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Progressive lengthening of 3′ untranslated regions of mRNAs by alternative cleavage and polyadenylation in cellular senescence of mouse embryonic fibroblasts

By Miao Han, Guoliang Lv, Hongbo Nie, Ting Shen, Yichi Niu, Xueping Li, Meng Chen, Xia Zheng, Wei Li, Chen Ding, Gang Wei, Jun Gu, Xiao-Li Tian, Yufang Zheng, Xinhua Liu, Jinfeng Hu, Wei Tao, Ting Ni

Posted 11 Nov 2015
bioRxiv DOI: 10.1101/031302

ABSTRACT Background Cellular senescence has historically been viewed as an irreversible cell cycle arrest that acts to prevent cancer. Recent discoveries demonstrated that cellular senescence also played a vital role in normal embryonic development, tissue renewal and senescence-related diseases. Alternative cleavage and polyadenylation (APA) is an important layer of post-transcriptional regulation, which has been found playing an essential role in development, activation of immune cells and cancer progression. However, the role of APA in the process of cellular senescence remains unclear. Materials and Methods We applied high-throughput paired-end polyadenylation sequencing (PA-seq) and strand-specific RNA-seq sequencing technologies, combined systematic bioinformatics analyses and experimental validation to investigate APA regulation in different passages of mouse embryonic fibroblasts (MEFs) and in aortic vascular smooth muscle cells of rats (VSMCs) with different ages. Results Based on PA-seq, we found that genes in senescent cells tended to use distal pA sites and an independent bioinformatics analysis for RNA-seq drew the same conclusion. In consistent with these global results, both the number of genes significantly preferred to use distal pAs in senescent MEFs and VSMCs were significantly higher than genes tended to use proximal pAs. Interestingly, the expression levels of genes preferred to use distal pAs in senescent MFEs and VSMCs tended to decrease, while genes with single pAs did not show such trend. More importantly, genes preferred to use distal pAs in senescent MFEs and VSMCs were both enriched in common senescence-related pathways, including ubiqutin mediated proteolysis, regulation of actin cytoskeleton, cell cycle and wnt signaling pathway. By cis-elements analyses, we found that the longer 3'UTR; UTRs of the genes tended to use distal pAs progressively can introduce more conserved binding sites of senescence-related miRNAs and RBPs. Furthermore, 375 genes with progressive 3'UTR; UTR lengthening during MEF senescence tended to use more strong and conserved polyadenylation signal (PAS) around distal pA sites and this was accompanied the observation that expression level of core factors involved in cleavage and polyadenylation complex was decreased. Conclusions Our finding that genes preferred distal pAs in senescent mouse and rat cells provide new insights for aging cells' posttranscriptional gene regulation in the view of alternative polyadenylation given senescence response was thought to be a tumor suppression mechanism and more genes tended to use proximal pAs in cancer cells. In short, APA was a hidden layer of post-transcriptional gene expression regulation involved in cellular senescence.

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