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YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle

GSE247254 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 121 samples Submitted 2024/06/17 Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 121 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
121 samples: 37 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.
Paper
YY1-controlled regulatory connectivity and transcription are influenced by the cell cycleNature genetics · 2024
Summary (written by the submitters)
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion.
Read the full summary ↓
Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer-promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer-promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1's architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.
Published in
YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle
Lam JC, Aboreden NG, Midla SC et al. · Nature genetics 2024 · PMID 39210046 · doi:10.1038/s41588-024-01871-y
This dataset
Open GSE247254 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 GSE247254_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 PRJNA1036696 and SRA study SRP470649. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39210046) ↗
Study design
37 conditions, mostly in duplicate
G1E-ER4_anatelo_YY1_ChIPseq ×3 G1E-ER4_prometa_YY1_ChIPseq ×3 YY1aid_async_auxin_Pol2_ChIPseq ×3 YY1aid_async_auxin_YY1_ChIPseq ×3 YY1aid_async_untreated_Pol2_ChIPseq ×3 YY1aid_async_untreated_YY1_ChIPseq ×3 YY1aid_earlyG1_auxin_Pol2_ChIPseq ×3 YY1aid_earlyG1_untreated_Pol2_ChIPseq ×3 +58 more

Supports a between-group comparison across 92 samples.

How we read this: 37 replicated groups read from 121 sample titles; they account for 92 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

+ 81 more — browse all 121 samples with per-sample file links →

Datasets on a similar topic

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