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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE277950 | GEO | 2024/10/16

REPOSITORIES: GEO

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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.

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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.

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Project description:We report the effect of splicing upon O-GlcNAc perturbation with OGT inhibitor or OGA inhibitor. We found that splicing is acutely affected through our phosphoproteomics data when cells are treated with OGT inhibitor. By obtaining the various splicing events that are affected by OGT or OGA inhibition, we found that O-GlcNAc is a major regulator of detained introns splicing. At early time point, we observed highly specific splicing of OGT/OGA detained introns to buffer O-GlcNAc changes. At longer time point, ~80% of the total detained introns are affected by O-GlcNAc perturbation, while the rest of canonical splicing events are only minimally affected (~ 5%).

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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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Ogt Controls Adult Neurogenesis through Modulating Notch Signaling Activity in Mice

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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]

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

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

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Project description:TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation. We found that OGT interacts with TET2 tightly. Using ChIP-seq with specific antibodies, we tested the co-localization of TET2 and OGT in genome level.

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Project description:OGT (O-GlcNAc transferase) is the distinctive enzyme responsible for catalyzing O-GlcNAc to the serine or threonine residues of thousands of cytoplasm and nuclear proteins that are involved in DNA damage, RNA splicing, and transcription preinitiation and initiation complex assembly. However, the molecular mechanism by OGT regulating gene transcription remains elusive. Using proximity labeling based mass spectrometry, we searched for functional partners of OGT and found that Dot1L, the conserved and unique histone methyltransferase mediated histone H3 lys79 methylation required for gene transcription, DNA damage repair, cell proliferation, and embryo development, interacts with OGT. Although this specific interaction does not regulate the enzymatic activity of Dot1L, it facilitates OGT-dependent histones O-GlcNAcylation. Moreover, OGT associates with Dot1L at transcription start sites, and depleting Dot1L decreased OGT associated with chromatin globally. Notably, downregulation of Dot1L reduces the levels of histone H2B S112 O-GlcNAcylation and histone H2B K120 ubiquitination in vivo, which are associated with gene transcription regulation. Taken together, these results reveal a Dot1L-dependent O-GlcNAcylation of chromatin.

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