title: Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.
abstract: 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 38 639 Pol-II promoters, including 12 270 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.
authors.affiliation: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Sun
authors.forename: Jiejun
authors.initials: J
authors.lastname: Wu
authors.forename: Priyankara
authors.initials: P
authors.lastname: Wickramasinghe
authors.forename: Sharmistha
authors.initials: S
authors.lastname: Pal
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.forename: Anirban
authors.initials: A
authors.lastname: Bhattacharyya
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Agosto-Perez
authors.forename: Louise C
authors.initials: LC
authors.lastname: Showe
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D016678:Genome; D051379:Mice; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000592:standards; D014158:Transcription, Genetic
chemical_list: D012319:RNA Polymerase II