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Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

ABSTRACT: Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

PROVIDER: PRJNA1005639 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25646471.fastq.gz	Fastqsanger.gz
	SRR25646472.fastq.gz	Fastqsanger.gz
	SRR25646473.fastq.gz	Fastqsanger.gz
	SRR25646474.fastq.gz	Fastqsanger.gz
	SRR25646475.fastq.gz	Fastqsanger.gz

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Phosphorylation controls mRNA retention via nuclear speckle cohesion - cellular fractionation data

Project description:Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During mitosis, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify PP1 phosphatases as responsible for counteracting kinase-mediated dissolution. Their overexpression increases speckle cohesion and leads to retention of polyadenylated RNA within speckles and the nucleus. By performing APEX2 proximity labeling combined with RNA-sequencing, we characterized the association of specific RNAs with nuclear speckles depending on their cohesion state. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm, particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increased with greater nuclear speckle cohesion, the ratios of most mRNA species to each other were constant, indicating non-selective, or proportional, retention. We then explored whether nuclear speckle cohesion changes in response to environmental perturbations associated with changes in kinase or phosphatase activity. We found that cellular responses to heat shock, oxidative stress, and hypoxia include changes to the cohesion of nuclear speckles and mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization.

2024-11-10 | GSE240883 | GEO

Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

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Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

Project description:Phosphorylation controls mRNA retention via nuclear speckle cohesion - APEX2-seq

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Phosphorylation controls mRNA retention via nuclear speckle cohesion during environmental perturbations

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Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention

Project description:Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify the PP1 family as the phosphatases that counteract kinase-mediated dissolution. PP1 overexpression increases speckle cohesion and leads to retention of polyadenylated RNA within speckles and the nucleus. Using APEX2 proximity labeling combined with RNA-sequencing, we characterized the relationship between the cohesion of nuclear speckles and the recruitment of specific RNAs. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm, particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increased with nuclear speckle cohesion, the ratios of most mRNA species to each other were constant, indicating non-selective, or proportional, retention. We then explored whether nuclear speckle cohesion changes in response to environmental perturbations associated with changes in kinase or phosphatase activity. We found that cellular responses to heat shock, oxidative stress, and hypoxia include changes to the cohesion of nuclear speckles and mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization.

2024-11-28 | PXD055775 | Pride

Phosphorylation controls mRNA retention via nuclear speckle cohesion during environmental perturbations

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

2024-11-10 | GSE240892 | GEO

Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

Project description:Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

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Disruption of nuclear speckle integrity dysregulates RNA splicing in C9ORF72-FTD/ALS

Project description:Dysregulation of RNA processing contributes to neurodegenerative diseases, especially amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Expansion of an intronic (GGGGCC)n repeat within the C9ORF72 gene is the most common cause of both FTD and ALS (C9-FTD/ALS), characterized with aberrant repeat RNA foci in the nucleus and noncanonical translation-produced dipeptide repeat (DPR) protein inclusions in the cytoplasm. Here we elucidate that the (GGGGCC)n repeat RNA co-localizes with nuclear speckles and alters their phase separation properties and granule dynamics. Moreover, the essential nuclear speckle scaffold protein SRRM2 is sequestered into the poly-GR cytoplasmic inclusions in C9-FTD/ALS mouse model and patient postmortem tissues, exacerbating the nuclear speckle dysfunction. Impaired nuclear speckle integrity induces global exon-skipping and intron retention in human iPSC-derived neurons. Similar alternative splicing changes can be found in patient postmortem tissues. This work identified novel molecular mechanism of global RNA splicing defects by impaired nuclear speckle function in C9-FTD/ALS and revealed novel potential biomarkers or therapeutic targets.

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UBL5 is essential for pre-mRNA splicing and sister chromatid cohesion in human cells

Project description:UBL5 is an atypical ubiquitin-like protein, whose function in metazoans remains largely unexplored. We show that UBL5 is required for sister chromatid cohesion maintenance in human cells. UBL5 primarily associates with spliceosomal proteins, and UBL5 depletion decreases pre-mRNA splicing efficiency, leading to globally enhanced intron retention. Defective sister chromatid cohesion is a general consequence of dysfunctional pre-mRNA splicing, resulting from the selective downregulation of the cohesion protection factor Sororin. As the UBL5 yeast orthologue, Hub1, also promotes spliceosome functions, our results show that UBL5 plays an evolutionary conserved role in pre-mRNA splicing, the integrity of which is essential for the fidelity of chromosome segregation.

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Project description:RNA-fractionation sequencing

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