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Series GSE220569 Query DataSets for GSE220569
Status Public on Jun 07, 2023
Title Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [Mnase-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Pioneer transcription factors, by interacting with nucleosomes, scan silent, compact chromatin to target regulatory sequences, enabling cooperative binding events that modulate local chromatin structure and gene activity. However, not all cognate motifs are targeted by pioneer factors and dynamic scanning parameters required to scan compact chromatin are unknown. A combined genomics and single-molecule tracking approach shows that to target DNase-resistant, low-histone turnover sites, pioneer factors FOXA1 and SOX2 display opposite dynamics of chromatin scanning: slow, with low nucleoplasmic diffusion and stable interactions, versus fast, with high nucleoplasmic diffusion and transient interactions, respectively. Despite such differences, the ability of FOXA1 and SOX2 to scan low-mobility chromatin, mediated by protein domains outside of the respective DNA binding domains, leads to targeting silent chromatin. By contrast, non-pioneer HNF4A predominantly targets DNase-sensitive, nucleosome-depleted regions. We conclude that the targeting of compact chromatin sites by pioneer factors can be performed through diverse dynamic processes.
Micrococcol nuclease digestion and sequencing (MNase-seq) of human BJ fibroblasts
 
Overall design Andrew,Katznelson
 
Contributor(s) Lerner J, Zaret K
Citation(s) 37405916
Submission date Dec 08, 2022
Last update date Sep 06, 2023
Contact name Kenneth S. Zaret
E-mail(s) zaret@pennmedicine.upenn.edu
Phone 2155735813
Organization name University of Pennsylvania School of Medicine
Department Cell and Developmental Biology
Lab Zaret lab
Street address 9-132, SCTR, 3400 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104-5157
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (2)
GSM6806989 hBJ,MNaseSeq,rep1
GSM6806990 hBJ,MNaseSeq,rep2
This SubSeries is part of SuperSeries:
GSE220570 Different chromatin scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2
Relations
BioProject PRJNA910209

Download family Format
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Supplementary file Size Download File type/resource
GSE220569_MNase_hFib_hg19.bw 455.3 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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