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Neurological Cockayne Syndrome Results from R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation

GSE226204 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 37 samples Submitted 2024/07/29 Platform GPL24676Platform GPL11154Platform GPL24247Platform GPL28038Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 37 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
37 samples: 17 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
Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription ElongationNature communications · 2024
Summary (written by the submitters)
Mutations in the Cockayne Syndrome group B (CSB) gene cause severe neurodevelopmental defects and premature aging. As a member of the SWI/SNF family of chromatin remodelers, CSB is best known for its role in transcription-coupled nucleotide excision (TC-NER), but this function neither explains the major disease phenotype nor offers any clue about the selective vulnerability in neurons.
Read the full summary ↓
Pursuing Cockayne Syndrome-associated genome instability, we uncover an intrinsic mechanism by which elongating RNA polymerase II (RNAPII) undergoes transient pausing at internal T-runs where CSB is required to push RNAPII forward. Consequently, CSB deficiency retards RNAPII elongation in these regions, and when coupled upstream G-rich sequences, such functional defects are further amplified to induce genome instability via augmented R-loop formation. As such R-loop prone motifs are proportionally represented in long genes that predominately function in neurons, this mechanism provides critical insights into selective neuronal vulnerability. Moreover, because of divergent intronic sequences between mice and humans, this mechanism also explains why mice deficient for CSB do not develop severe neurological abnormalities as seen in humans, suggesting that the manifestation of Cockayne Syndrome phenotype results from progressive genome evolution in mammals.
Published in
Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation
Zhang X, Xu J, Hu J et al. · Nature communications 2024 · PMID 39019869 · doi:10.1038/s41467-024-50298-w
This dataset
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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 GSE226204_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 PRJNA939159 and SRA study SRP424857. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39019869) ↗
Study design
17 conditions, mostly in duplicate
CSB_ChIP ×2 PolII_ChIP_siNC ×2 PolII_ChIP_siNC_input ×2 PolII_ChIP_siCSB ×2 PolII_ChIP_siCSB_input ×2 PRO_siNC ×2 PRO_siCSB ×2 chr_RNA_siNC ×2 +12 more

Supports a between-group comparison across 34 samples.

How we read this: 17 replicated groups read from 37 sample titles; they account for 34 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
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