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

Abstract

Alternative 3 0 -terminal exons, which use intronic polyadenylation sites, are generally less conserved and expressed at lower levels than the last exon of genes. Here we discover a class of human genes, in which the last exon appeared recently during evolution, and the major gene product uses an alternative 3 0 -terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3 0 -terminal exons are downregulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein HuR/ ELAVL1 is a major regulator of this specific set of alternative 3 0 -terminal exons. HuR binding to the alternative 3 0 -terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3 0 -terminal exons.

Decoding Transcriptome Dynamics of Genome-Encoded Polyadenylation and Autoregulation with Small-Molecule Modulators of Alternative Polyadenylation

“…We thereby identified five molecules (SN38, camptothecin [CPT], febuxostat, T4 [6,7-dimethoxy-2-((4-phenyl-3,6-dihydropyridin-1 (2H)-yl)methyl) quinazoline-4(3H)-one], T5 [3-cyclobutyl-6-(2-naphthylmethyl)-2,7-dihydro-4H-pyrazolo [3,4-b]pyridin-4-one]) as hit compounds (Figures 1E and 1F). SN38 and CPT are topoisomerase inhibitors (TOPOi), which were previously reported to be APA modulators (Dutertre et al, 2014). This indicated that the initial cell-based reporter screen was sufficiently sensitive and specific to detect APA modulators.…”

“…Chemical biology approaches have been useful to clarify the molecular mechanisms, regulation, and functions of cellular processes involved in RNA-processing pathways such as alternative splicing (Salton and Misteli, 2016). Topoisomerase inhibitors were reported to modulate CR-APA by dissociation from human antigen R in pre-mRNA (Dutertre et al, 2014). However, no APA-specific inhibitors or modulators have been identified.…”

HuR-Dependent Editing of a New Mineralocorticoid Receptor Splice Variant Reveals an Osmoregulatory Loop for Sodium Homeostasis

“…For instance, HuR was shown to promote skipping of exon 6 in the transcript of the apoptosis receptor Fas, resulting in the generation of a soluble isoform that prevents programmed cell death 30 . HuR binding to the alternative 3′-terminal exon in pre-messenger target transcripts has been also shown to promote their splicing 31 . Since we have recently demonstrated that HuR constitutes a major mediator of hypotonicity-induced increase in MR expression under hypotoncity (see Lema et al ., 2017, submitted), we speculated that HuR might also participate to the processing of MR transcript in renal cells.…”

PCF11 links alternative polyadenylation to formation and spontaneous regression of neuroblastoma

“…We depleted 174 proteins including all known factors involved in pre-mRNA 3'end cleavage and polyadenylation in eukaryotes 8 and selected key factors regulating transcriptional activities, splicing, RNA turnover and other functions [23][24][25][26][27][28][29][30][31][32] which could directly or indirectly modulate TREND ( Supplementary Table 2) 5 . Probing the efficiency of RNAi-mediated depletion revealed a dropout rate (i.e.…”