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The PNUTS phosphatase complex controls transcription pause release [ChIP-Seq]

GSE271891 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 94 samples Submitted 2024/11/26 Platform GPL19415
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 94 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
94 samples: 32 conditions, mostly in triplicateGroups 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
The PNUTS phosphatase complex controls transcription pause releaseMolecular cell · 2024
Summary (written by the submitters)
Gene expression is regulated by controlling distinct steps of the transcriptional cycle, including initiation, pausing, elongation, and termination. Kinases phosphorylate RNA Polymerase II and associated factors to control transitions between these steps and act as central gene regulatory nodes. Similarly, phosphatases that dephosphorylate these components are emerging as important regulators of transcription, though their roles remain less well understood.
Read the full summary ↓
Here we discover that the mouse PNUTS-PP1 phosphatase complex plays an essential role in controlling transcription pause release in addition to its previously described function in transcription termination. Transcription pause release by the PNUTS complex is essential for almost all RNA Pol II-dependent gene transcription, relies on its PP1 phosphatase subunit, and controls the phosphorylation of factors required for pause release and elongation. Together, these findings reveal an essential new role for a phosphatase complex in transcription pause release and shows that the PNUTS complex is essential for RNA Pol II-dependent transcription.
Published in
The PNUTS phosphatase complex controls transcription pause release
Kelley JR, Dimitrova E, Maciuszek M et al. · Molecular cell 2024 · PMID 39603239 · doi:10.1016/j.molcel.2024.10.045
This dataset
Open GSE271891 in finder → Find more ChIP / ATAC / CUT&Tag 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 GSE271891_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1133811 and SRA study SRP518942. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39603239) ↗
Study design
32 conditions, mostly in triplicate
PNUTSdTAG_CDK9_dTAG ×4 PNUTSdTAG_CDK9_UNT ×4 PNUTSdTAG_NELF_dTAG ×4 PNUTSdTAG_NELF_UNT ×4 PNUTSdTAG-TFIIS-UNT ×3 PNUTSdTAG-TFIIS-dTAG ×3 PNUTSdTAG-INT11-UNT ×3 PNUTSdTAG-INT11-dTAG ×3 +24 more

Supports a between-group comparison across 94 samples.

How we read this: 32 replicated groups read from 94 sample titles; they account for 94 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

+ 54 more — browse all 94 samples with per-sample file links →

Datasets on a similar topic

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