Pre-mRNA Splicing in the Nuclear Landscape

Abstract

Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5′-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.

Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns

“…This length distribution influences chromatin architecture and RNA Pol II in human cells (Bieberstein et al, 2012). An obvious suggestion is that pre-mRNA substrates with very long first exons are spliced inefficiently; we speculate that the nuclear cap-binding complex at the transcript's 5 0 end, which typically promotes splicing (Carrocci and Neugebauer, 2019), may be too far away from the intron to perform this role. Indeed, cap-dependent splicing is inhibited when first exons are lengthened (Lewis et al, 1996).…”

A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses

“…The 30 and 20 kb viral RNA genomes are then generated in the nucleus of cells transfected with CPER-generated DNA and exported into the cytoplasm, where they initiate the generation of authentic viruses, i.e., viruses with replicative and pathogenic characteristics (for SARS-CoV-2) indistinguishable from WT viruses. Remarkably, the CPER method described herein reliably and rapidly produces authentic viruses despite (i) the large genome sizes that would likely exacerbate misassembly errors, (ii) the presence of nuclear RNA splicing activities 54 , (iii) the multiple processes required for nuclear export and translation of RNA 55 , and (iv) the presence of host cell enzymes that degrade viral RNA 56 , 57 . Thus, genome size does not appear to be a limitation for the CPER methodology, which bodes well for future studies of RNA viruses with larger genomes, such as the recently discovered planarian secretory cell nidovirus that has a ~41 kb genome 58 .…”

The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II

“…Interestingly, the rate of the Pol II affects Ubx spliced target genes differently. Thus, Ubx may regulate splicing via various molecular mechanisms, such as by promoting the recruitment of splicing activators (SR proteins) or repressors (hnRNP), by modifying the RNA folding or impacting on the chromatin landscape (Carrocci and Neugebauer, 2019; Saldi et al, 2016, Carnesecchi et al, 2018). Taken together, this further extend the possible combination of Hox molecular mode of actions.…”

“…Splicing is regulated at several levels in the nucleus (Bentley, 2014; Chen and Manley, 2009; Galganski et al, 2017; Spector and Lamond, 2011; Wahl et al, 2009). Notably, it mainly happens co-transcriptionally (Blencowe, 2006; Hegele et al, 2012; Wahl et al, 2009) and depends on the RNA Polymerase II (Pol II) elongation activity (Bentley, 2014; Carrocci and Neugebauer, 2019; Khodor et al, 2011; de la Mata et al, 2003; Oesterreich et al, 2011; Saldi et al, 2016). Remarkably, a single pre-mRNA can be spliced in different ways thereby diversifying transcript isoforms and proteins (Blencowe, 2006).…”