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Splicing factors and chromatin organization enhance exon recognition by alleviating constraints generated by gene nucleotide composition bias

ABSTRACT: To characterize the rules governing exon recognition during splicing, we analyzed RNA-seq datasets and identified ~4,000 GC-rich and ~5,000 AT-rich exons, labelled GC-exons and AT-exons, respectively whose inclusion depends on different sets of splicing factors. We show that a high GC-load is associated with predicted RNA secondary structures at 5'ss and that GC-exons are dependent on U1 snRNP-associated proteins. Meanwhile, a high AT-load is associated with a large number of decoy splicing-related signals upstream exons such as the number of branchpoints and SF1- or U2AF65-binding sites and AT-exons are dependent on U2 snRNP-associated proteins. Nucleotide composition bias also influences local chromatin organization. Since the GC content of exons correlates with that of their hosting-genes, -isochores and – topologically-associated domains, we propose that regional nucleotide composition bias leaves a footprint locally, at the exon level, inducing, during splicing, constraints that are alleviated by the local chromatin organization and specific splicing factors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138397 | GEO | 2019/10/25

REPOSITORIES: GEO

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A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly post-transcriptional

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2007-01-22 | GSE6417 | GEO

Gene architecture directs splicing outcome in separate nuclear spatial regions

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SF3B1 association with chromatin determines splicing outcomes

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SF3B1 association with chromatin determines splicing outcomes

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2015-02-10 | E-GEOD-64078 | biostudies-arrayexpress

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2018-08-07 | GSE106578 | GEO

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