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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE277952 | GEO | 2024/10/14

REPOSITORIES: GEO

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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 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 [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

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

| PRJNA1164790 | ENA

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]

| PRJNA1164796 | ENA

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 [RNA-seq II]

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

| PRJNA1164795 | ENA

Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing.

Project description:The expression of intron-containing genes in eukaryotes requires generation of protein-coding messenger RNAs (mRNAs) via RNA splicing, whereby the spliceosome removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must ensure accurate removal of highly diverse introns. We show that Sde2 is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain (referred to as Sde2-C). Precursor processing after the first di-glycine motif by the ubiquitin-specific proteases Ubp5 and Ubp15 generates a short-lived activated Sde2-C fragment with an N-terminal lysine residue, which subsequently gets incorporated into spliceosomes. Absence of Sde2 or defects in Sde2 activation both result in inefficient excision of selected introns from a subset of pre-mRNAs. Sde2 facilitates spliceosomal association of Cactin/Cay1, with a functional link between Sde2 and Cactin further supported by genetic interactions and pre-mRNA splicing assays. These findings suggest that ubiquitin-like processing of Sde2 into a short-lived activated form may function as a checkpoint to ensure proper splicing of certain pre-mRNAs in fission yeast.

| S-EPMC5753039 | biostudies-other

Balance between MAT2A intron detention and splicing is determined cotranscriptionally.

Project description:Transcriptome analysis of human cells has revealed that intron retention controls the expression of a large number of genes with diverse cellular functions. Detained introns (DI) constitute a subgroup of transcripts with retained introns that are not exported to the cytoplasm but instead remain in the nucleus. Previous studies reported that the splicing of DIs in the CLK1 transcript is post-transcriptionally induced to produce mature mRNA in the absence of new transcription. Thus, CLK1-DI serves as a precursor or "reservoir" for the CLK1 mRNA. However, whether this is a universal mechanism for gene regulation by intron detention remains unknown. The MAT2A gene encodes S-adenosylmethionine (SAM) synthetase and it contains a DI that is regulated in response to intracellular SAM levels. We used three independent assays to assess the precursor-product relationship between MAT2A-DI and MAT2A mRNA. In contrast to CLK1-DI, these data support a model in which the MAT2A-DI transcript is not a precursor to mRNA but is instead a "dead-end" RNA fated for nuclear decay. Additionally, we show that in SAM-deprived conditions the cotranscriptional splicing of MAT2A detained introns increases. We conclude that polyadenylated RNAs with DIs can have at least two distinct fates. They can serve as nuclear reservoirs of pre-mRNAs available for rapid induction by the cell, or they constitute dead-end RNAs that are degraded in the nucleus.

| S-EPMC5959247 | biostudies-literature

A Role of U12 Intron in Proper Pre-mRNA Splicing of Plant Cap Binding Protein 20 Genes.

Project description:The nuclear cap-binding complex (CBC) is composed of two cap-binding proteins: CBP20 and CBP80. The CBP20 gene structure is highly conserved across land plant species. All studied CBP20 genes contain eight exons and seven introns, with the fourth intron belonging to the U12 class. This highly conserved U12 intron always divides the plant CBP20 gene into two parts: one part encodes the core domain containing the RNA binding domain (RBD), and the second part encodes the tail domain with a nuclear localization signal (NLS). In this study, we investigate the importance of the U12 intron in the Arabidopsis thaliana CBP20 gene by moving it to different intron locations of the gene. Relocation of the U12 intron resulted in a significant decrease in the U12 intron splicing efficiency and the accumulation of wrongly processed transcripts. These results suggest that moving the U12 intron to any other position of the A. thaliana CBP20 gene disturbs splicing, leading to substantial downregulation of the level of properly spliced mRNA and CBP20 protein. Moreover, the replacement of the U12 intron with a U2 intron leads to undesired alternative splicing events, indicating that the proper localization of the U12 intron in the CBP20 gene secures correct CBP20 pre-mRNA maturation and CBP20 protein levels in a plant. Surprisingly, our results also show that the efficiency of U12 splicing depends on intron length. In conclusion, our study emphasizes the importance of proper U12 intron localization in plant CBP20 genes for correct pre-mRNA processing.

| S-EPMC5932401 | biostudies-literature

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