Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional activity regulates alternative cleavage and polyadenylation


ABSTRACT: Genes containing multiple polyadenylation (polyA) sites express mRNA isoforms with variable 3’ untranslated regions (3’UTRs). We found that short and long 3’UTR isoforms were relatively more abundant when genes were highly and lowly expressed, respectively, in human and mouse cells. Consistently, upregulated and downregulated genes were more likely to have shortened and lengthened 3’UTRs, respectively, when genes changed expression under different cell conditions or in response to extracellular stimuli. Using nuclear run-on assays, we found that RNA polymerase II (Pol II) was more likely to pause at the polyA site of highly expressed genes than that of lowly expressed ones. Moreover, in line with the difference in polyA site usage, highly expressed genes tend to have higher H3K4me3 and H3K36me3 levels but a lower density of nucleosome around promoter-proximal polyA sites relative to distal ones. Taken together, our results indicate that the efficiency of 3’ end processing is generally coupled to transcriptional activity, leading to modulation of polyA site choice by transcription and thus connecting transcriptional control with post-transcriptional regulation via pre-mRNA processing. Nascent RNA sequencing of C2C12 cell

ORGANISM(S): Mus musculus

SUBMITTER: Zhe Ji 

PROVIDER: E-GEOD-26512 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional activity regulates alternative cleavage and polyadenylation.

Ji Zhe Z   Luo Wenting W   Li Wencheng W   Hoque Mainul M   Pan Zhenhua Z   Zhao Yun Y   Tian Bin B  

Molecular systems biology 20110927


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  ...[more]

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