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The p400 complex promotes HIV-1 latency by suppressing 1 viral transcription and altering the host cell state [RNA-seq]

GSE280360 Homo sapiens (human) RNA-seq (gene expression) 52 samples Submitted 2025/08/19 Platform GPL30173Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 52 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
52 samples: 20 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
The p400 complex promotes HIV-1 latency by suppressing viral transcription and altering the host cell stateNucleic acids research · 2025
Summary (written by the submitters)
Eradicating HIV-1 is complicated by latently infected CD4+T cells harboring repressed HIV-1 proviruses that can reactivate. Using a pooled shRNAmir screen of all human chromatin regulators we identified previously unappreciated factors that govern HIV-1 latency and reactivation. Depletion of EP400 and DMAP1, core subunits of the multifunctional p400 complex, strongly derepressed HIV-1 transcription in Jurkat and primary CD4+T cells.
Read the full summary ↓
EP400/DMAP1 co-localize with paused RNA Polymerase II (RNAPII) at the transcriptional start sites (TSS) of protein-coding genes, limiting RNAPII pause release, with HIV-1 elongation particularly affected. TNF-⍺ stimulation robustly promotes co-recruitment of RNAPII, EP400, and DMAP1 across the HIV-1 genome, which is distinct from other genes where this co-recruitment occurs mainly at the TSS. Depletion of EP400/DMAP1 reactivated HIV transcription independently of histone variant exchange and KAT5 activity, and increased gene expression of key T cell factors known to trans-activate HIV-1. Thus, the p400 complex is a host restriction factor that blocks RNAPII transcriptional elongation at the HIV-1 locus and creates a CD4+T cell state unfavorable for HIV-1 transcription.
Published in
The p400 complex promotes HIV-1 latency by suppressing viral transcription and altering the host cell state
Mori LP, Li C, Venables T et al. · Nucleic acids research 2025 · PMID 40842241 · doi:10.1093/nar/gkaf764
This dataset
Open GSE280360 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 GSE280360_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 PRJNA1177980 and SRA study SRP540941. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40842241) ↗
Study design
20 conditions, mostly in triplicate
productive_shCD8B_3_BC ×3 latent_shCD8B_3_BC ×3 productive_shCD19_4_BC ×3 latent_shCD19_4_BC ×3 productive_shEP400_4_BC ×3 latent_shEP400_4_BC ×3 productive_shDMAP1_2_BC ×3 latent_shDMAP1_2_BC ×3 +12 more

Supports a between-group comparison across 52 samples.

How we read this: 20 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

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