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Letter

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

¹ Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093-0653, USA; ² UCSD Bioinformatics Graduate Program, UCSD, La Jolla, California 92093-0653, USA; ³ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; ⁴ Department of Medicine, UCSD School of Medicine, La Jolla, California 92093-0660, USA; ⁵ NimbleGen Systems Inc., Madison, Wisconsin 53711, USA; ⁶ Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, California 92093-0653, USA

By integrating genome-wide maps of RNA polymerase II (Polr2a) binding with gene expression data and H3ac and H3K4me3 profiles, we characterized promoters with enriched activity in mouse embryonic stem cells (mES) as well as adult brain, heart, kidney, and liver. We identified 24,000 promoters across these samples, including 16,976 annotated mRNA 5' ends and 5153 additional sites validating cap-analysis of gene expression (CAGE) 5' end data. We showed that promoters with CpG islands are typically non-tissue specific, with the majority associated with Polr2a and the active chromatin modifications in nearly all the tissues examined. By contrast, the promoters without CpG islands are generally associated with Polr2a and the active chromatin marks in a tissue-dependent way. We defined 4396 tissue-specific promoters by adapting a quantitative index of tissue-specificity based on Polr2a occupancy. While there is a general correspondence between Polr2a occupancy and active chromatin modifications at the tissue-specific promoters, a subset of them appear to be persistently marked by active chromatin modifications in the absence of detectable Polr2a binding, highlighting the complexity of the functional relationship between chromatin modification and gene expression. Our results provide a resource for exploring promoter Polr2a binding and epigenetic states across pluripotent and differentiated cell types in mammals.

⁸ Corresponding author.

E-mail biren{at}ucsd.edu, rgreen{at}nimblegen.com; fax: (858) 534-7750.

[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to the Gene Expression Omnibus under accession no. GSE7688 [NCBI GEO] .]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.6654808

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