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

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

PROVIDER: PRJNA779795 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16922635_1.fastq.gz	Fastqsanger.gz
	SRR16922635_2.fastq.gz	Fastqsanger.gz
	SRR16922637_1.fastq.gz	Fastqsanger.gz
	SRR16922637_2.fastq.gz	Fastqsanger.gz
	SRR16922639_1.fastq.gz	Fastqsanger.gz

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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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[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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[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.

2022-07-07 | GSE188650 | GEO

SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23

Project description:Here we characterized SRSF1’s interactome using proximity labeling and mass spectrometry. This approach yielded 190 proteins enriched in the SRSF1 samples, independently of the N- or C-terminal location of the biotin-labeling domain. The detected proteins reflect established functions of SRSF1 in pre-mRNA splicing and reveal additional connections to spliceosome proteins, in addition to other recently identified functions. We validated a robust interaction with the spliceosomal RNA helicase DDX23/PRP28 using bimolecular fluorescence complementation and in vitro binding assays. The interaction is mediated by the N-terminal RS-like domain of DDX23 and both RRM1 and the RS domain of SRSF1.

2024-04-30 | PXD048180 | Pride

[SHAPE-MaP_10_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 | GSE202785 | GEO

[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

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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Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Project description:Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome. 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.

2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress

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.

| S-EPMC2673513 | biostudies-literature

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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