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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
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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.
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Overall design |
Jonathan,Lerner
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Contributor(s) |
Katznelson A, Zaret K |
Citation(s) |
37405916 |
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Submission date |
Dec 08, 2022 |
Last update date |
Sep 06, 2023 |
Contact name |
Kenneth S. Zaret |
E-mail(s) |
zaret@pennmedicine.upenn.edu
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Phone |
2155735813
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Organization name |
University of Pennsylvania School of Medicine
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Department |
Cell and Developmental Biology
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Lab |
Zaret lab
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Street address |
9-132, SCTR, 3400 Civic Center Boulevard
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City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104-5157 |
Country |
USA |
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Platforms (1) |
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Samples (26)
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GSM6806959 |
FOXA1,HALO,hBJ,rep1 |
GSM6806960 |
FOXA1,HALO,hBJ,rep1,input |
GSM6806961 |
FOXA1,HALO,hBJ,rep2 |
GSM6806962 |
FOXA1,HALO,hBJ,rep2,input |
GSM6806963 |
FOXA1dbd,HALO,hBJ,rep1 |
GSM6806964 |
FOXA1dbd,HALO,hBJ,rep1,input |
GSM6806965 |
FOXA1dbd,HALO,hBJ,rep2 |
GSM6806966 |
FOXA1dbd,HALO,hBJ,rep2,input |
GSM6806967 |
FOXA1nhaa,HALO,hBJ,rep1 |
GSM6806968 |
FOXA1nhaa,HALO,hBJ,rep1,input |
GSM6806969 |
FOXA1nhaa,HALO,hBJ,rep2 |
GSM6806970 |
FOXA1nhaa,HALO,hBJ,rep2,input |
GSM6806971 |
FOXA1rraa,HALO,hBJ,rep1 |
GSM6806972 |
FOXA1rraa,HALO,hBJ,rep1,input |
GSM6806973 |
FOXA1rraa,HALO,hBJ,rep2 |
GSM6806974 |
FOXA1rraa,HALO,hBJ,rep2,input |
GSM6806975 |
HNF4A,HALO,hBJ,rep1 |
GSM6806976 |
HNF4A,HALO,hBJ,rep1,input |
GSM6806977 |
HNF4A,HALO,hBJ,rep2 |
GSM6806978 |
HNF4A,HALO,hBJ,rep2,input |
GSM6806979 |
H2Bhalo,t0,rep1 |
GSM6806980 |
H2Bhalo,t0,rep2 |
GSM6806981 |
H2Bhalo,t0,input |
GSM6806982 |
H2Bhalo,t6,rep1 |
GSM6806983 |
H2Bhalo,t6,rep2 |
GSM6806984 |
H2Bhalo,t6,input |
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This SubSeries is part of SuperSeries: |
GSE220570 |
Different chromatin scanning modes lead to targeting of compacted chromatin by pioneer factors FOXA1 and SOX2 |
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Relations |
BioProject |
PRJNA910211 |
Supplementary file |
Size |
Download |
File type/resource |
GSE220567_RAW.tar |
4.0 Gb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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