Transcription outcome of promoters enriched in histone variant H3.3 defined by positioning of H3.3 and local chromatin marks

Biochemical and Biophysical Research Communications
Eivind G LundErwan Delbarre

Abstract

Replication-independent histone variant H3.3 is incorporated into distinct genomic regions including promoters. However topology of promoter-associated H3.3 in relation to chromatin modifications and transcriptional outcome is not known, providing no insight on any distinction between H3.3-containing active and inactive promoters. Here, we report algorithms providing information on gene expression status as a function of density and position of multiple chromatin marks on promoters. We identify a relationship between promoter enrichment in epitope-tagged H3.3 or its canonical isoform H3.2 and corresponding transcriptional outcomes, as a function of sub-promoter positioning of DNA methylation and H3K4me3, H3K9me3 and H3K27me3. We identify a low-frequency configuration of H3.3 and H3K9me3 co-occupancy associated with transcriptional activity, while H3.3 and H3K27me3 promoters are invariably inactive. We unveil H3.3 and DNA methylated promoters whose transcription outcome depends on H3.3 sub-promoter positioning. Our results indicate how spatially restricted positioning of H3.3 may add another layer of transcription regulation.

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Citations

Dec 4, 2012·Molecular Cell·Joshua C BlackJohnathan R Whetstine
Aug 7, 2013·Trends in Biochemical Sciences·David ClynesRichard J Gibbons
Jul 10, 2012·Cell Metabolism·Chao Lu, Craig B Thompson
Sep 10, 2014·Current Biology : CB·Alexander FreyJulian E Sale
Jun 5, 2013·American Journal of Human Genetics·Yee Him CheungNada Jabado
Aug 4, 2012·Current Opinion in Pharmacology·Rui Chen, Michael Snyder
Jan 2, 2013·The Lancet Oncology·Joon-Hyung KimJeffrey P Greenfield
Dec 18, 2014·Biophysical Journal·Jochen ErlerJörg Langowski
Sep 16, 2014·Seminars in Radiation Oncology·Alexander K Diaz, Suzanne J Baker
Oct 15, 2013·Cell·Cameron W BrennanUNKNOWN TCGA Research Network

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