Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

Abstract

The rate of RNA polymerase II (Pol II) elongation can influence splice site selection in nascent transcripts, yet the extent and physiological relevance of this kinetic coupling between transcription and alternative splicing (AS) is not well understood. We performed experiments to perturb Pol II elongation and then globally compared AS patterns with genome-wide Pol II occupancy. RNA binding and RNA processing functions were significantly enriched among the genes with Pol II elongation inhibition-dependent changes in AS. Under conditions that interfere with Pol II elongation, including cell stress, increased Pol II occupancy was detected in the intronic regions flanking the alternative exons in these genes, and these exons generally became more included. A disproportionately high fraction of these exons introduced premature termination codons that elicited nonsense-mediated mRNA decay (NMD), thereby further reducing transcript levels. Our results provide evidence that kinetic coupling between transcription, AS, and NMD affords a rapid mechanism by which cells can respond to changes in growth conditions, including cell stress, to coordinate the levels of RNA processing factors with mRNA levels.

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

“…As expected from previous studies and from its ability to inhibit transcription elongation [20][21][22] , CPT favored inclusion more often than exclusion of cassette exons (Fig. 1c).…”

“…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.…”

“…Several genes involved in the DNA damage response, such as MDM2 that encodes the main repressor of p53, are regulated at the splicing level in response to genotoxic agents 16 . Recently, UV irradiation and the topoisomerase (TOP) I inhibitor, camptothecin (CPT), were shown to increase the inclusion of many cassette exons through an inhibition of transcription elongation, which gives more time for the cotranscriptional recognition and inclusion of alternative exons [19][20][21] . CPT also induces skipping of a set of exons, in part by disrupting the interaction between the EWS and YB-1 proteins 22 .…”

Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes

“…On the one hand, reduction of RNAPII elongation rate with CPT or DRB led to the expected increase of alternative exon inclusion. 30 On the other hand, use of RNAPII mutants that have either faster or slower elongation rates yielded alternative splicing changes in both directions, i.e., increase and decrease of inclusion of alternative exons. 31 It also be noted that a recent study demonstrated that slower transcriptional elongation led to increased skipping of an alternative exon instead of the expected increased inclusion, through recruiting a splicing silencer protein to its target sequence on the pre-mRNA.…”

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

“…However, several recent reports show that the splicing efficiency of specific subsets of transcripts changes in different environmental conditions 12 or when splicing-related proteins are mutated. 13,14 Mutations that alter transcription elongation rates or treatment with drugs that affect transcription can change alternative splicing outcomes in metazoa [15][16][17][18][19][20] and splicing efficiency in yeast. 8,21,22 For example, splicing of the DYN2 alternative splicing reporter pre-mRNA in S. cerevisiae changes when transcription elongation is slowed using the small molecules 6-Azauracil or mycophenolic acid, or by mutating the RNA Pol II subunit Rpb2.…”