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Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - Cytoplasm Nucleoplasm Chromatin Fractions

ABSTRACT: Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - Cytoplasm Nucleoplasm Chromatin Fractions

PROVIDER: PRJNA1149822 | ENA |

REPOSITORIES: ENA

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Productive mRNA chromatin escape is promoted by PRMT5 activity - Cytoplasm Nucleoplasm Chromatin Fractions

Project description:Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) —but not type I PRMT inhibition—leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.

2025-09-01 | GSE275215 | GEO

Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm.

Project description:RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA-protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins-SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation-interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP. As expected, SRSF3 and SRSF7 targets were detected in all fractions, with intron, snoRNA and lncRNA interactions enriched in the nucleus. Cytoplasmically-bound mRNAs reflected distinct functional groupings, suggesting coordinated translation regulation. Surprisingly, hundreds of cytoplasmic intron targets were detected. These cytoplasmic introns were found to be highly conserved and introduced premature termination codons into coding regions. However, many intron-retained mRNAs were not substrates for nonsense-mediated decay (NMD), even though they were detected in polysomes. These findings suggest that intron-retained mRNAs in the cytoplasm have previously uncharacterized functions and/or escape surveillance. Hence, Fr-iCLIP detects the cellular location of RNA-protein interactions and provides insight into co-transcriptional, post-transcriptional and cytoplasmic RBP functions for coding and non-coding RNAs.

| S-EPMC5737842 | biostudies-literature

Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB.

Project description:Protein Arginine Methyltransferase 5 (PRMT5) regulates RNA splicing and transcription by symmetric dimethylation of arginine residues (Rme2s/SDMA) in many RNA binding proteins. However, the mechanism by which PRMT5 couples splicing to transcriptional output is unknown. Here, we demonstrate that a major function of PRMT5 activity is to promote chromatin escape of a novel, large class of mRNAs that we term Genomically Retained Incompletely Processed Polyadenylated Transcripts (GRIPPs). Using nascent and total transcriptomics, spike-in controlled fractionated cell transcriptomics, and total and fractionated cell proteomics, we show that PRMT5 inhibition and knockdown of the PRMT5 SNRP (Sm protein) adapter protein pICln (CLNS1A) -but not type I PRMT inhibition-leads to gross detention of mRNA, SNRPB, and SNRPD3 proteins on chromatin. Compared to most transcripts, these chromatin-trapped polyadenylated RNA transcripts have more introns, are spliced slower, and are enriched in detained introns. Using a combination of PRMT5 inhibition and inducible isogenic wildtype and arginine-mutant SNRPB, we show that arginine methylation of these snRNPs is critical for mediating their homeostatic chromatin and RNA interactions. Overall, we conclude that a major role for PRMT5 is in controlling transcript processing and splicing completion to promote chromatin escape and subsequent nuclear export.

| S-EPMC11326253 | biostudies-literature

Productive mRNA chromatin escape is promoted by PRMT5 activity - mRNA Seq PRMT5 pICln RIOK1 CoPR5 kd

Project description:Productive mRNA chromatin escape is promoted by PRMT5 activity - mRNA Seq PRMT5 pICln RIOK1 CoPR5 kd

| PRJNA1149820 | ENA

ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling

Project description:ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling

| PRJNA1096325 | ENA

Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB -PROSeq after PRMT inhibition and Dexamethasone treatment

Project description:Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB -PROSeq after PRMT inhibition and Dexamethasone treatment

| PRJNA1149825 | ENA

Allele specific analysis of the immunoglobulin heavy chain locus by simultaneous analysis of the productive and the non-productive allele through paired-end 4C sequencing analysis in mature B cells

Project description:In developing B cells the immunoglobulin heavy chain (IgH) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH allele to pericentromeric heterochromatin. Here we used an allele-specific chromosome conformation capture combined with sequencing (4C-seq) approach to unambigously follow the individual IgH alleles in mature B lymphocytes. Despite their physical and functional difference, productive and non-productive IgH alleles in B cells and unrearranged IgH alleles in T cells share many chromosomal contacts and largely reside in active chromatin. In brain, however, the locus resides in a different, repressive environment. We conclude that IgH adopts a lymphoid-specific nuclear location that is however unrelated to maintenance of allelic exclusion. We additionally find that in mature B cells - but not in T cells – the distal VH regions of both IgH alleles position themselves away from active chromatin. This, we speculate, may help to restrict enhancer activity to the productively rearranged VH promoter element. Allele specific analysis of the nuclear organization of the IgH locus in resting and activated B cells and T cells and fetal brain cells

2013-06-01 | E-GEOD-47128 | biostudies-arrayexpress

CD32A Immunoprecipitation in K562 Cell Membrane and Cytoplasm Fractions

Project description:Here we interrogate CD32A protein interactions in the cytoplasm and membrane fractions isolated from the human AML cell lines K562 wild-type and knockout for CD32A. Cells were fractionated prior to incubation with CD32A antibody and subsequent samples isolated using protein agarose beads.

2023-09-05 | PXD042514 | Pride

Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - PROSeq Nascent Transcriptome after PRMT inhibition 15m 3hr

Project description:Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB - PROSeq Nascent Transcriptome after PRMT inhibition 15m 3hr

| PRJNA1149821 | ENA

Rbfox1, Rbfox2, and Rbfox3 iCLIP from mouse brain nuclear fractions

Project description:In this study we analyze the in vivo recruitment of mouse brain nuclear Rbfox proteins to RNA using individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP). Rbfox1, Rbfox, 2, and Rbfox3 iCLIP libraries were constructed from high molecular weight (HMW) nuclear fraction containing chromatin and the soluble nucleoplasm.

2016-04-21 | GSE76475 | GEO

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