GEO series

Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [CUT&Tag]

GSE297589 Homo sapiens; Mus musculus Genome binding/occupancy profiling by high throughput sequencing 38 samples Submitted 2025/06/05 Platform GPL34281Platform GPL34328

Summary

5-azacytidine (5-azaC) is a DNA hypomethylating agent clinically used to improve outcomes in myeloid malignancies. However, 5-azaC treatment causes gene dysregulation inconsistent with DNA hypomethylation changes. Some patients benefited from 5-azaC treatment did not display notable DNA demethylation. These observations suggest alternative mechanisms of action by 5-azaC. As a ribonuleoside analogue, 5-azaC is more readily incorporated into nascent RNA. Here, we demonstrate that RNA 5-methycytosine (m5C) depletion by 5-azaC treatment, particularly at early time points, is sufficient to induce leukemia cell death. In contrast to its DNA demethylation function, the RNA-dependent process by 5-azaC causes transcriptional repression, disrupting genes involved in cell cycle regulation and DNA repair. Mechanistically, 5-azaC impairs two specific m5C-mediated transcriptional regulatory pathways. First, depletion of m5C in chromatin-associated RNA (caRNA) disrupts the MBD6-mediated H2AK119ub removal. In parallel, this also impairs SRSF2 recruitment and the downstream H3K27ac deposition by p300. Indeed, loss of the caRNA methyltransferase NSUN2 caused prolonged cell cycle, defective DNA repair, and shifted hematopoietic lineage commitment toward erythropoiesis, mirroring the effects of 5-azaC treatment. Furthermore, we performed leukemia cell line screen and identifies that TET2 and IKZF1 depletion can sensitize 5-azaC treatment, consistent with the observed RNA-dependent cytotoxicity of 5-azaC in leukemia cells. In summary, our findings highlight the transcription regulation by 5-azaC through depleting caRNA m5C, providing insights into the mechanism of action for 5-azaC, the prediction of its efficacy, and future directions for therapy developments based on 5-azaC.

This dataset

Open GSE297589 in finder → Find more ChIP / ATAC / CUT&Tag datasets →

Download

Direct links to NCBI, no account and no request form: the whole study as GSE297589_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 38 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1265226 and SRA study SRP586366. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 conditions, mostly in triplicate

MOLM13, H2AK119ub, Ctrl, ×3 MOLM13, H2AK119ub, 5azaC, ×3 MOLM13, H3K27ac, Ctrl, ×3 MOLM13, H3K27ac, 5azaC, ×3 SKM1, H3K27ac, Ctrl, ×3 SKM1, H3K27ac, 5azaC, ×3 SKM1, tetshNSUN2, H3K27ac, Ctrl, ×3 SKM1, tetshNSUN2, H3K27ac, Dox, ×3 +6 more

Supports a between-group comparison across 38 samples.

14 replicated groups read from 38 sample titles; they account for 38 of them. Check it against the sample list below before relying on it.

Similar datasets

Search all ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.