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Series GSE241281 Query DataSets for GSE241281
Status Public on Apr 23, 2024
Title Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [GRO-seq]
Organism Homo sapiens
Experiment type Other
Summary The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ~200-250bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased the pause ratio at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, proteins that interact with the N-terminal transactivation domain (e.g. histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (e.g. TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.
Overall design To profile the effects of ZFX on Pol2 pausing in human cell lines. siRNA knockdowns with siZFX and a control siRNA oligo were performed in LN-229 cells with 2 biological replicates. 293T cells and 293T cells with ZFX and ZNF711 knockouts (DKO) were also performed with 2 biological replicates.
Contributor(s) Hsu E, Hutchison KR, Liu Y, Nicolet CM, Schreiner SM, Zemke NR, Farnham PJ
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NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM133450 Characterization of a novel family of human transcription factors that bind at +240 downstream of the transcription start site. UNIVERSITY OF SOUTHERN CALIFORNIA Peggy J Farnham
P30 CA014089 Administrative Supplements for P30 Cancer Centers Support Grants (CCSG) to Enhance the Utility of Data Available through the Childhood Cancer Data Initiative (CCDI) Ecosystem UNIVERSITY OF SOUTHERN CALIFORNIA Caryn Lerman
F32 CA264890 How does the ubiquitously expressed ZFX mediate cell type-specific transcriptional regulation UNIVERSITY OF SOUTHERN CALIFORNIA Emily Hsu
Submission date Aug 21, 2023
Last update date Apr 24, 2024
Contact name Peggy J Farnham
Organization name University of Southern California
Department Biochemistry and Molecular Medicine
Street address 1450 Biggy St, NRT6514
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (8)
GSM7720585 HEK293T, WT, groseq, Rep1
GSM7720586 HEK293T, DKO, groseq, Rep1
GSM7720587 HEK293T, WT, groseq, Rep2
This SubSeries is part of SuperSeries:
GSE241284 Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters
BioProject PRJNA1007637

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Supplementary file Size Download File type/resource
GSE241281_RAW.tar 1.2 Gb (http)(custom) TAR (of BIGWIG)
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Raw data are available in SRA

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