title: Transcriptional activity regulates alternative cleavage and polyadenylation.
abstract: Genes containing multiple pre-mRNA cleavage and polyadenylation sites, or polyA sites, express mRNA isoforms with variable 3' untranslated regions (UTRs). By systematic analysis of human and mouse transcriptomes, we found that short 3'UTR isoforms are relatively more abundant when genes are highly expressed whereas long 3'UTR isoforms are relatively more abundant when genes are lowly expressed. Reporter assays indicated that polyA site choice can be modulated by transcriptional activity through the gene promoter. Using global and reporter-based nuclear run-on assays, we found that RNA polymerase II is more likely to pause at the polyA site of highly expressed genes than that of lowly expressed ones. Moreover, highly expressed genes tend to have a lower level of nucleosome but higher H3K4me3 and H3K36me3 levels at promoter-proximal polyA sites relative to distal ones. Taken together, our results indicate that polyA site usage is generally coupled to transcriptional activity, leading to regulation of alternative polyadenylation by transcription.
authors.affiliation: Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Ji
authors.forename: Wenting
authors.initials: W
authors.lastname: Luo
authors.forename: Wencheng
authors.initials: W
authors.lastname: Li
authors.forename: Mainul
authors.initials: M
authors.lastname: Hoque
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Pan
authors.forename: Yun
authors.initials: Y
authors.lastname: Zhao
authors.forename: Bin
authors.initials: B
authors.lastname: Tian
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism; D006801:Humans; D008745:Methylation; D051379:Mice; D015341:Nucleic Acid Probes; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D011061:Poly A / Q000032:analysis* / Q000235:genetics; D026723:Polyadenylation; D059367:RNA Cleavage; D059368:RNA Isoforms / Q000235:genetics / Q000378:metabolism*; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D006657:Histones; D015341:Nucleic Acid Probes; D009707:Nucleosomes; D059368:RNA Isoforms; D012322:RNA Precursors; D012333:RNA, Messenger; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins; D011061:Poly A