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Alternative splicing decouples local from global PRC2 activity

GSE223666 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 87 samples Submitted 2024/03/18 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 87 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
87 samples: 38 conditions, mostly in duplicateGroups 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
Alternative splicing decouples local from global PRC2 activityMolecular cell · 2024
Summary (written by the submitters)
PRC2 mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of H3K27. This complex interacts with sets of accessory factors forming two distinct subtypes (PRC2.1 and PRC2.2) that differ in their action and chromatin targeting mechanisms. However, the underlying molecular mechanisms orchestrating PRC2 assembly are not yet understood.
Read the full summary ↓
Here, we report the identification of an alternative splicing event involving that alternative splicing of the PRC2 core component SUZ12 exon 4 which generates two isoforms coexisting in the same cell in virtually all tissues and developmental stages. Skipping this exon generates a previously uncharacterized isoform (SUZ12S) that forces the formation of the PRC2.1 subtype and favors PRC2 dimerization. Our results suggest that while SUZ12L is needed for maintenance of global H3K27 methylation levels, While SUZ12S is necessary and sufficient to ensure correct repression of Polycomb target genes via promoter-proximal H3K27me3 deposition, the full-length SUZ12L isoform is needed for maintenance of global H3K27 methylation levels. Lastly, we show that mouse embryonic stem cells lacking either of the two isoforms display impaired exit from pluripotency upon differentiation stimulus. Our findings thus reveal evidence for the existence of a physiological mechanism regulating PRC2 assembly and higher order interactions, with an impact on H3K27 methylation and gene repression.
Published in
Alternative splicing decouples local from global PRC2 activity
Arecco N, Mocavini I, Blanco E et al. · Molecular cell 2024 · PMID 38452766 · doi:10.1016/j.molcel.2024.02.011
This dataset
Open GSE223666 in finder → Find more mouse 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 GSE223666_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 PRJNA927240 and SRA study SRP418969. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38452766) ↗
Study design
38 conditions, mostly in duplicate
RNA_NP_WT ×4 H3K27me3_WT ×3 H3K27me3_Deltaex4 ×3 H3K27me3_KO ×3 RNA_WT ×3 RNA_KO ×3 H3K27me3_CSex4 ×2 Suz12_WT ×2 +34 more

Supports a between-group comparison across 83 samples.

How we read this: 38 replicated groups read from 87 sample titles; they account for 83 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

+ 47 more — browse all 87 samples with per-sample file links →

Datasets on a similar topic

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