GEO series

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

GSE240883 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2024/11/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 15 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: 15 samples: 5 × chromatin, vs 5 × cytoplasm, vs 5 × nucleus,Groups 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 GSE240883 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 GSE240883_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 PRJNA1005639 and SRA study SRP455198. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39755675) ↗

Study design

5 × chromatin, vs 5 × cytoplasm, vs 5 × nucleus,

Supports a between-group comparison across 15 samples.

How we read this: 3 replicated groups read from 15 sample titles; they account for 15 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

GSM7711257 chromatin, rep 1 chromatin,
GSM7711258 chromatin, rep 2 chromatin,
GSM7711259 chromatin, rep 3 chromatin,
GSM7711260 chromatin, rep 4 chromatin,
GSM7711261 chromatin, rep 5 chromatin,
GSM7711262 cytoplasm, rep 1 cytoplasm,
GSM7711263 cytoplasm, rep 2 cytoplasm,
GSM7711264 cytoplasm, rep 3 cytoplasm,
GSM7711265 cytoplasm, rep 4 cytoplasm,
GSM7711266 cytoplasm, rep 5 cytoplasm,
GSM7711267 nucleus, rep 1 nucleus,
GSM7711268 nucleus, rep 2 nucleus,
GSM7711269 nucleus, rep 3 nucleus,
GSM7711270 nucleus, rep 4 nucleus,
GSM7711271 nucleus, rep 5 nucleus,

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