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PHF2 maintains neural progenitor genome stability by preserving pericentric heterochromatin integrity (ChIP-Seq)

GSE242383 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 19 samples Submitted 2024/06/17 Platform GPL23479
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 19 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
19 samples: 8 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
PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferationEMBO reports · 2024
Summary (written by the submitters)
Heterochromatin stability is crucial for progenitor proliferation during development. It relays on the maintenance of local hubs of H3K9me. However, the mechanisms underlying the establishment of competent local levels of H3K9me remain poorly understood. To address this intriguing question, we used a neural stem cell (NSC) model to analyze the significance of the H3K9me2 demethylase PHF2, which is crucial for progenitor proliferation.
Read the full summary ↓
Through mass spectroscopy and genome-wide assays, we uncovered that PHF2 interacts with heterochromatin components and it is enriched at pericentromeric heterochromatin (PcH) boundaries. This binding is essential for maintaining silenced the satellite repeats and to prevent DNA damage and genome instability. To do that, PHF2 balances H3K9me3 levels at these boundaries to ensure high H3K9me3 levels at satellite repeats. Mechanistically, we discover that while its catalytic and PHD domains are indispensable, the intrinsically disordered region within PHF2 is dispensable for stabilizing PcH. Altogether, our study sheds light on the intricate relationship between heterochromatin stability and progenitor proliferation during mammalian neurogenesis.
Published in
PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation
Aguirre S, Pappa S, Serna-Pujol N et al. · EMBO reports 2024 · PMID 38890452 · doi:10.1038/s44319-024-00178-7
This dataset
Open GSE242383 in finder → Find more mouse 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 GSE242383_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 PRJNA1014578 and SRA study SRP459482. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38890452) ↗
Study design
8 conditions, mostly in duplicate
shCT K9me3 ×2 shCT K4me3 ×2 shPHF2 K9me3 ×2 shPHF2 K4me3 ×2 PHF2 input ×2 PHF2 ×2 PHF2 NIH ×2 PHF2 2 ×2 +3 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 19 sample titles; they account for 16 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
Datasets on a similar topic

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