GEO series

METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin [Nascent RNA-seq]

GSE243987 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/12/01 Platform GPL30209

At a glance

RNA-seq (gene expression) · human · 16 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: Homo sapiens (human)
Samples: 16 samples: 8 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.

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 GSE243987 in finder → Find more human 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 GSE243987_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 PRJNA1020846 and SRA study SRP463124. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in duplicate

293T, 10min, RNA-seq ×2 293T, 20min, RNA-seq ×2 293T, 30min, RNA-seq ×2 293T, 60min, RNA-seq ×2 METTL3 knockout, 10min, RNA-seq ×2 METTL3 knockout, 20min, RNA-seq ×2 METTL3 knockout, 30min, RNA-seq ×2 METTL3 knockout, 60min, RNA-seq ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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

GSM7802816 293T, 10min, RNA-seq rep1 293T, 10min, RNA-seq
GSM7802817 293T, 10min, RNA-seq rep2 293T, 10min, RNA-seq
GSM7802818 293T, 20min, RNA-seq rep1 293T, 20min, RNA-seq
GSM7802819 293T, 20min, RNA-seq rep2 293T, 20min, RNA-seq
GSM7802820 293T, 30min, RNA-seq rep1 293T, 30min, RNA-seq
GSM7802821 293T, 30min, RNA-seq rep2 293T, 30min, RNA-seq
GSM7802822 293T, 60min, RNA-seq rep1 293T, 60min, RNA-seq
GSM7802823 293T, 60min, RNA-seq rep2 293T, 60min, RNA-seq
GSM7802824 METTL3 knockout, 10min, RNA-seq rep1 METTL3 knockout, 10min,…
GSM7802825 METTL3 knockout, 10min, RNA-seq rep2 METTL3 knockout, 10min,…
GSM7802826 METTL3 knockout, 20min, RNA-seq rep1 METTL3 knockout, 20min,…
GSM7802827 METTL3 knockout, 20min, RNA-seq rep2 METTL3 knockout, 20min,…
GSM7802828 METTL3 knockout, 30min, RNA-seq rep1 METTL3 knockout, 30min,…
GSM7802829 METTL3 knockout, 30min, RNA-seq rep2 METTL3 knockout, 30min,…
GSM7802830 METTL3 knockout, 60min, RNA-seq rep1 METTL3 knockout, 60min,…
GSM7802831 METTL3 knockout, 60min, RNA-seq rep2 METTL3 knockout, 60min,…

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, histone
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
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
GSE256116 DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states 36 samples shares h3k9, chromatin, promotes
GSE255352 Hypoxia promotes histone H3K9 lactylation to enhance LAMC2 transcription in esophageal squamous cell carcinoma 16 samples shares h3k9, promotes, 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.