Open AccessTranscriptional activity regulates alternative cleavage and polyadenylation
Author(s) -
Ji Zhe,
Luo Wenting,
Li Wencheng,
Hoque Mainul,
Pan Zhenhua,
Zhao Yun,
Tian Bin
Publication year - 2011
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2011.69
Subject(s) - polyadenylation , biology , gene isoform , gene , untranslated region , primary transcript , three prime untranslated region , transcription (linguistics) , promoter , genetics , regulation of gene expression , rna polymerase ii , reporter gene , cleavage and polyadenylation specificity factor , transcriptional regulation , exon , gene expression , microbiology and biotechnology , alternative splicing , messenger rna , linguistics , philosophy
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.