GEO series

Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [RNA-Seq]

GSE241276 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/04/23 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 8 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: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promotersNucleic acids research · 2024

Summary (written by the submitters)

The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ~200-250bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased the pause ratio at ZFX-regulated promoters.

Read the full summary ↓

To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, proteins that interact with the N-terminal transactivation domain (e.g. histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (e.g. TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.

Published in

Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

Hsu E, Hutchison K, Liu Y et al. · Nucleic acids research 2024 · PMID 38726870 · doi:10.1093/nar/gkae372

This dataset

Open GSE241276 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 GSE241276_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 PRJNA1007634 and SRA study SRP456245. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38726870) ↗

Study design

8 conditions, mostly in triplicate

LN-229, siControl ×3 LN-229, siZFX ×3 LN-229, siZNF593 ×3 LN-229, siControl_2 ×3 LN-229, siZFX siZNF593 ×3 293T, DKO, wtZFX ×3 293T, DKO, pCMV6 ×3 293T, DKO, ZFX12_13 ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM7720370 LN-229, siControl_rep1 LN-229, siControl
GSM7720371 LN-229, siControl_rep2 LN-229, siControl
GSM7720372 LN-229, siControl_rep3 LN-229, siControl
GSM7720373 LN-229, siZFX_rep1 LN-229, siZFX
GSM7720374 LN-229, siZFX_rep2 LN-229, siZFX
GSM7720375 LN-229, siZFX_rep3 LN-229, siZFX
GSM7720376 LN-229, siZNF593_rep1 LN-229, siZNF593
GSM7720377 LN-229, siZNF593_rep2 LN-229, siZNF593
GSM7720378 LN-229, siZNF593_rep3 LN-229, siZNF593
GSM7720379 LN-229, siControl_2_rep1 LN-229, siControl_2
GSM7720380 LN-229, siControl_2_rep2 LN-229, siControl_2
GSM7720381 LN-229, siControl_2_rep3 LN-229, siControl_2
GSM7720382 LN-229, siZFX siZNF593_rep1 LN-229, siZFX siZNF593
GSM7720383 LN-229, siZFX siZNF593_rep2 LN-229, siZFX siZNF593
GSM7720384 LN-229, siZFX siZNF593_rep3 LN-229, siZFX siZNF593
GSM7720385 293T, DKO, wtZFX_rep1 293T, DKO, wtZFX
GSM7720386 293T, DKO, wtZFX_rep2 293T, DKO, wtZFX
GSM7720387 293T, DKO, wtZFX_rep3 293T, DKO, wtZFX
GSM7720388 293T, DKO, pCMV6_rep1 293T, DKO, pCMV6
GSM7720389 293T, DKO, pCMV6_rep2 293T, DKO, pCMV6
GSM7720390 293T, DKO, pCMV6_rep3 293T, DKO, pCMV6
GSM7720391 293T, DKO, ZFX12_13_rep1 293T, DKO, ZFX12_13
GSM7720392 293T, DKO, ZFX12_13_rep2 293T, DKO, ZFX12_13
GSM7720393 293T, DKO, ZFX12_13_rep3 293T, DKO, ZFX12_13

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