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Landscape of Star-PAP mRNA association along with its co-regulator RBM10 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

ABSTRACT: Landscape of Star-PAP mRNA association along with its co-regulator RBM10 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

PROVIDER: PRJNA757275 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15594015.fastq.gz	Fastqsanger.gz
	SRR15594016.fastq.gz	Fastqsanger.gz
	SRR15594017.fastq.gz	Fastqsanger.gz
	SRR15594018.fastq.gz	Fastqsanger.gz

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Landscape of Star-PAP mRNA association along with its co-regulator RBM10 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

Project description:We employed HITS-CLIP to map genome wide Star-PAP mRNA binding and define the role of RBM10 on global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP which is diminished on cellular Star-PAP depletion. HITs-CLIP data analysis of RBM10 knockdown and pulldown with anti Star-PAP antibody on HEK293 cells indicates significance of RBM10 in Star-PAP and mRNA association.

2021-08-25 | GSE182643 | GEO

Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association.

Project description:Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3'-UTR processing, we observed a high association of Star-PAP at the 3'-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3'-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.

| S-EPMC8469156 | biostudies-literature

RNA-seq of RBM10 in LUAD cell lines

Project description:RNA-seq in isogenic RBM10-proficient and RBM10-deficient cells derived from lung adenocarcinoma cell lines HCC827 (parental and RBM10 knockout; control siRNA and RBM10 siRNA) and NCI-H1299 (parental and RBM10 knockout).

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CRISPR-Cas9 RBM10 synthetic lethality screen

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Global analysis of alternative splicing regulated by RBM10

Project description:RBM10 is an RNA binding protein that was identified as a component of spliceosome complex, suggesting its potential role in splicing regulation. However, the direct experimental evidence for this function has been lacking. Here we characterized in vivo RBM10-RNA interactions and investigated the role of RBM10 in splicing regulation at the global level. We observed significant RBM10-RNA interactions in the vicinity of splice sites and identified hundreds of splicing changes following perturbation of cellular RBM10 abundance. A RNA splicing map integrating the binding pattern and splicing profiles revealed a significant correlation between RBM10-enhanced exon skipping events and its binding close to the splicing sites of both upstream and downstream introns. Furthermore, we demonstrated the splicing defects in a patient carrying a RBM10 mutation. Overall, our data provided insights into the mechanistic model of RBM10-mediated splicing regulation and established genomic resources for future studies on its function in different pathophysiological contexts.

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Global analysis of alternative splicing regulated by RBM10

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RBM5 and RBM10

Project description:RBM5 and RBM10

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Characterization of RBM10 interactome in unchallenged and MK1775-treated cells

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Identification of RBM5 and RBM10-dependent splicing events in 293Flp-In cells.

Project description:RBM5 and RBM10 are RNA-binding proteins and splicing regulators. These two proteins are putative paralogs in mammalian cells, sharing common domain organization and extensive protein sequence similarity, but their RNA-binding preferences differ. We developed a sensitive system to identify splicing events regulated by RBM5 and/or RBM10, deleting all RBM5 alleles in 293Flp-In cells, and reducing the expression of RBM10, which is partially rescued by activation of a cryptic exon (CE) in one of the RBM10 alleles. RBM5 or RBM10 transgenes were then introduced in these RBM5-null, RBM10 mutant cells (RBM5-/-;RBM10-/CE), allowing controlled protein expression, induced with Doxycycline. Using this system we identify thousands of RBM5 and RBM10-regulated cassette exons, and note a substantial overlap between the two sets.

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Rbm10 promotes heterochromatin assembly by interacting with Clr6 and chromatin remodeling complexes

Project description:Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses confirmed that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodeling complexes known to be essential for heterochromatin silencing. We propose that Rbm10 serves as a platform to recruit Clr6 and chromatin remodelers to mediate heterochromatin formation. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.

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