GEO series

Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chipseq_MED1_RAW2647]

GSE245579 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 2 samples Submitted 2024/11/19 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 2 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: 2 samples
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: Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxideMolecular cell · 2024

Summary (written by the submitters)

Histone modifying enzymes depend on the availability of cofactors, with acetyl-CoA being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA producing enzymes are also delivered to the nucleus suggests that high concentrations of metabolites generated locally may impact acetylation of histones and other nuclear substrates and eventually control gene regulation.

Read the full summary ↓

Here we show that 2-ketoacid dehydrogenases were stably associated with the Mediator complex in macrophages, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in LPS-stimulated macrophages, inhibited both the activity of 2-ketoacid dehydrogenases and their association with Mediator. Consequently, NO reduced de novo histone acetylation at genomic regions with high acetyl-CoA deposition rates. Our findings indicate that a local supply of acetyl-CoA generated by Mediator-bound 2-ketoacid dehydrogenases is required to maximize acetylation of histone tails at sites of elevated HAT activity.

Published in

Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide

Russo M, Gualdrini F, Vallelonga V et al. · Molecular cell 2024 · PMID 38242130 · doi:10.1016/j.molcel.2023.12.033

This dataset

Open GSE245579 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 GSE245579_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 PRJNA1029018 and SRA study SRP466838. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38242130) ↗

Samples in this study

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

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GSE245442 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chipseq_H3K27ac_spikein] 36 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production
GSE245444 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chipseq_panAc_spikein] 12 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production
GSE245580 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chrom_RNAseq] 18 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production
GSE245445 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chrom_RNAseq_iNOS1400W] 18 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production
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GSE301366 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-seq mouse, CTCF, SMC1, MED1] 24 samples shares med1
GSE255473 Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (ATAC-seq_shMed1) 9 samples shares med1

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