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[SHAPE-MaP_10_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

ABSTRACT: Please refer to the summary of the Superseries.

ORGANISM(S): Human adenovirus 2

PROVIDER: GSE202785 | GEO | 2022/07/07

REPOSITORIES: GEO

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[SHAPE-MaP_4_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

Project description:Please refer to the summary of the Superseries.

2022-07-07 | GSE188649 | GEO

[RNP-MaP] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

Project description:Please refer to the summary of the Superseries.

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[SHAPE-MaP_4_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

Project description:[SHAPE-MaP_4_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

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[SHAPE-MaP_10_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

Project description:[SHAPE-MaP_10_mM] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

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[RNP-MaP] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

Project description:[RNP-MaP] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions

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Exon-independent recruitment of SRSF1 is mediated by U1 snRNP stem-loop 3.

Project description:SRSF1 protein and U1 snRNPs are closely connected splicing factors. They both stimulate exon inclusion, SRSF1 by binding to exonic splicing enhancer sequences (ESEs) and U1 snRNPs by binding to the downstream 5' splice site (SS), and both factors affect 5' SS selection. The binding of U1 snRNPs initiates spliceosome assembly, but SR proteins such as SRSF1 can in some cases substitute for it. The mechanistic basis of this relationship is poorly understood. We show here by single-molecule methods that a single molecule of SRSF1 can be recruited by a U1 snRNP. This reaction is independent of exon sequences and separate from the U1-independent process of binding to an ESE. Structural analysis and cross-linking data show that SRSF1 contacts U1 snRNA stem-loop 3, which is required for splicing. We suggest that the recruitment of SRSF1 to a U1 snRNP at a 5'SS is the basis for exon definition by U1 snRNP and might be one of the principal functions of U1 snRNPs in the core reactions of splicing in mammals.

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Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.

Project description:Most human protein-encoding genes contain multiple exons that are spliced together, frequently in alternative arrangements, by the spliceosome. It is established that U1 snRNP is an essential component of the spliceosome, in human consisting of RNA and ten proteins, several of which are post-translationally modified and exist as multiple isoforms. Unresolved and challenging to investigate are the effects of these post translational modifications on the dynamics, interactions and stability of the particle. Using mass spectrometry we investigate the composition and dynamics of the native human U1 snRNP and compare native and recombinant complexes to isolate the effects of various subunits and isoforms on the overall stability. Our data reveal differential incorporation of four protein isoforms and dynamic interactions of subunits U1-A, U1-C and Sm-B/B'. Results also show that unstructured post-translationally modified C-terminal tails are responsible for the dynamics of Sm-B/B' and U1-C and that their interactions with the Sm core are controlled by binding to different U1-70k isoforms and their phosphorylation status in vivo. These results therefore provide the important functional link between proteomics and structure as well as insight into the dynamic quaternary structure of the native U1 snRNP important for its function.

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Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.

Project description:Human spliceosomal U1 small nuclear ribonucleoprotein particles (snRNPs), which consist of U1 small nuclear RNA and ten proteins, recognize the 5' splice site within precursor messenger RNAs and initiate the assembly of the spliceosome for intron excision. An electron density map of the functional core of U1 snRNP at 5.5 A resolution has enabled us to build the RNA and, in conjunction with site-specific labelling of individual proteins, to place the seven Sm proteins, U1-C and U1-70K into the map. Here we present the detailed structure of a spliceosomal snRNP, revealing a hierarchical network of intricate interactions between subunits. A striking feature is the amino (N)-terminal polypeptide of U1-70K, which extends over a distance of 180 A from its RNA binding domain, wraps around the core domain consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. The structure of U1 snRNP provides insights into U1 snRNP assembly and suggests a possible mechanism of 5'-splice-site recognition.

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SAM68 interaction with U1A modulates U1 snRNP recruitment and regulates mTor pre-mRNA splicing.

Project description:Src associated in mitosis (SAM68) plays major roles in regulating RNA processing events, such as alternative splicing and mRNA translation, implicated in several developmental processes. It was previously shown that SAM68 regulates the alternative splicing of the mechanistic target of rapamycin (mTor), but the mechanism regulating this process remains elusive. Here, we report that SAM68 interacts with U1 small nuclear ribonucleoprotein (U1 snRNP) to promote splicing at the 5' splice site in intron 5 of mTor. We also show that this direct interaction is mediated through U1A, a core-component of U1snRNP. SAM68 was found to bind the RRM1 domain of U1A through its C-terminal tyrosine rich region (YY domain). Deletion of the U1A-SAM68 interaction domain or mutation in SAM68-binding sites in intron 5 of mTor abrogates U1A recruitment and 5' splice site recognition by the U1 snRNP, leading to premature intron 5 termination and polyadenylation. Taken together, our results provide the first mechanistic study by which SAM68 modulates alternative splicing decision, by affecting U1 snRNP recruitment at 5' splice sites.

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Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly.

Project description:Alternative splicing is responsible for much of the transcriptomic and proteomic diversity observed in eukaryotes and involves combinatorial regulation by many cis-acting elements and trans-acting factors. SR and hnRNP splicing regulatory proteins often have opposing effects on splicing efficiency depending on where they bind the pre-mRNA relative to the splice site. Position-dependent splicing repression occurs at spliceosomal E-complex, suggesting that U1 snRNP binds but cannot facilitate higher order spliceosomal assembly. To test the hypothesis that the structure of U1 snRNA changes during activation or repression, we developed a method to structure-probe native U1 snRNP in enriched conformations that mimic activated or repressed spliceosomal E-complexes. While the core of U1 snRNA is highly structured, the 5' end of U1 snRNA shows different SHAPE reactivities and psoralen crosslinking efficiencies depending on where splicing regulatory elements are located relative to the 5' splice site. A motif within the 5' splice site binding region of U1 snRNA is more reactive toward SHAPE electrophiles when repressors are bound, suggesting U1 snRNA is bound, but less base-paired. These observations demonstrate that splicing regulators modulate splice site selection allosterically.

| S-EPMC7491332 | biostudies-literature

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