missatgers
dc.title Human genes with CpG island promoters have a distinct transcription-associated chromatin organization
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/gb-2012-13-11-r110
dc.relation.projectID info:eu-repo/grantAgreement/EC/ERC/276741
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011-30246
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/RYC-2010-07114
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2008-00365
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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