Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans [RESEARCH]

Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. While many documented examples of splicing differences between broad tissue-types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. Using Translating Ribosome Affinity Purification coupled with deep-sequencing (TRAP-seq) in C. elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, conserved across Caenorhabditis species and enriched in specific cis regulatory motifs. Utilizing this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5' splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons b...

Source: Genome Research - October 30, 2020 Category: Genetics & Stem Cells Authors: Koterniak, B., Pilaka, P. P., Gracida, X., Schneider, L.-M., Pritišanac, I., Zhang, Y., Calarco, J. A. Tags: RESEARCH Source Type: research