Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay

Abstract

Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic analysis integrating three data sources, eCLIP assays for a large RBP panel, shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq, to identify novel such autoregulatory feedback loops. We show that RBPs frequently bind their own pre-mRNAs, their exons respond prominently to NMD pathway disruption, and that the responding exons are enriched with nearby eCLIP peaks. We confirm previously proposed models of autoregulation in SRSF7 and U2AF1 genes and present two novel models, in which (i) SFPQ binds its mRNA and promotes switching to an alternative distal 3′-UTR that is targeted by NMD, and (ii) RPS3 binding activates a poison 5′-splice site in its pre-mRNA that leads to a frame shift and degradation by NMD. We also suggest specific splicing events that could be implicated in autoregulatory feedback loops in RBM39, HNRNPM, and U2AF2 genes. The results are available through a UCSC Genome Browser track hub.

SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly

“…(2) SRSF7 binds strongly to the PCE and intron 3 in WT cells (ref. 16 , this study). (3) Introns 3 and 5 are retained in cancer cell lines that overexpress SRSF7 (MCF-7, A549; data not shown).…”

“…SRSF7 was also suggested to regulate its own transcript levels through the inclusion of an ultraconserved alternative exon, called poison cassette exon (PCE), a process referred to as unproductive splicing. The PCE contains a premature termination codon (PTC) and causes the rapid cytoplasmic degradation of the transcript by NMD 15,16 . SRSF7 transcript levels are also crossregulated by SRSF3, which binds to the PCE and promotes its inclusion 17 .…”

Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential

“…A number of splicing factors are known to auto-regulate their own expression or regulate the expression of other splicing factors through alternative splicing coupled with NMD (Änkö et al 2012; Dredge and Jensen 2011;Jangi et al 2014;Jumaa and Nielsen 1997;McGlincy et al 2010;Pervouchine et al 2019;Rossbach et al 2009;Saltzman et al 2008;Saltzman, Pan, and Blencowe 2011;Spellman, Llorian, and Smith 2007;Sun et al 2010;Sureau et al 2001). Many of these NMD-coupled splicing events (including all those in the SR gene family) are associated with a highly conserved or ultraconserved element (Bejerano et al 2004) of the human genome, indicating a potential role for these elements in the regulation of alternative splicing coupled with NMD (Lareau, Brooks, et al 2007;Ni et al 2007).…”

Autoregulation of Many Yeast Ribosomal Proteins Discovered by Efficient Search for Feedback Regulation

“…Although less well-studied, autoregulation also occurs for proteins involved in post-transcriptional steps of gene expression. For example, many splicing factors regulate their own expression [13][14][15][16][17] . Recently developed methods for high-throughput analysis of RNA-protein interactions have identified many RNAbinding proteins, some of which are associated with their own mRNAs [18][19][20][21][22][23][24][25] .…”