|
| Status |
Public on Jun 23, 2021 |
| Title |
Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code [in vitro] |
| Organism |
Human adenovirus 2 |
| Experiment type |
Other
|
| Summary |
The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML – a model pre-mRNA substrate – guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. We further find that the pre-mRNA segments potentially interacting with the early spliceosomal component U1 snRNP are distributed across the intron, that there is a spatial proximity of 5′ and 3′ splice sites within the pre-mRNA scaffold, and that an interplay exists between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components can 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 provides a conceptual basis to analyze the contribution of recognizable three-dimensional structural scaffolds to the splicing code across the mammalian transcriptome.
|
| |
|
| Overall design |
Estimation of SHAPE reactivity by SHAPE-MaP of Adenovirus 2 major late transcript IVS1 and its mutants
|
| |
|
| Contributor(s) |
Saha K, Ghosh G |
| Citation(s) |
34161584 |
| |
| Submission date |
Apr 23, 2021 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Kaushik Saha |
| E-mail(s) |
ksaha79@googlemail.com
|
| Organization name |
University of California San Diego
|
| Department |
Chemistry and Biochemistry
|
| Lab |
NSB 3325A
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0375 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL30034 |
Illumina MiSeq (Human adenovirus 2) |
|
| Samples (50)
|
|
| This SubSeries is part of SuperSeries: |
| GSE173178 |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code |
|
| Relations |
| BioProject |
PRJNA724661 |
| SRA |
SRP316024 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE173175_3AG_Ad3AG.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_5GU_Ad5GU.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_8Ad3_Ad3.shape.gz |
1.3 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_8Ad5_Ad5.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_8AdBS_AdBS.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_8Ad_AdML.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3ESESR5_Ad3ESE.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3ESESRbuf_Ad3ESE.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3SR1_Ad3.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3SR5_Ad3.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3SRbuf_Ad3.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad3_Ad3.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad5_Ad5.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_AdSR1_Ad.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_AdSRbuf_Ad.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_AdU1_AdML.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_Ad_AdML.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_D2D3_Ad.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_D2D5_Ad.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
| GSE173175_D2D6_Ad.shape.gz |
1.4 Kb |
(ftp)(http) |
SHAPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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