E2F mediates enhanced alternative polyadenylation in proliferation

Abstract

BackgroundThe majority of mammalian genes contain multiple poly(A) sites in their 3' UTRs. Alternative cleavage and polyadenylation are emerging as an important layer of gene regulation as they generate transcript isoforms that differ in their 3' UTRs, thereby modulating genes' response to 3' UTR-mediated regulation. Enhanced cleavage at 3' UTR proximal poly(A) sites resulting in global 3' UTR shortening was recently linked to proliferation and cancer. However, mechanisms that regulate this enhanced alternative polyadenylation are unknown.ResultsHere, we explored, on a transcriptome-wide scale, alternative polyadenylation events associated with cellular proliferation and neoplastic transformation. We applied a deep-sequencing technique for identification and quantification of poly(A) sites to two human cellular models, each examined under proliferative, arrested and transformed states. In both cell systems we observed global 3' UTR shortening associated with proliferation, a link that was markedly stronger than the association with transformation. Furthermore, we found that proliferation is also associated with enhanced cleavage at intronic poly(A) sites. Last, we found that the expression level of the set of genes that encode for 3'-end processing proteins is globally elevated in proliferation, and that E2F transcription factors contribute to this regulation.ConclusionsOur results comprehensively identify alternative polyadenylation events associated with cellular proliferation and transformation, and demonstrate that the enhanced alternative polyadenylation in proliferative conditions results not only in global 3' UTR shortening but also in enhanced premature cleavage in introns. Our results also indicate that E2F-mediated co-transcriptional regulation of 3'-end processing genes is one of the mechanisms that links enhanced alternative polyadenylation to proliferation.

A recently evolved class of alternative 3′-terminal exons involved in cell cycle regulation by topoisomerase inhibitors

“…Second, while the role of ALEs and intronic polyA sites in cellular processes is only emerging 11,15 , with different patterns of regulation associated with proliferation depending on cell models 5,6 , our data establish a role of ALE regulation in cell responses to TOP inhibitors. Interestingly, the preferential repression of intragenic polyA sites by DOXO is reminiscent of the recent finding that a UV mimetic reduces the use of internal polyA sites in many yeast genes 24 .…”

“…ALEs are widely regulated in a tissue-specific manner 14 , but little is known about their dynamic regulation. Interestingly, internal ALEs are preferentially upregulated during neuron activation 15 ; a similar regulation was found during cell proliferation in one study 6 , but not in another 5 . Thus, little is known about ALE regulation on a large scale.…”

“…Thus, cell responses to DNA damage may involve the coordinated regulation of both nuclear and cytoplasmic sets of transcripts by HuR. Large-scale regulation of alternative polyadenylation and splicing are increasingly involved in cellular processes, including proliferation and genotoxic responses, respectively [1][2][3][4][5][6][7][8]16,[19][20][21] . In this context, our data provide several advances.…”

“…Large numbers of alternatively spliced exons are coordinately regulated during various processes, including notably cell differentiation and cancer 1,2 , but studies mainy focused on cassette exons. Likewise, alternative polyA sites are widely regulated during several processes, most notably cell proliferation, where shorter forms are preferentially expressed [3][4][5][6][7] , but studies mainly focused on tandem polyA sites, which are located in the same exon. Thus, little is known about the regulation of alternative 3 0 terminal exons, also called alternative last exons (ALEs), which are found in 43,000 human genes and correspond to the alternative use of intronic polyA sites in a splicing-dependent manner [7][8][9] .…”

Alternative polyadenylation: New insights from global analyses

“…In differentiated cells, polyadenylation shifts to the distal PASs that have canonical cis-elements (likely stronger sites). Interestingly, both microarray and sequencing analyses suggest that most core 39 processing factors are expressed at higher levels in proliferating cells than in differentiated or resting cells Elkon et al 2012). Therefore, higher levels of 39 processing factors in proliferating cells may promote the recognition of weaker proximal PAS, while the limited amounts of 39 processing factors in differentiated cells may be preferentially recruited to the stronger distal PASs.…”