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Status |
Public on Jun 23, 2021 |
Title |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code [In Vivo] |
Organism |
Human adenovirus 2 |
Experiment type |
Other
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Summary |
The specific recognition of splice signals at or near the exon-intron junctions is not explained by their weak conservation across the mammalian transcriptome and postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of a pre-mRNA guiding early spliceosomal components to the splice signal sequences. We find that mutation in non-cognate splice signal sequences of a model pre-mRNA substrate could impede recruitment of early spliceosomal components due to disruption of global structure of the pre-mRNA. We also find distribution of pre-mRNA segments potentially interacting with early spliceosomal component U1 snRNP across the intron, spatial proximity of 5′ and 3′ splice sites within the pre-mRNA scaffold, and an interplay between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components could recognize a three-dimensional structural scaffold beyond the short splice signal sequences and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This work provides a conceptual base to extend our understanding of prevalence, distribution, and splicing regulatory potential of recognizable three-dimensional structural scaffolds across the mammalian transcriptome.
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Overall design |
Estimation of in vivo SHAPE reactivity by SHAPE-MaP of Adenovirus 2 major late transcript IVS1 and its mutants
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Contributor(s) |
Saha K, Ghosh G |
Citation(s) |
34161584 |
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Submission date |
Apr 23, 2021 |
Last update date |
Jun 24, 2021 |
Contact name |
Kaushik Saha |
E-mail(s) |
ksaha79@googlemail.com
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Organization name |
University of California San Diego
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Department |
Chemistry and Biochemistry
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Lab |
NSB 3325A
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Street address |
9500 Gilman Drive
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093-0375 |
Country |
USA |
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Platforms (1) |
GPL30034 |
Illumina MiSeq (Human adenovirus 2) |
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Samples (9)
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This SubSeries is part of SuperSeries: |
GSE173178 |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code |
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Relations |
BioProject |
PRJNA724662 |
SRA |
SRP316027 |