GEO series

METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin (ChIP-Seq)

GSE220868 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/12/01 Platform GPL30209

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: 10 samples: 2 × HEK293T, H3K9Ac-ChIP, vs 2 × METTL3 knockout, H3K9Ac-ChIP, vs 2 × METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, vs 2 × METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP,Groups 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.

Summary (written by the submitters)

METTL3 constitutes the catalytic subunit of the major methyltransferase complex mediating the formation of N6-methyladenosine (m6A) in mRNA. Although the resulting m6A is known to regulate numerous cellular processes, the protein interaction network of this complex remains largely unknown. Here, we employed ascorbate peroxidase-based proximity labeling followed by LC-MS/MS analysis to examine systematically the interaction proteins of METTL3 and METTL14 in HEK293T cells.

Read the full summary ↓

Aside from many proteins involved in mRNA splicing, a subset of histone regulatory proteins are enriched in the proximity proteome of METTL3, including histone acetyltransferase 1 (HAT1). In addition, genetic ablation of METTL3 led to reduced chromatin occupancy of HAT1 isoform-a, which is expressed exclusively in the nucleus, and diminished H3K9Ac in HEK293T cells, especially in retrotransposons. Depletion of HAT1 led to diminished H3K9Ac, which could be restored by wild-type HAT but not the one fused with the nuclear export sequence (NES) of PKI to remove it from the nucleus. Our in vitro acetylation assay further confirmed the acetylation activity of HAT1 isoform-a on nucleosome histone H3K9. The reduced retrotransposons H3K9Ac in METTL3-/- cells could be restored by ectopic expression of wild-type METTL3, but not its catalytically inactive D395A mutant. Together, we assessed the protein interactome of METTL3, uncovered a new function of HAT1 in acetylating H3K9 in chromatin, and revealed a crosstalk between METTL3-mediated formation of m6A and HAT1-catalyzed formation of H3K9Ac in chromatin.

This dataset

Open GSE220868 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 GSE220868_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 PRJNA911778 and SRA study SRP412834. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × HEK293T, H3K9Ac-ChIP, vs 2 × METTL3 knockout, H3K9Ac-ChIP, vs 2 × METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, vs 2 × METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 8 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

GSM6824876 HEK293T, Input
GSM6824877 METTL3 knockout, Input
GSM6824878 HEK293T, H3K9Ac-ChIP, rep1 HEK293T, H3K9Ac-ChIP,
GSM6824879 HEK293T, H3K9Ac-ChIP, rep2 HEK293T, H3K9Ac-ChIP,
GSM6824880 METTL3 knockout, H3K9Ac-ChIP, rep1 METTL3 knockout, H3K9Ac…
GSM6824881 METTL3 knockout, H3K9Ac-ChIP, rep2 METTL3 knockout, H3K9Ac…
GSM6824882 METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, rep1 METTL3 knockout with wi…
GSM6824883 METTL3 knockout with wildtype METTL3 rescue, H3K9Ac-ChIP, rep2 METTL3 knockout with wi…
GSM6824884 METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP, rep1 METTL3 knockout with mu…
GSM6824885 METTL3 knockout with mutated METTL3 rescue, H3K9Ac-ChIP, rep2 METTL3 knockout with mu…

Datasets on a similar topic

GSE220870 METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin 43 samples shares mettl3, h3k9, acetyltransferase, acetylation, recruitment, chromatin, promotes
GSE243987 METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin [Nascent RNA-seq] 16 samples shares mettl3, h3k9, acetyltransferase, acetylation, recruitment, chromatin, promotes
GSE256116 DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states 36 samples shares h3k9, chromatin, promotes
GSE256135 DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states 77 samples shares h3k9, chromatin, promotes
GSE288140 HDAC2-Mediated Recruitment of METTL3 to Chromatin Regulates Human Embryonic Stem Cell Differentiation 74 samples shares mettl3, recruitment, chromatin
GSE282925 DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states [RNA-Seq] 12 samples shares h3k9, chromatin, promotes
GSE256114 DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states 12 samples shares h3k9, chromatin, promotes
GSE285328 Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin [RNA-seq] 6 samples shares mettl3, acetylation, chromatin

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