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Series GSE145160 Query DataSets for GSE145160
Status Public on Apr 30, 2020
Title Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Our study focuses on a family of ubiquitously expressed human C2H2 zinc finger proteins comprised of ZFX, ZFY, and ZNF711. Although their protein structure suggests that ZFX, ZFY, and ZNF711 are transcriptional regulators, the mechanisms by which they influence transcription have not yet been elucidated. We used CRISPR-mediated deletion to create bi-allelic knockouts of ZFX and/or ZNF711 in female HEK293T cells (which naturally lack ZFY). We found that loss of either ZFX or ZNF711 reduced cell growth and that the double knockout cells have major defects in proliferation. RNA-seq analysis revealed that thousands of genes showed altered expression in the double knockout clones, suggesting that these TFs are critical regulators of the transcriptome. To gain insight into how these TFs regulate transcription, we created mutant ZFX proteins and analyzed them for DNA binding and transactivation capability. We found that zinc fingers 11-13 are necessary and sufficient for DNA binding and, in combination with the N terminal region, constitute a functional transactivator. Our functional analyses of the ZFX family provides important new insights into transcriptional regulation in human cells by members of the large, but under-studied family of C2H2 zinc finger proteins.
 
Overall design RNA-seq, ChIP-seq, ChIP-exo, (and EPIC array (GSE148960)) in HEK293T kidney cells and 22Rv1 prostate cells
 
Contributor(s) Ni W
Citation(s) 32406922
Submission date Feb 12, 2020
Last update date Aug 21, 2023
Contact name Weiya Stephanie Ni
E-mail(s) weiyani@usc.edu
Phone (626) 560-8660
Organization name University of Southern California
Street address 1450 Biggy Street
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
 
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (58)
GSM4307732 HEK293T, Control - RNAseq, rep1
GSM4307733 HEK293T, Control - RNAseq, rep2
GSM4307734 HEK293T, Control - RNAseq, rep3
Relations
BioProject PRJNA606250
SRA SRP248416

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
GSE145160_RAW.tar 2.8 Gb (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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