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PreprintCited by 25RNA Research and SplicingRNA and protein synthesis mechanismsRNA regulation and disease

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Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing

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Saha, Kaushik, England, Whitney, Fernandez, Mike Minh, Biswas, Tapan, Spitale, Robert C., Ghosh, Gourisankar·2018·Nucleic Acids Research
DOI 10.1101/292003PMC PMC7293017

Preprint — published as 10.1093/nar/gkaa358 · Paper page

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Abstract

Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem-loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.

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Metadata

Authors
Saha, K., England, W., Fernandez, M. M., Biswas, T., Spitale, R. C., & Ghosh, G.
Affiliations
  • University of California San Diego (US)
  • University of California, Irvine (US)
Corresponding author
  • Spitale, Robert C.
  • Ghosh, Gourisankar
ORCID
Venue
Nucleic Acids Research
Publisher
openRxiv
Published
2018-03-30
Volume
48
Issue
11
Pages
6294-6309
ISSN
0305-1048 (ISSN-L)
DOI
10.1101/292003
PMC
PMC7293017
OpenAlex
W3024286496
Cited by
25
References
1
Citations by year
2026: 1 · 2025: 4 · 2023: 4 · 2022: 4 · 2021: 10 · 2020: 2
FWCI
1.62
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • Leona M. and Harry B. Helmsley Charitable Trust
  • National Institutes of Health
  • National Human Genome Research Institute (UM1HG009443)
  • National Institute of General Medical Sciences (R01GM085490, R01GM084277)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
intron retention, alternative splicing, exonic splicing enhancers, pre-mRNA secondary structure, splice site recognition, splicing factors, mouse transcriptome, RNA structure
MeSH terms
Mouse Embryonic Stem Cells, Adenoviridae, Animals, Base Sequence, Enhancer Elements, Genetic, Exons, Introns, Mutation, RNA Precursors, RNA Splicing, Spliceosomes, Base Pairing, Gene Silencing, Mice, beta-Globins, Transcriptome

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