GEO series

Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chrom_RNAseq_iNOS1400W]

GSE245445 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/11/19 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 18 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 18 samples: 6 conditions, mostly in triplicateGroups 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: 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 GSE245445 in finder → Find more mouse RNA-seq 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 GSE245445_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1028521 and SRA study SRP466515. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38242130) ↗

Study design

6 conditions, mostly in triplicate

INH_LPS_16h ×3 INH_LPS_8h ×3 INH ×3 LPS_16h ×3 LPS_8h ×3 UT ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM7842875 INH_LPS_16h_R1 INH_LPS_16h
GSM7842876 INH_LPS_16h_R2 INH_LPS_16h
GSM7842877 INH_LPS_16h_R3 INH_LPS_16h
GSM7842878 INH_LPS_8h_R1 INH_LPS_8h
GSM7842879 INH_LPS_8h_R2 INH_LPS_8h
GSM7842880 INH_LPS_8h_R3 INH_LPS_8h
GSM7842881 INH_R1 INH
GSM7842882 INH_R2 INH
GSM7842883 INH_R3 INH
GSM7842884 LPS_16h_R1 LPS_16h
GSM7842885 LPS_16h_R2 LPS_16h
GSM7842886 LPS_16h_R3 LPS_16h
GSM7842887 LPS_8h_R1 LPS_8h
GSM7842888 LPS_8h_R2 LPS_8h
GSM7842889 LPS_8h_R3 LPS_8h
GSM7842890 UT_R1 UT
GSM7842891 UT_R2 UT
GSM7842892 UT_R3 UT

Datasets on a similar topic

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, histone
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, histone
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, histone
GSE227963 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Med1_Chipseq] 4 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production, histone
GSE245579 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chipseq_MED1_RAW2647] 2 samples shares 2-ketoacid, mediator-bound, dehydrogenases, acetylation, acetyl-coa, production, histone

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.