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Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters

Ni, Weiya and Perez, Andrew A. and Schreiner, Shannon and Nicolet, Charles M. and Farnham, Peggy J. (2020) Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. Nucleic Acids Research, 48 (11). pp. 5986-6000. ISSN 0305-1048. PMCID PMC7293018. doi:10.1093/nar/gkaa384.

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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.

Item Type:Article
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URLURL TypeDescription CentralArticle
Ni, Weiya0000-0002-8821-7786
Perez, Andrew A.0000-0002-8723-4859
Schreiner, Shannon0000-0002-8458-5362
Nicolet, Charles M.0000-0003-3036-8925
Farnham, Peggy J.0000-0003-4469-7914
Additional Information:© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 16 February 2020; Revision received: 09 April 2020; Accepted: 04 May 2020; Published: 14 May 2020. We thank the UCLA Technology Center for Genomics & Bioinformatics for sequencing ChIP-seq and RNA-seq samples, Novogene for sequencing RNA-seq samples, Peconic Genomics ( for assistance with the ChIP-exo experiments, ECLIPSE Bioinovations ( for assistance with the eCLIP experiments, the USC Center for High Performance Computing (, the USC Norris Comprehensive Cancer Center Flow Cytometry and Immune Monitoring Core (supported in part by the National Cancer Institute Cancer Center Shared Grant award P30CA014089 and the USC Office of the Provost and Dean's Development Funds at the Keck School of Medicine of USC) for single cell sorting and cell cycle analysis (, the USC Norris Molecular Genomics Core Facility for assistance with the DNA methylation EPIC arrays, the USC Office of Research, and the Norris Medical Library for pathway analysis software. We thank Dr. Kristian Helin for the gift of a ZNF711 antibody and Dr. Suhn Rhie for helpful discussions and instruction concerning data analysis. Data Availability: The ChIP-seq, ChIP-exo, RNA-seq, and DNA methylation EPIC data are available in NCBI’s Gene Expression Omnibus ( and are accessible through GEO Series accession number GSE145160. Funding: National Institutes of Health [R01CA136924, P30CA014089]. Funding for open access charge: National Institutes of Health [R01CA136924]. Conflict of interest statement. None declared.
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University of Southern CaliforniaUNSPECIFIED
Issue or Number:11
PubMed Central ID:PMC7293018
Record Number:CaltechAUTHORS:20200522-121905575
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Official Citation:Weiya Ni, Andrew A Perez, Shannon Schreiner, Charles M Nicolet, Peggy J Farnham, Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters, Nucleic Acids Research, Volume 48, Issue 11, 19 June 2020, Pages 5986–6000,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103417
Deposited By: Tony Diaz
Deposited On:22 May 2020 20:51
Last Modified:16 Nov 2021 18:21

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