Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

Hao Sun, Jiejun Wu, Priyankara Wickramasinghe, Sharmistha Pal, Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Louise C. Showe, Tim H.M. Huang, Ramana V. Davuluri

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


Alternative promoters that are differentially used in various cellular contexts and tissue types add to the transcriptional complexity in mammalian genome. Identification of alternative promoters and the annotation of their activity in different tissues is one of the major challenges in understanding the transcriptional regulation of the mammalian genes and their isoforms. To determine the use of alternative promoters in different tissues, we performed ChIP-seq experiments using antibody against RNA Pol-II, in five adult mouse tissues (brain, liver, lung, spleen and kidney). Our analysis identified 38639 Pol-II promoters, including 12270 novel promoters, for both protein coding and non-coding mouse genes. Of these, 6384 promoters are tissue specific which are CpG poor and we find that only 34 of the novel promoters are located in CpG-rich regions, suggesting that novel promoters are mostly tissue specific. By identifying the Pol-II bound promoter(s) of each annotated gene in a given tissue, we found that 37 of the protein coding genes use alternative promoters in the five mouse tissues. The promoter annotations and ChIP-seq data presented here will aid ongoing efforts of characterizing gene regulatory regions in mammalian genomes.

Original languageEnglish (US)
Pages (from-to)190-201
Number of pages12
JournalNucleic acids research
Issue number1
StatePublished - Jan 2011
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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