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Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants [Histone LCD]

GSE287065 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2026/03/09 Platform GPL34328
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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
48 samples: 24 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.
Summary (written by the submitters)
Intrinsically disordered regions (IDRs) are well-known facilitators of chromatin regulation, but their role as regulatory restraints remains underexplored. Here, we reveal that the C-terminal IDR of mammalian ALKBH5 anchors its main activity to mRNA, limiting chromatin engagement in mouse embryonic stem cells (mESCs). IDR deletion redirects ALKBH5 to chromatin-associated non-coding RNAs, driving widespread chromatin opening and transcriptional activation.
Read the full summary ↓
This mechanism extends to histone demethylases, where IDR deletion also results in broad removal of repressive histone marks, leading to increased chromatin accessibility and activation of transposable elements. Leveraging these insights, we engineered plant ALKBH5 homologs with IDR deletion. Overexpression of these IDR-deleted plant RNA demethylases could promote Arabidopsis root growth and significantly increase rice yield. Our findings uncover a conserved role for IDRs in restraining chromatin interaction to control chromatin state and establish a new strategy of crop engineering using plant proteins to increase biomass and yield.
This dataset
Open GSE287065 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 GSE287065_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 PRJNA1211080 and SRA study SRP557674. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
24 conditions, mostly in duplicate
ATAC KDM4A del-IDR OE ×2 ATAC KDM4A FL OE ×2 ATAC KDM4B del-IDR OE ×2 ATAC KDM4B FL OE ×2 ATAC KDM6B del-IDR OE ×2 ATAC KDM6B FL OE ×2 ATAC KDM6A del-IDR OE ×2 ATAC KDM6A FL OE ×2 +16 more

Supports a between-group comparison across 48 samples.

How we read this: 24 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.