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MePCE promotes Homologous Recombination through coordinating R-loop resolution at DNA Double Stranded Breaks (ChIP-Seq & DRIP-seq)

GSE261535 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/05/23 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
MePCE promotes homologous recombination through coordinating R-loop resolution at DNA double-stranded breaksCell reports · 2025
Summary (written by the submitters)
MePCE is a multifunctional protein that regulates the Positive Transcription Elongation Factor b (P-TEFb) partitioning between the nucleosol and chromatin. While the role of MePCE in sequestering P-TEFb in the nucleoplasm through the 7SK ribonuclear protein complex (RNPc) is well understood, its functions on chromatin remain obscure. In order to address this gap in our knowledge, we performed mass spectrometry of MePCE interactors on chromatin.
Read the full summary ↓
Our analysis revealed that chromatin-associated-MePCE mainly interacts with factors involved in R-loop processing and DNA repair factors. Consistent with this initial finding, MePCE is rapidly recruited to laser-mediated DNA damage and AsiSI-mediated DNA double stranded breaks (DSBs). Moreover, MePCE depletion specifically impairs DSB repair by homologous recombination (HR). To explore the molecular mechanism behind the observed HR defect, we took advantage of an inducible AsiSI system to analyze the effect of MePCE depletion in DSB repair factor recruitment and R-loop levels at over 100 genomic site-specific DSBs. Consistent with impaired HR, MePCE depletion decreases RAD51 loading and enhances R-loop levels specifically at DSBs. Analysis of R-loop protein complexes by mass spectrometry revealed that in addition to decreasing specific R-loop processing factors and chromatin remodelers, MePCE depletion increased the interaction with R-loops of the other constitutive member of the 7SK RNPc, LARP7, which is degraded by BRCA1/BARD1 upon DSB. Overall, our results uncover dynamic regulation of the 7SK RNPc at DSBs during the repair process and explain the recently observed synthetic lethality of MePCE and BRCA1 deficiency.
Published in
MePCE promotes homologous recombination through coordinating R-loop resolution at DNA double-stranded breaks
Devanathan SK, Li YR, Shelton SB et al. · Cell reports 2025 · PMID 40411785 · doi:10.1016/j.celrep.2025.115740
This dataset
Open GSE261535 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 GSE261535_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 PRJNA1087397 and SRA study SRP495078. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40411785) ↗
Study design
18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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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