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Author Notes:

Work Phone :404-727-8491 FAX : 404-727-3746 E-mail Address : xcheng@emory.edu

Y.L. performed crystallographic and DNAbinding experiments; Y.O.O. performed protein purification and helped with fluorescence polarization assays; Y.Z. analyzed published Klf4 ChIP-seq profiles; H.H. performed binding assays with unmodified and hemimethylated DNA; X.Z. initiated this project and together with X.C. organized and designed the scope of the study; R.M.B. and X.C. examined potential to predict methyl-CpG binding proteins from the primary sequences.

And all were involved in analyzing data and preparing the manuscript.

The authors thank Brenda Baker at the organic synthesis unit of New England Biolabs for synthesizing the oligonucleotides.

Conflict of interest statement. None declared.

Subjects:

Research Funding:

National Institutes of Health (NIH) [GM049245-20 to X.C.]

The Emory University School of Medicine supported the use of Southeast Regional Collaborative Access Team (SER-CAT) 22-BM beamline at the Advanced Photon Source, Argonne National Laboratory.

Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science

Georgia Research Alliance Eminent Scholar (to X.C.)

Funding for open access charge: Waived by Oxford University Press.

Structural basis for Klf4 recognition of methylated DNA

Tools:

Journal Title:

Nucleic Acids Research

Volume:

Volume 42, Number 8

Publisher:

, Pages 4859-4867

Type of Work:

Article | Final Publisher PDF

Abstract:

Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg–Glu pair.

Copyright information:

© The Author(s) 2014. Published by Oxford University Press.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 3.0 Unported License (http://creativecommons.org/licenses/by/3.0/).

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