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Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation

GSE279769 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2025/11/03 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 7 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
Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbationNature communications · 2025
Summary (written by the submitters)
The development of selective ligands to target DNA G-quadruplexes (G4s) has been pivotal in revealing their role in transcriptional regulation. However, most of the ligands described to date lack intra-G4 selectivity, severely limiting their potential for uncovering the biological function of individual G4s across the genome. To overcome these limitations, we developed ATENA (Approach to Target Exact Nucleic Acid alternative structures).
Read the full summary ↓
ATENA relies on the chemical modification of established G4-ligands to enable their conjugation onto a catalytically inactive Cas9 protein (dCas9) using HaloTag, allowing for the targeting of individual G4s in living cells. We have systematically screened the length of the PEG-linkers connecting the G4-ligands to the HaloTag and sgRNA sequences to attain optimal G4 engagement both in vitro and in cells. Using optimized conditions, we leveraged ATENA to demonstrate how the selective targeting of the well-studied G4 in the promoter of the oncogene c-MYC suppresses its transcription exclusively from the P1 promoter. We also show that positioning ligands in the proximity of regulatory elements suppresses c-MYC transcription in a G4-independent manner, highlighting the importance of appropriate design to measure genuine G4-mediated transcriptional changes. We also demonstrate that selective targeting of a G4 in the PVT1 promoter can either stimulate or repress its transcription depending on the type of G4-ligand used, indicating that functional responses associated with G4-stabilization can highly depend on the type of ligand used. We further harnessed ATENA to study transcriptional perturbation associated with cell-specific G4s, revealing that the functional responses associated with these structures are tightly linked with the expression levels of the targeted gene. Our study provides critical insights into G4-based therapeutic design, offering an innovative platform to investigate G4 biology with high precision.
Published in
Chemically modified CRISPR-Cas9 enables targeting of individual G-quadruplex and i-motif structures, revealing ligand-dependent transcriptional perturbation
Nuccio SP, Cadoni E, Nikoloudaki R et al. · Nature communications 2025 · PMID 41366211 · doi:10.1038/s41467-025-67074-z
This dataset
Open GSE279769 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 GSE279769_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 PRJNA1174229 and SRA study SRP539233. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41366211) ↗
Study design
7 conditions, mostly in triplicate
MCF7, DMSO, ×3 MCF7, DC34, ×3 MCF7, PyPDS, ×3 MCF7dCas9Halo,sgRNAMYC-19,DMSO, ×3 MCF7dCas9Halo,sgRNAMYC-19,Cl-PDS2, ×3 MCF7dCas9Halo,sgRNAMYC-NTC,DMSO, ×3 MCF7dCas9Halo,sgRNAMYC-NTC,Cl-PDS2, ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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
Datasets on a similar topic

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