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Series GSE203640 Query DataSets for GSE203640
Status Public on Apr 29, 2024
Title Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To dissect the molecular mechanisms of the transcription factor FOXA2 accessing nucleosomal targets and controlling cell fates, we combined live-cell single-molecule imaging, genome editing, chromatin binding, chromatin accessibility, and RNA sequence analysis. Using the hESC differentiation cellular system to anterior primitive streak (APS) and definitive endoderm (DE), we demonstrated by RNA-seq that FOXA2 is a lineage-determining transcription factor for DE formation and that its intrinsically disordered C-terminal domain (CTD) is essential for its normal function. Through ChIP-seq and ATAC-seq at multiple time points of exogenous expression, we also showed that the CTD is required for FOXA2 effectively accessing targets in closed chromatin and altering chromatin accessibility. Together with the single-molecule kinetics captured by fluorescence microscopy, this study uncovers new mechanistic insights on the activity of lineage-determining transcription factors in engaging chromatin and accessing nucleosomal targets.
 
Overall design We generated homozygous genome-edited human embryonic stem cell lines (H7 hESC) with deletion of the entire protein-coding region, or the CTD, or both the CTD and NTD at the FOXA2 locus. Wild-type and edited hESCs were differentiated to APS and DE for poly-A RNA-seq. We generated U2OS cell lines with inducible expression of FOXA1/2/3 and SOX2 full length and mutants with the Tet-on system. Cells were induced with Dox for 4 days for ChIP-seq and ATAC-seq.
RNA-Seq of poly-A enriched RNA in human H7 embryonic stem cells (undifferentiated, APS and DE stages), homozygous Halo-FOXA2 knock-in clone KI14, FOXA2 knock-out clones KO1, KO21, KO30, homozygous delta C-teminus FOXA2 clone dC11, and homozygous delta C- and N-termini clone dCdN10.
 
Contributor(s) Niu D, Cattoglio C, Deng W
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Submission date May 23, 2022
Last update date Apr 30, 2024
Contact name Wulan Deng
E-mail(s) denglabpku@outlook.com
Organization name Peking University
Department BIOPIC
Street address Beijing Haidian District Yiheyuan Road #5
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (11)
GSM6181133 WT_ES
GSM6181134 WT_APS
GSM6181135 WT_DE
This SubSeries is part of SuperSeries:
GSE203650 Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells
Relations
BioProject PRJNA841659

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE203640_RAW.tar 165.8 Mb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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