Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins

Abstract 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.

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ZiF-Predict: A Web Tool for Predicting DNA-Binding Specificity in C2H2 Zinc Finger Proteins

Genomics Proteomics & Bioinformatics ◽

10.1016/s1672-0229(10)60013-7 ◽

2010 ◽

Vol 8 (2) ◽

pp. 122-126 ◽

Cited By ~ 13

Author(s):

Bhuvan Molparia ◽

Kanav Goyal ◽

Anita Sarkar ◽

Sonu Kumar ◽

Durai Sundar

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Binding Specificity ◽

Zinc Finger Proteins ◽

Web Tool ◽

C2h2 Zinc Finger ◽

Dna Binding Specificity

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Characterization and design of C2H2 zinc finger proteins as custom DNA binding domains

10.31274/etd-180810-4325 ◽

2008 ◽

Author(s):

Jeffry D. Sander

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Proteins ◽

C2h2 Zinc Finger ◽

Dna Binding Domains ◽

Binding Domains

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Faculty Opinions recommendation of Reduction in DNA-binding affinity of Cys2His2 zinc finger proteins by linker phosphorylation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1019055.215578 ◽

2004 ◽

Author(s):

Philip Dawson

Keyword(s):

Dna Binding ◽

Binding Affinity ◽

Zinc Finger ◽

Zinc Finger Proteins ◽

Dna Binding Affinity

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Identification of non-Ser/Thr-Pro consensus motifs for Cdk1 and their roles in mitotic regulation of C2H2 zinc finger proteins and Ect2

Scientific Reports ◽

10.1038/srep07929 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 32

Author(s):

Kazuhiro Suzuki ◽

Kosuke Sako ◽

Kazuhiro Akiyama ◽

Michitaka Isoda ◽

Chiharu Senoo ◽

...

Keyword(s):

Zinc Finger ◽

Zinc Finger Proteins ◽

C2h2 Zinc Finger ◽

Consensus Motifs ◽

Mitotic Regulation

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Characterization of the DNA Binding Activity of the ZFY Zinc Finger Domain

Biochemistry ◽

10.1021/bi9018626 ◽

2010 ◽

Vol 49 (4) ◽

pp. 679-686 ◽

Cited By ~ 4

Author(s):

Jennifer Grants ◽

Erin Flanagan ◽

Andrea Yee ◽

Paul J. Romaniuk

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Binding Activity ◽

Zinc Finger Domain ◽

Dna Binding Activity

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Advances in the Regulation of Epidermal Cell Development by C2H2 Zinc Finger Proteins in Plants

Frontiers in Plant Science ◽

10.3389/fpls.2021.754512 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guoliang Han ◽

Yuxia Li ◽

Ziqi Qiao ◽

Chengfeng Wang ◽

Yang Zhao ◽

...

Keyword(s):

Cell Fate ◽

Zinc Finger ◽

Epidermal Cell ◽

Stress Responses ◽

Root Hairs ◽

Zinc Finger Proteins ◽

Cell Development ◽

Salt Glands ◽

Plant Adaptation ◽

C2h2 Zinc Finger

Plant epidermal cells, such as trichomes, root hairs, salt glands, and stomata, play pivotal roles in the growth, development, and environmental adaptation of terrestrial plants. Cell fate determination, differentiation, and the formation of epidermal structures represent basic developmental processes in multicellular organisms. Increasing evidence indicates that C2H2 zinc finger proteins play important roles in regulating the development of epidermal structures in plants and plant adaptation to unfavorable environments. Here, we systematically summarize the molecular mechanism underlying the roles of C2H2 zinc finger proteins in controlling epidermal cell formation in plants, with an emphasis on trichomes, root hairs, and salt glands and their roles in plant adaptation to environmental stress. In addition, we discuss the possible roles of homologous C2H2 zinc finger proteins in trichome development in non-halophytes and salt gland development in halophytes based on bioinformatic analysis. This review provides a foundation for further study of epidermal cell development and abiotic stress responses in plants.

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Single amino acid exchanges in separate domains of the Drosophila serendipity delta zinc finger protein cause embryonic and sex biased lethality.

Genetics ◽

10.1093/genetics/131.4.905 ◽

1992 ◽

Vol 131 (4) ◽

pp. 905-916 ◽

Cited By ~ 2

Author(s):

M Crozatier ◽

K Kongsuwan ◽

P Ferrer ◽

J R Merriam ◽

J A Lengyel ◽

...

Keyword(s):

Amino Acid ◽

Dna Binding ◽

Zinc Finger ◽

Zinc Finger Protein ◽

Essential Gene ◽

Larval Instar ◽

Single Amino Acid ◽

Isolation And Characterization ◽

Finger Protein

Abstract The Drosophila serendipity (sry) delta (delta) zinc finger protein is a sequence-specific DNA binding protein, maternally inherited by the embryo and present in nuclei of transcriptionally active cells throughout fly development. We report here the isolation and characterization of four ethyl methanesulfate-induced zygotic lethal mutations of different strengths in the sry delta gene. For the stronger allele, all of the lethality occurs during late embryogenesis or the first larval instar. In the cases of the three weaker alleles, most of the lethality occurs during pupation; moreover, those adult escapers that emerge are sterile males lacking partially or completely in spermatozoa bundles. Genetic analysis of sry delta thus indicates that it is an essential gene, whose continued expression throughout the life cycle, notably during embryogenesis and pupal stage, is required for viability. Phenotypic analysis of sry delta hemizygote escaper males further suggests that sry delta may be involved in regulation of two different sets of genes: genes required for viability and genes involved in gonadal development. All four sry delta alleles are fully rescued by a wild-type copy of sry delta, but not by an additional copy of the sry beta gene, reinforcing the view that, although structurally related, these two genes exert distinct functions. Molecular characterization of the four sry delta mutations revealed that these mutations correspond to single amino acid replacements in the sry delta protein. Three of these replacements map to the same (third out of seven) zinc finger in the carboxy-terminal DNA binding domain; interestingly, none affects the zinc finger consensus residues. The fourth mutation is located in the NH2-proximal part of the protein, in a domain proposed to be involved in specific protein-protein interactions.

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