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HMJSL C. Neoformans splicing factor knockout RNA-seq

ABSTRACT: We determined that over 60 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. We found they govern splicing efficiency of introns with divergent spacing between intron elements. Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites. Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G-patch/helicase pair that promotes splicing fidelity. We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.

ORGANISM(S): Cryptococcus neoformans

PROVIDER: GSE168814 | GEO | 2021/03/13

REPOSITORIES: GEO

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The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells

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2014-05-30 | E-GEOD-56878 | biostudies-arrayexpress

The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells

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PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects

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Stalled spliceosomes are a signal for RNAi-mediated genome defense

Project description:Using the yeast Cryptococcus neoformans, we describe a mechanism by which transposons are initially targeted for RNAi-mediated genome defense. We show that intron-containing mRNA precursors template siRNA synthesis. We identify a Spliceosome-Coupled And Nuclear RNAi (SCANR) complex required for siRNA synthesis and demonstrate that it physically associates with the spliceosome. We find that RNAi target transcripts are distinguished by suboptimal introns and abnormally high occupancy on spliceosomes. Functional investigations demonstrate that the stalling of mRNA precursors on spliceosomes is required for siRNA accumulation. Lariat debranching enzyme is also necessary for siRNA production, suggesting a requirement for processing of stalled splicing intermediates. We propose that recognition of mRNA precursors by the SCANR complex is in kinetic competition with splicing, thereby promoting siRNA production from transposon transcripts stalled on spliceosomes. Disparity in the strength of gene expression signals encoded by transposons versus genes offers an avenue for the evolution of genome defense. Small RNA profile of wild-type Cryptococcus neoformans was determined by deep sequencing using the Illumina SBS platform

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The histone variant H2A.Z promotes splicing of weak introns (array)

Project description:Multiple lines of evidence implicate chromatin in the regulation of pre-mRNA splicing. However, the influence of chromatin factors on co-transcriptional splice-site usage remains unclear. Here we investigated the function of the highly conserved histone variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast, Schizosaccharomyces pombe. Using Epistatic Mini-Array Profiles (EMAPs) to survey the genetic interaction landscape of the Swr1 nucleosome remodeling complex, which deposits H2A.Z, we uncovered evidence for functional interactions with components of the spliceosome. In support of these genetic connections, splicing-specific microarrays show that H2A.Z and the Swr1 ATPase are required during temperature stress for the efficient splicing of a sub-set of introns. Notably, affected introns are enriched for H2A.Z occupancy, and more likely to contain non-consensus splice sites. To test the significance of the latter correlation, we mutated the splice sites in an affected intron to consensus and found this suppressed the requirement for H2A.Z in splicing of that intron. These data suggest that H2A.Z occupancy promotes co-transcriptional splicing of sub-optimal introns that may otherwise be discarded via proofreading ATPases. Consistent with this model, we show that over-expression of splicing ATPase Prp16 suppresses both the growth and splicing defects seen in the absence of H2A.Z.

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