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Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [ChIP-seq]

GSE329244 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 64 samples Submitted 2026/04/29 Platform GPL34290

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 64 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: Mus musculus (mouse)
Samples: 64 samples: 32 conditions, mostly in duplicateGroups 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.

Summary (written by the submitters)

Polycomb group (PcG) proteins safeguard cell identity by maintaining target genes in a transcriptionally repressed state through depositing two histone marks, H2A lysine-119 ubiquitination (H2AK119ub1) and H3 lysine-27 trimethylation (H3K27me3). BAP1 and UTX are thought to erase these marks during transcription activation, but their exact roles remain unclear.

Read the full summary ↓

Here we observe a rapid loss of H2AK119ub1, followed by a reduction in H3K27me3 levels at promoters upon transcription induction, coinciding with a swift dissociation of PRCs. With an acute degradation system, we show that BAP1 and UTX are dispensable for transcription activation or the dissolution of PcG repressive marks. Instead, they promote enhancer establishment during cell fate transition independent of their eraser enzymatic activity. Therefore, our study provides novel mechanistic insights that the dissolution of PcG-marks is transcription-dependent while UTX and BAP1 primarily function as bridging factors to construct enhancers, rather than as erasers of PcG memory.

This dataset

Open GSE329244 in finder → Find more mouse 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 GSE329244_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 PRJNA1458197 and SRA study SRP695313. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

32 conditions, mostly in duplicate

BAP1,+IAA,0,119ub1, ×2 BAP1,+IAA,3,119ub1, ×2 BAP1,+IAA,6,119ub1, ×2 BAP1,+IAA,24,119ub1, ×2 BAP1,-IAA,0,119ub1, ×2 BAP1,-IAA,3,119ub1, ×2 BAP1,-IAA,6,119ub1, ×2 BAP1,-IAA,24,119ub1, ×2 +24 more

Supports a between-group comparison across 64 samples.

How we read this: 32 replicated groups read from 64 sample titles; they account for 64 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

GSM9699939 BAP1,+IAA,0,119ub1,rep1 BAP1,+IAA,0,119ub1,
GSM9699940 BAP1,+IAA,0,119ub1,rep2 BAP1,+IAA,0,119ub1,
GSM9699941 BAP1,+IAA,3,119ub1,rep1 BAP1,+IAA,3,119ub1,
GSM9699942 BAP1,+IAA,3,119ub1,rep2 BAP1,+IAA,3,119ub1,
GSM9699943 BAP1,+IAA,6,119ub1,rep1 BAP1,+IAA,6,119ub1,
GSM9699944 BAP1,+IAA,6,119ub1,rep2 BAP1,+IAA,6,119ub1,
GSM9699945 BAP1,+IAA,24,119ub1,rep1 BAP1,+IAA,24,119ub1,
GSM9699946 BAP1,+IAA,24,119ub1,rep2 BAP1,+IAA,24,119ub1,
GSM9699947 BAP1,-IAA,0,119ub1,rep1 BAP1,-IAA,0,119ub1,
GSM9699948 BAP1,-IAA,0,119ub1,rep2 BAP1,-IAA,0,119ub1,
GSM9699949 BAP1,-IAA,3,119ub1,rep1 BAP1,-IAA,3,119ub1,
GSM9699950 BAP1,-IAA,3,119ub1,rep2 BAP1,-IAA,3,119ub1,
GSM9699951 BAP1,-IAA,6,119ub1,rep1 BAP1,-IAA,6,119ub1,
GSM9699952 BAP1,-IAA,6,119ub1,rep2 BAP1,-IAA,6,119ub1,
GSM9699953 BAP1,-IAA,24,119ub1,rep1 BAP1,-IAA,24,119ub1,
GSM9699954 BAP1,-IAA,24,119ub1,rep2 BAP1,-IAA,24,119ub1,
GSM9699955 BAP1,+IAA,2i,K4me1,rep1 BAP1,+IAA,2i,K4me1,
GSM9699956 BAP1,+IAA,2i,K4me1,rep2 BAP1,+IAA,2i,K4me1,
GSM9699957 BAP1,-IAA,2i,K4me1,rep1 BAP1,-IAA,2i,K4me1,
GSM9699958 BAP1,-IAA,2i,K4me1,rep2 BAP1,-IAA,2i,K4me1,
GSM9699959 BAP1,+IAA,FA,K4me1,rep1 BAP1,+IAA,FA,K4me1,
GSM9699960 BAP1,+IAA,FA,K4me1,rep2 BAP1,+IAA,FA,K4me1,
GSM9699961 BAP1,-IAA,FA,K4me1,rep1 BAP1,-IAA,FA,K4me1,
GSM9699962 BAP1,-IAA,FA,K4me1,rep2 BAP1,-IAA,FA,K4me1,
GSM9699963 BAP1,+IAA,FA,WT,K4me1,rep1 BAP1,+IAA,FA,WT,K4me1,
GSM9699964 BAP1,+IAA,FA,WT,K4me1,rep2 BAP1,+IAA,FA,WT,K4me1,
GSM9699965 BAP1,+IAA,FA,C91A,K4me1,rep1 BAP1,+IAA,FA,C91A,K4me1,
GSM9699966 BAP1,+IAA,FA,C91A,K4me1,rep2 BAP1,+IAA,FA,C91A,K4me1,
GSM9699967 UTX,+IAA,0,K27me3,rep1 UTX,+IAA,0,K27me3,
GSM9699968 UTX,+IAA,0,K27me3,rep2 UTX,+IAA,0,K27me3,
GSM9699969 UTX,+IAA,3,K27me3,rep1 UTX,+IAA,3,K27me3,
GSM9699970 UTX,+IAA,3,K27me3,rep2 UTX,+IAA,3,K27me3,
GSM9699971 UTX,+IAA,6,K27me3,rep1 UTX,+IAA,6,K27me3,
GSM9699972 UTX,+IAA,6,K27me3,rep2 UTX,+IAA,6,K27me3,
GSM9699973 UTX,+IAA,24,K27me3,rep1 UTX,+IAA,24,K27me3,
GSM9699974 UTX,+IAA,24,K27me3,rep2 UTX,+IAA,24,K27me3,
GSM9699975 UTX,-IAA,0,K27me3,rep1 UTX,-IAA,0,K27me3,
GSM9699976 UTX,-IAA,0,K27me3,rep2 UTX,-IAA,0,K27me3,
GSM9699977 UTX,-IAA,3,K27me3,rep1 UTX,-IAA,3,K27me3,
GSM9699978 UTX,-IAA,3,K27me3,rep2 UTX,-IAA,3,K27me3,

+ 24 more — browse all 64 samples with per-sample file links →

Datasets on a similar topic

GSE329243 Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [CUT&Tag] 16 samples shares bap1, utx, establishment, dispensable, activation, essential, polycomb, bivalent
GSE329245 Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [RNA-seq] 24 samples shares bap1, utx, establishment, dispensable, activation, essential, polycomb, bivalent
GSE267538 Nr5a2 is dispensable for ZGA but essential for morula development 537 samples shares dispensable, essential
GSE312320 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq, 2] 132 samples shares establishment, activation
GSE309423 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation [ChIP-Seq] 42 samples shares establishment, activation
GSE267536 Nr5a2 is dispensable for ZGA but essential for morula development [ATAC-seq] 23 samples shares dispensable, essential
GSE254023 The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq) 12 samples shares dispensable, essential
GSE223673 Nr5a2 is dispensable for ZGA but essential for morula development [RNA-seq] 514 samples shares dispensable, essential

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