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Rnf20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α [tPol2_MLE12_ChIP-Seq]

GSE231314 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2025/03/20 Platform GPL28457
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
12 samples: 3 × MLE12_Rnf20_CTR_Pol2_chipseq_IP vs 3 × MLE12_Rnf20_HET_Pol2_chipseq_IP vs 3 × MLE12_Rnf20_CTR_Pol2_chipseq_INPUT vs 3 × MLE12_Rnf20_HET_Pol2_chipseq_INPUTGroups 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
RNF20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1αNature communications · 2025
Summary (written by the submitters)
Defective DNA repair and metabolic rewiring are highly intertwined in promoting the development and progression of cancer. However, the molecular players at the interface of these processes remain largely unexplored. Here we show that the Rnf20-HIF1α axis links the DNA damage response and metabolic reprogramming in lung cancer. Haploinsufficiency of Rnf20, catalyzing histone H2B monoubiquitylation (H2Bub1), dramatically increases the occurrence of spontaneous lung adenocarcinoma and small cell lung carcinoma (SCLC) in mice.
Read the full summary ↓
Mechanistically, ablation of a single Rnf20 allele resulted in insufficient Rnf20-H2Bub1-p53-mediated control and induced pronounced defects in DNA repair, increased cell growth, epithelial-to-mesenchymal transition (EMT), and metabolic rewiring via HIF1α-mediated RNA polymerase II promoter-proximal pause release, which was independent of H2Bub1. Importantly, RNF20 levels are decreased in lung adenocarcinoma and SCLC patients, and this decrease negatively correlates with the expression of HIF1α target genes, suggesting HIF1α inhibition as a promising therapeutic approach for lung cancer patients with decreased RNF20 activity.
Published in
RNF20 links the DNA damage response and metabolic rewiring in lung cancer through HIF1α
Liu H, Tang Y, Singh A et al. · Nature communications 2025 · PMID 40436847 · doi:10.1038/s41467-025-60223-4
This dataset
Open GSE231314 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 GSE231314_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 PRJNA963201 and SRA study SRP435177. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40436847) ↗
Study design
3 × MLE12_Rnf20_CTR_Pol2_chipseq_IP vs 3 × MLE12_Rnf20_HET_Pol2_chipseq_IP vs 3 × MLE12_Rnf20_CTR_Pol2_chipseq_INPUT vs 3 × MLE12_Rnf20_HET_Pol2_chipseq_INPUT

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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