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Author Notes:

To whom correspondence should be addressed. Tel: +1 713 834 6274; Email: xcheng5@mdanderson.org

Correspondence may also be addressed to Taiping Chen. Tel: +1 512 237 9479; Email: tchen2@mdanderscon.org

The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

Author Contributions: R.R. performed protein purification, DNA-binding experiments, crystallization and X-ray data collection;

J.R.H. performed X-ray data collection and structure determination;

S.H. generated Zbtb24- and Cdca7-deficient mESC lines and stable mESC clones expressing WT and mutant ZBTB24 and performed molecular and cellular experiments to characterize the ICF2 missense mutations;

Y.Z. participated in molecular and cellular experiments;

A.K.S. performed ChIP; L.D.C. performed deep sequencing under the supervision of J.S;

Y.L. and K.L. performed bioinformatics analysis;

H.H. made expression constructs and performed protein purification and DNA binding assays;

C.S.L.K. and R.R. generated R390S mutant;

X.Z. participated in experimental design and discussions throughout the study;

T.C. and X.C. conceived the project, supervised the experimental work and wrote the manuscript.

We thank Z. Ying, B. Liu, H. Zhao, N. Veland, J. Dan and T. Hamidi in the Chen laboratory for discussion and technical assistance, B. Baker at New England Biolabs for synthesizing oligonucleotides, and A. Setili and Y. Cao in the Cheng laboratory for help with protein purification and technique supports.

Conflict of interest statement. None declared.

Subjects:

Research Funding:

U.S. National Institutes of Health (NIH) [1R01AI1214030A1 to T.C.; GM049245-24 to X.C.;

CA16672 to the CCSG Cores at MD Anderson Cancer Center];

the Cancer Prevention and Research Institute of Texas [RR160029 to X.C., RP170002 to J.S.]

Thomas Endowment fellowship (to Y.Z.).

Funding for open access charge: NIH.

Keywords:

  • Science & Technology
  • Life Sciences & Biomedicine
  • Biochemistry & Molecular Biology
  • ZINC-FINGER
  • IMMUNODEFICIENCY SYNDROME
  • CENTROMERIC INSTABILITY
  • CHROMOSOME INSTABILITY
  • FACIAL ANOMALIES
  • ICF
  • METHYLATION
  • RECOGNITION
  • MUTATIONS
  • DNMT3A

Structural basis of specific DNA binding by the transcription factor ZBTB24

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Journal Title:

Nucleic Acids Research

Volume:

Volume 47, Number 16

Publisher:

, Pages 8388-8398

Type of Work:

Article | Final Publisher PDF

Abstract:

ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes-the other three being DNMT3B, CDCA7 and HELLS-that are mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a genetic disorder characterized by DNA hypomethylation and antibody deficiency. The molecular mechanisms by which ZBTB24 regulates gene expression and the biological functions of ZBTB24 are poorly understood. Here, we identified a 12-bp consensus sequence [CT(G/T)CCAGGACCT] occupied by ZBTB24 in the mouse genome. The sequence is present at multiple loci, including the Cdca7 promoter region, and ZBTB24 binding is mostly associated with gene activation. Crystallography and DNA-binding data revealed that the last four of the eight zinc fingers (ZFs) (i.e. ZF5-8) in ZBTB24 confer specificity of DNA binding. Two ICF missense mutations have been identified in the ZBTB24 ZF domain, which alter zinc-binding cysteine residues. We demonstrated that the corresponding C382Y and C407G mutations in mouse ZBTB24 abolish specific DNA binding and fail to induce Cdca7 expression. Our analyses indicate and suggest a structural basis for the sequence specific recognition by a transcription factor centrally important for the pathogenesis of ICF syndrome.

Copyright information:

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/).
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