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SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq II]

ABSTRACT: SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq II]

PROVIDER: PRJNA1164795 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30786728.fastq.gz	Fastqsanger.gz
	SRR30786729.fastq.gz	Fastqsanger.gz
	SRR30786730.fastq.gz	Fastqsanger.gz
	SRR30786731.fastq.gz	Fastqsanger.gz
	SRR30786732.fastq.gz	Fastqsanger.gz

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SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [CRISPR]

Project description:In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing. To do this, we performed CRISPR knockout screens using the Brunello knockout library on Thiamet G (TG)-treated HCT116 cells containing an O-GlcNAc responsive GFP reporter (GFP-β-OGT) integrated at the AAVS1 locus. Knockout of negative regulatory factors which regulate OGT intron 4 detention lead to increased GFP expression. Using replicate screens and further biochemical validation, we identified SFSWAP as one of the top hits affecting OGT intron 4 detention.

2024-10-16 | GSE277949 | GEO

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]

Project description:In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing using a CRISPR knockout screen in an O-GlcNAc responsive GFP reporter cell line. In order to characterize the functions of the protein, we performed siRNA mediated knockdown of SFSWAP followed by RNA-seq analysis under untreated conditions. Alternate splicing analysis using rMATS (and other tools) revealed enhanced splicing of retained introns and increased inclusion of cassette exons upon knockdown of SFSWAP, supporting an inhibitory role for SFSWAP in splicing.

2024-10-16 | GSE277950 | GEO

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq II]

Project description:In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing using a CRISPR knockout screen in an O-GlcNAc responsive GFP reporter cell line. In order to characterize the functions of the protein, we performed siRNA mediated knockdown of SFSWAP followed by RNA-seq analysis under TG-treated conditions. In addition, we performed the same analysis under UPF1 knockdown conditions to stabilize NMD targeted transcripts. Alternate splicing analysis using rMATS (and other tools) revealed enhanced splicing of retained introns and increased inclusion of cassette exons upon knockdown of SFSWAP, supporting an inhibitory role for SFSWAP in splicing.

2024-10-16 | GSE277951 | GEO

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

Project description:SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

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SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [CRISPR]

Project description:SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [CRISPR]

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SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing.

Project description:O-GlcNAcylation is the reversible post-translational addition of β-N-acetylglucosamine to serine and threonine residues of nuclear and cytoplasmic proteins. It plays an important role in several cellular processes through the modification of thousands of protein substrates. O-GlcNAcylation in humans is mediated by a single essential enzyme, O-GlcNAc transferase (OGT). OGT, together with the sole O-GlcNAcase OGA, form an intricate feedback loop to maintain O-GlcNAc homeostasis in response to changes in cellular O-GlcNAc using a dynamic mechanism involving nuclear retention of its fourth intron. However, the molecular mechanism of this dynamic regulation remains unclear. Using an O-GlcNAc responsive GFP reporter cell line, we identify SFSWAP, a poorly characterized splicing factor, as a trans-acting factor regulating OGT intron detention. We show that SFSWAP is a global regulator of retained intron splicing and exon skipping that primarily acts as a negative regulator of splicing. In contrast, knockdown of SFSWAP leads to reduced inclusion of a 'decoy exon' present in the OGT retained intron which may mediate its role in OGT intron detention. Global analysis of decoy exon inclusion in SFSWAP and UPF1 double knockdown cells indicate altered patterns of decoy exon usage. Together, these data indicate a role for SFSWAP as a global negative regulator of pre-mRNA splicing and positive regulator of intron retention.

| S-EPMC11507684 | biostudies-literature

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]

Project description:SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]

| PRJNA1164794 | ENA

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-14 | GSE277952 | GEO

CRISPR screen identifies NUDT21 as a regulator of intron detention of the SAM synthetase MAT2A RNA

Project description:The only S-adenosymethionine (SAM) synthetase expressed in most human cells, MAT2A, is regulated by intron detention. Using a GFP fusion reporter, we conducted a CRISPR screen to identify regulators of this alternative splicing event. The screen identified METTL16, a known regulator of this process, and NUDT21. NUDT21 encodes the CFIm25 protein a member of the CFIm complex involved in alternative polyadenylation. Validation and follow-up studies support the idea that CFIm25 and the larger CFIm complex plays an unanticipated role in splicing of the MAT2A detained intron.

2021-05-04 | GSE172217 | GEO

NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA

Project description:NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA

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