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Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery

GSE272562 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 46 samples Submitted 2025/04/08 Platform GPL30882Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 46 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
46 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machineryNucleic acids research · 2025
Summary (written by the submitters)
The silencing of adeno-associated virus (AAV) vectors over time poses a challenge to the development of effective gene therapies. Here, we describe a bioorthogonal platform for tuning AAV expression, enabling the controlled activation of viral transgenes after transduction. This platform uses a small, synthetic DNA binding protein embedded in the AAV genome coupled with a heterobifunctional small molecule that recruits endogenous transcriptional machinery to chemically induce transgene expression in a dose-dependent and reversible manner.
Read the full summary ↓
In human cells, this strategy successfully activates AAV expression across different viral serotypes, cassette configurations, and transgene payloads. Epigenomic analysis reveals that this technology facilitates direct and specific recruitment of the transcriptional regulator BRD4 to AAV genomes. Our results demonstrate that the expression of native AAV genomes can be tuned through chemically induced proximity (CIP), opening the possibility of a new class of AAV vectors that can be dynamically potentiated.
Published in
Dynamic activation of rAAV transgene expression by a small molecule that recruits endogenous transcriptional machinery
Wasserman SR, Muron S, Lee HR et al. · Nucleic acids research 2025 · PMID 40298110 · doi:10.1093/nar/gkaf345
This dataset
Open GSE272562 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE272562_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1137350 and SRA study SRP520807. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40298110) ↗
Study design
12 conditions, mostly with about 4 replicates each
U2OS BRD4 no treatment ×4 U2OS BRD4 C207 treatment ×4 U2OS H3K9ac no treatment ×4 U2OS H3K9ac C207 treatment ×4 U2OS H3K27ac no treatment ×4 U2OS H3K27ac C207 treatment ×4 U2OS cells, no infection, DMSO, ×4 U2OS cells, no infection, 300 nM C207, ×4 +5 more

Supports a between-group comparison across 45 samples.

How we read this: 12 replicated groups read from 46 sample titles; they account for 45 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

+ 6 more — browse all 46 samples with per-sample file links →

Datasets on a similar topic

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