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Series GSE220567 Query DataSets for GSE220567
Status Public on Jun 07, 2023
Title Distinct Chromatin Scanning Modes Lead to Targeting of Compacted Chromatin by Pioneer Factors FOXA1 and SOX2 [ChIP-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.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HNF4A, FOXA1, FOXA1-DBD, FOXA1-NHAA, FOXA1-RRAA, as well as H2B-HALO after ectopic expression in human BJ fibroblast cells.
 
Overall design Jonathan,Lerner
 
Contributor(s) Katznelson A, 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 (26)
GSM6806959 FOXA1,HALO,hBJ,rep1
GSM6806960 FOXA1,HALO,hBJ,rep1,input
GSM6806961 FOXA1,HALO,hBJ,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 PRJNA910211

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE220567_RAW.tar 4.0 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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