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DNA methylation status determines the sensitivity of repeats to restriction by the HUSH-MORC2 complex [CUT&RUN]

GSE240384 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 42 samples Submitted 2024/03/26 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 42 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
Homo sapiens (human)
Samples
42 samples: 16 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
DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressorNature communications · 2024
Summary (written by the submitters)
The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1.
Read the full summary ↓
Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
Published in
DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor
Pandiloski N, Horváth V, Karlsson O et al. · Nature communications 2024 · PMID 39214989 · doi:10.1038/s41467-024-50765-4
This dataset
Open GSE240384 in finder → Find more human 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 GSE240384_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 PRJNA1003476 and SRA study SRP454069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39214989) ↗
Study design
16 conditions, mostly in duplicate
CR117_LV3599_Control_IgG ×2 CR112_LV3599_Control_H3K9me3 ×2 CR117_LV3599_Control_H3K4me3 ×2 CR112_LV3688_MORC2_CRISPRi_H3K9me3 ×2 CR117_LV3688_MORC2_CRISPRi_H3K4me3 ×2 CR117_LV3691_TASOR_CRISPRi_H3K9me3 ×2 CR117_LV3691_TASOR_CRISPRi_H3K4me3 ×2 CR114_LV3393_Control_IgG ×2 +18 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 42 sample titles; they account for 32 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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