GEO series

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Mnase-seq]

GSE234251 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 21 samples Submitted 2024/03/11 Platform GPL19057

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 21 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: 21 samples: 9 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: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCFNature genetics · 2024

Summary (written by the submitters)

Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediate these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits.

Read the full summary ↓

Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes cause only moderate effects on the chromatin landscape, while removal of the NURF specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility bound CTCF is nevertheless impaired in function resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.

Published in

Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF

Iurlaro M, Masoni F, Flyamer IM et al. · Nature genetics 2024 · PMID 38816647 · doi:10.1038/s41588-024-01767-x

This dataset

Open GSE234251 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 GSE234251_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 PRJNA980630 and SRA study SRP441370. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38816647) ↗

Study design

9 conditions, mostly in duplicate

MNaseSeq_ESC_bptf_ko_A ×3 MNaseSeq_ESC_cecr2_ko_B ×3 MNaseSeq_ESC_wt_B ×3 MNaseSeq_ESC_acf1_ko_C ×2 MNaseSeq_ESC_rsf1_ko_A ×2 MNaseSeq_ESC_tip5_ko_A ×2 MNaseSeq_ESC_wstf_ko_A ×2 MNaseSeq_ESC_wt_A ×2 +1 more

Supports a between-group comparison across 21 samples.

How we read this: 9 replicated groups read from 21 sample titles; they account for 21 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

GSM7458212 MNaseSeq_ESC_acf1_ko_C_rep1 MNaseSeq_ESC_acf1_ko_C
GSM7458213 MNaseSeq_ESC_acf1_ko_C_rep2 MNaseSeq_ESC_acf1_ko_C
GSM7458214 MNaseSeq_ESC_bptf_ko_A_rep1 MNaseSeq_ESC_bptf_ko_A
GSM7458215 MNaseSeq_ESC_bptf_ko_A_rep2 MNaseSeq_ESC_bptf_ko_A
GSM7458216 MNaseSeq_ESC_bptf_ko_A_rep3 MNaseSeq_ESC_bptf_ko_A
GSM7458217 MNaseSeq_ESC_cecr2_ko_B_rep1 MNaseSeq_ESC_cecr2_ko_B
GSM7458218 MNaseSeq_ESC_cecr2_ko_B_rep2 MNaseSeq_ESC_cecr2_ko_B
GSM7458219 MNaseSeq_ESC_cecr2_ko_B_rep3 MNaseSeq_ESC_cecr2_ko_B
GSM7458220 MNaseSeq_ESC_rsf1_ko_A_rep1 MNaseSeq_ESC_rsf1_ko_A
GSM7458221 MNaseSeq_ESC_rsf1_ko_A_rep2 MNaseSeq_ESC_rsf1_ko_A
GSM7458222 MNaseSeq_ESC_tip5_ko_A_rep1 MNaseSeq_ESC_tip5_ko_A
GSM7458223 MNaseSeq_ESC_tip5_ko_A_rep2 MNaseSeq_ESC_tip5_ko_A
GSM7458224 MNaseSeq_ESC_wstf_ko_A_rep1 MNaseSeq_ESC_wstf_ko_A
GSM7458225 MNaseSeq_ESC_wstf_ko_A_rep2 MNaseSeq_ESC_wstf_ko_A
GSM7458226 MNaseSeq_ESC_wt_A_rep1 MNaseSeq_ESC_wt_A
GSM7458227 MNaseSeq_ESC_wt_A_rep2 MNaseSeq_ESC_wt_A
GSM7458228 MNaseSeq_ESC_wt_B_rep1 MNaseSeq_ESC_wt_B
GSM7458229 MNaseSeq_ESC_wt_B_rep2 MNaseSeq_ESC_wt_B
GSM7458230 MNaseSeq_ESC_wt_B_rep3 MNaseSeq_ESC_wt_B
GSM7458231 MNaseSeq_ESC_wt_C_rep1 MNaseSeq_ESC_wt_C
GSM7458232 MNaseSeq_ESC_wt_C_rep2 MNaseSeq_ESC_wt_C

Datasets on a similar topic

GSE234273 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [ChIP-seq] 32 samples shares iswi, nurf, ctcf, accessibility, systematic, assessment, subunits
GSE234288 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Cut&Run] 12 samples shares iswi, nurf, ctcf, accessibility, systematic, assessment, subunits
GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares iswi, nurf, ctcf, accessibility, systematic, assessment, subunits
GSE287375 CTCF-RNA interactions orchestrate cell-specific chromatin loop organization [ChIP-seq] 54 samples shares ctcf
GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares ctcf
GSE253692 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [mESC_d0246_CTCF_MBD3_ChIP_Seq] 36 samples shares ctcf
GSE243710 Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq] 33 samples shares ctcf
GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares ctcf

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