GEO series

m6A sites in the coding region trigger translation-dependent mRNA decay (RNA-seq)

GSE248571 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/11/20 Platform GPL30173Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 32 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: 32 samples: 10 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: m6A sites in the coding region trigger translation-dependent mRNA decayMolecular cell · 2024

Summary (written by the submitters)

N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. In this study, we reveal that m6A sites in the coding sequence (CDS) trigger CDS–m6A decay (CMD), a novel mRNA decay pathway that is distinct from previously reported m6A-dependent degradation mechanisms.

Read the full summary ↓

Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors of m6A-mediated RNA decay. Mechanistically, CMD depends on translation whereby m6A deposition in the CDS induces ribosome pausing and transcript destabilization. We found that the target transcripts of CMD are recognized by the m6A reader protein YTHDF2, selectively enriched in processing bodies (P-bodies) and degraded via the decapping factor DCP2. Our findings highlight CMD as a previously unknown pathway for m6A-mediated decay, which is particularly important for controlling the expression of developmental regulators and retrogenes.

Published in

m6A sites in the coding region trigger translation-dependent mRNA decay

Zhou Y, Ćorović M, Hoch-Kraft P et al. · Molecular cell 2024 · PMID 39577428 · doi:10.1016/j.molcel.2024.10.033

This dataset

Open GSE248571 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 GSE248571_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 PRJNA1044802 and SRA study SRP474024. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39577428) ↗

Study design

10 conditions, mostly in triplicate

HEK293T, DMSO, 9h, RNA-seq ×4 HEK293T, STM2457, 9h, RNA-seq ×4 HEK293T, DMSO, 6h, RNA-seq ×3 HEK293T, STM2457, 6h, RNA-seq ×3 HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq ×3 HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq ×3 HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, ×3 HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, ×3 +2 more

Supports a between-group comparison across 32 samples.

How we read this: 10 replicated groups read from 32 sample titles; they account for 32 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

GSM7917298 HEK293T, DMSO, 6h, RNA-seq rep1 HEK293T, DMSO, 6h, RNA-…
GSM7917299 HEK293T, DMSO, 6h, RNA-seq rep2 HEK293T, DMSO, 6h, RNA-…
GSM7917300 HEK293T, DMSO, 6h, RNA-seq rep3 HEK293T, DMSO, 6h, RNA-…
GSM7917301 HEK293T, STM2457, 6h, RNA-seq rep1 HEK293T, STM2457, 6h, R…
GSM7917302 HEK293T, STM2457, 6h, RNA-seq rep2 HEK293T, STM2457, 6h, R…
GSM7917303 HEK293T, STM2457, 6h, RNA-seq rep3 HEK293T, STM2457, 6h, R…
GSM7917304 HEK293T, DMSO, 9h, RNA-seq rep1 HEK293T, DMSO, 9h, RNA-…
GSM7917305 HEK293T, DMSO, 9h, RNA-seq rep2 HEK293T, DMSO, 9h, RNA-…
GSM7917306 HEK293T, DMSO, 9h, RNA-seq rep3 HEK293T, DMSO, 9h, RNA-…
GSM7917307 HEK293T, DMSO, 9h, RNA-seq rep4 HEK293T, DMSO, 9h, RNA-…
GSM7917308 HEK293T, STM2457, 9h, RNA-seq rep1 HEK293T, STM2457, 9h, R…
GSM7917309 HEK293T, STM2457, 9h, RNA-seq rep2 HEK293T, STM2457, 9h, R…
GSM7917310 HEK293T, STM2457, 9h, RNA-seq rep3 HEK293T, STM2457, 9h, R…
GSM7917311 HEK293T, STM2457, 9h, RNA-seq rep4 HEK293T, STM2457, 9h, R…
GSM7917312 HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep1 HEK293T, YTHDF2 KD, DMS…
GSM7917313 HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep2 HEK293T, YTHDF2 KD, DMS…
GSM7917314 HEK293T, YTHDF2 KD, DMSO, 6h, RNA-seq rep3 HEK293T, YTHDF2 KD, DMS…
GSM7917315 HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep1 HEK293T, YTHDF2 KD, STM…
GSM7917316 HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep2 HEK293T, YTHDF2 KD, STM…
GSM7917317 HEK293T, YTHDF2 KD, STM2457, 6h, RNA-seq rep3 HEK293T, YTHDF2 KD, STM…
GSM8424168 HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep1 HEK293T (RNA-Seq), DMSO…
GSM8424169 HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep2 HEK293T (RNA-Seq), DMSO…
GSM8424170 HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep3 HEK293T (RNA-Seq), DMSO…
GSM8424171 HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep1 HEK293T (RNA-Seq), STM2…
GSM8424172 HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep2 HEK293T (RNA-Seq), STM2…
GSM8424173 HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep3 HEK293T (RNA-Seq), STM2…
GSM8424174 HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep1 HEK293T (RNA-Seq), DMSO…
GSM8424175 HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep2 HEK293T (RNA-Seq), DMSO…
GSM8424176 HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep3 HEK293T (RNA-Seq), DMSO…
GSM8424177 HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep1 HEK293T (RNA-Seq), STM2…
GSM8424178 HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep2 HEK293T (RNA-Seq), STM2…
GSM8424179 HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep3 HEK293T (RNA-Seq), STM2…

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