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Polycomb sustains promoters in a deep OFF-state by limiting PIC formation to counteract transcription

GSE216636 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/05/29 Platform GPL19415
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
12 samples: 3 × RING1BmAID-TAF1dTAG-T7-UNT vs 3 × RING1BmAID-TAF1dTAG-T7-AUX vs 3 × RING1BmAID-TAF1dTAG-T7-Input-UNT vs 3 × RING1BmAID-TAF1dTAG-T7-Input-AUXGroups 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 Polycomb system sustains promoters in a deep OFF state by limiting pre-initiation complex formation to counteract transcriptionNature cell biology · 2024
Summary (written by the submitters)
The Polycomb system plays fundamental roles in regulating gene expression during mammalian development. However, how it controls transcription to enable gene repression has remained enigmatic. Here we employ rapid degron-based depletion coupled with live-cell transcription imaging and single-particle tracking to uncover how the Polycomb system controls transcription in single cells.
Read the full summary ↓
We discover that the Polycomb system is not a constitutive block to transcription but instead sustains a long-lived deep promoter OFF-state which limits the frequency with which the promoter can enter into a transcribing state. We demonstrate that Polycomb sustains this deep promoter OFF-state by counteracting the binding of factors that enable early transcription pre-initiation complex formation and show that this is necessary for gene repression. Together these important discoveries provide a new rationale for how the Polycomb system controls transcription and suggests a universal mechanism that could enable the Polycomb system to constrain transcription across diverse cellular contexts.
Published in
The Polycomb system sustains promoters in a deep OFF state by limiting pre-initiation complex formation to counteract transcription
Szczurek AT, Dimitrova E, Kelley JR et al. · Nature cell biology 2024 · PMID 39261718 · doi:10.1038/s41556-024-01493-w
This dataset
Open GSE216636 in finder → Find more 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 GSE216636_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 PRJNA894545 and SRA study SRP404705. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39261718) ↗
Study design
3 × RING1BmAID-TAF1dTAG-T7-UNT vs 3 × RING1BmAID-TAF1dTAG-T7-AUX vs 3 × RING1BmAID-TAF1dTAG-T7-Input-UNT vs 3 × RING1BmAID-TAF1dTAG-T7-Input-AUX

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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