DBMI Open Insights with Dmitri Pervouchine – 3/21

Thursday, March 21ST
Countway Library, 4th FL, Room 403, 12:30-1:30PM

Dmitri Pervouchine, PhD
Assistant Professor, Center of Life Sciences
Skolkovo Institute for Science and Technology

Integrative Transcriptomic Analysis Suggests Novel Autoregulatory Splicing Events coupled with Nonsense-Mediated mRNA Decay

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 (1) SFPQ binds its mRNA and promotes switching to an alternative distal 3′-UTR that is targeted by NMD, and (2) 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. Taken together, these findings indicate that autoregulatory negative feedback loop of alternative splicing and NMD is a ubiquitous form of post-transcriptional control of gene expression among splicing factors.