This work has attempted to identify which genes are most frequently targeted by differential splicing using both downloaded and original RNA-Seq data from several species and tissue types.
Abstract
Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short noncoding RNAs. In addition to full-length transcripts with all exons in the genomically encoded order, alternatively spliced transcripts can also be produced through alternative splicing of pre-mRNA. We have attempted to identify which genes are most frequently targeted by differential splicing using both downloaded and original RNA-Seq data from several species and tissue types. In order to identify splicing variation on an individual-to-individual basis, random contrasting of samples within compatible sets of samples was done. Both when analyzing sequence data from similar source material (same tissue from individuals kept under similar conditions) and when contrasting samples that are more different, such as different tissue types, genes associated with the splicing process itself seem to be the most recurring targets.
Abstract In contrast to canonical cis-splicing, trans-splicing combines exons from two distinct transcripts, yielding chimeric mRNAs. One striking example is the ubiquitously expressed modifier of the mdg4 (mod(mdg4)) locus in Drosophila, where all mRNAs spanning over 30 isoforms are generated exclusively by trans-spli...
I. Soldatova, O. Beginyazova, Oksana G Maksimenko et al.· Nucleic Acids Research· 0 citations
How splicing-dependent and splicing-independent activities are integrated are discussed and a framework in which splicing factors act as regulatory hubs coordinating gene expression across multiple layers is proposed.
M. J. Iglesias, Y. Agrofoglio, Lukasz Szewc et al.· TIBS -Trends in Biochemical...· 0 citations
Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive splice sites (RSSs), the intronic loci at which RS events occur, based on alignment of total RNA-seq data to short, customi...
David J. Bass, Steven L. Salzberg· bioRxiv· 0 citations
This review article scrutinizes the aberrations in RNA splicing linked to cancer and explores therapeutic endeavors directed at addressing mutations in RNA splicing.
This review describes how spliceosome assembly, splicing regulatory elements, splicing factors, epigenetic modifications, and post-transcriptional processes determine splice-site selection and suggests that safe clinical translation will require greater selectivity, reduced off-target toxicity, and preservation of esse...
Huining Huang, Yao Yu, Qian Zhou et al.· Molecular Biomedicine· 0 citations
The in vivo function of the conserved spliceosomal kinase PRPF-4 in C. elegans is investigated to establish PRPF-4 as a central regulator of RNA metabolism and demonstrate the far-reaching effects on gene expression caused by loss of core splicing components.
W. Barron, Xiaolu Wei, Sakia Ferdousy et al.· bioRxiv· 0 citations
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