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TET2 regulates histone H2AK119ub and leukemogenesis through LTR RNA m5C oxidation [seq_RNA-caRNA]

GSE241342 Homo sapiens (human) RNA-seq (gene expression) 29 samples Submitted 2024/07/25 Platform GPL24676Platform GPL24247
At a glance

RNA-seq (gene expression) · human · 29 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
29 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
RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesisNature · 2024
Summary (written by the submitters)
Mutation of TET2 drives myeloid malignancy progression. TET2 deficiency is known to cause a globally opened chromatin and activation of genes contributing to aberrant HSPC self-renewal. We show here that chromatin-associated retrotransposon RNA 5-methylcytosine (m5C), installed by NSUN2, can be recognized by the methyl-CpG-binding domain protein MBD6, which guides deubiquitylation of nearby histone H2AK119ub to promote an open chromatin state.
Read the full summary ↓
TET2 oxidizes m5C and antagonizes this MBD6-dependent H2AK119ub deubiquitylation. Thereby, TET2 depletion leads to globally decreased H2AK119ub, more open chromatin, and increased transcription in stem cells. TET2 mutant human leukemia became dependent on this gene activation pathway, with MBD6 silencing selectively inhibits proliferation of TET2 mutant leukemia in vitro and in vivo. Altogether, our findings reveal a previously unknown chromatin regulation pathway by TET2 through retrotransposon RNA m5C oxidation and identify the downstream MBD6 protein as a feasible target for developing therapies specific against TET2 mutant malignancies.
Published in
RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesis
Zou Z, Dou X, Li Y et al. · Nature 2024 · PMID 39358506 · doi:10.1038/s41586-024-07969-x
This dataset
Open GSE241342 in finder → Find more 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 GSE241342_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 PRJNA1007726 and SRA study SRP456234. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39358506) ↗
Study design
10 conditions, mostly in triplicate
mESC, Tet2 WT, caRNA, ×3 mESC, Pspc1 KO, caRNA, ×3 mESC, siControl, caRNA, ×3 mESC, siNsun2, caRNA, ×3 K562, TET2WT shControl, caRNA, ×3 K562, TETWT shMBD6, caRNA, ×3 K562, TET2KO shControl, caRNA, ×3 K562, TET2KO shMBD6, caRNA, ×3 +3 more

Supports a between-group comparison across 28 samples.

How we read this: 10 replicated groups read from 29 sample titles; they account for 28 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
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