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

Abstract

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Spliceosomal component PRP-40 is a central regulator of microexon splicing

“…Mammalian microexons tend to be frame preserving (multiples of 3 nt), such that inclusion or skipping of the microexon does not cause translational frameshifts. We likewise find that PRP-40regulated microexons show a strong preference for frame preservation (Figure 5C), in agreement with recent work on all detectable C. elegans microexons (Koterniak et al, 2020). We also tested whether the PRP-40-regulated microexons we identified are present in existing gene annotations and found that a substantial minority of microexons (30%) were previously unannotated, and a small number (4%) were previously annotated but considered constitutive exons (Figure 5D).…”

Bulk and single‐cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation

“…The differentially expressed isoforms with similar change using R package MFUZZ 80 . The 200 bp sequence of upstream and downstream intron flanking alternative exon was extracted using bedtools (version 2.30.0), and the enriched motifs were analysed modified from the previous study using HOMER findMotif.pl script with parameters: ‐len 6,8,10,12 81 . The significantly AS events were selected as regulated events, while the other events were selected as background events.…”

Wired for insight—recent advances in Caenorhabditis elegans neural circuits

“…In the nervous system, efforts to profile neuron-type transcriptomes began nearly two decades ago (ZHANG et al 2002), and have recently cumulated to the CeNGen initiative , which aims to establish a complete gene expression atlas for each neuron from larvae to adults. While conventional bulk RNAseq using dissociated and sorted neurons is a proven success (TAYLOR et al 2019), recent implementation of TRAP-seq (Translating Ribosome Affinity Purification) has uncovered neuronal-type mRNA splicing events (KOTERNIAK et al 2020). In combination with forward genetic screens using elegantly designed reporters that J o u r n a l P r e -p r o o f 8 detect alternative splicing in vivo (THOMPSON et al 2019), there is a greater anticipation to advance mechanistic understanding.…”