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

GSE240891 Homo sapiens (human) RNA-seq (gene expression) 64 samples Submitted 2024/11/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 64 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
64 samples: 16 conditions, mostly with about 5 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Phosphorylation of a nuclear condensate regulates cohesion and mRNA retentionNature communications · 2025
Summary (written by the submitters)
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.
Read the full summary ↓
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.
Published in
Phosphorylation of a nuclear condensate regulates cohesion and mRNA retention
McIntyre ABR, Tschan AB, Meyer K et al. · Nature communications 2025 · PMID 39755675 · doi:10.1038/s41467-024-55469-3
This dataset
Open GSE240891 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE240891_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1005653 and SRA study SRP455239. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39755675) ↗
Study design
16 conditions, mostly with about 5 replicates each
NLS, DMSO, biotinylated, ×5 NLS, DRB, biotinylated, ×5 NLS, GSK626616, biotinylated, ×5 NLS, Pladienolide-B, biotinylated, ×5 SON, DMSO, biotinylated, ×5 SON, DRB, biotinylated, ×5 SON, GSK626616, biotinylated, ×5 SON, Pladienolide-B, biotinylated, ×5 +10 more

Supports a between-group comparison across 62 samples.

How we read this: 16 replicated groups read from 64 sample titles; they account for 62 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 24 more — browse all 64 samples with per-sample file links →

Datasets on a similar topic

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