Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

Hideharu Hashimoto; Dongxue Wang; John R. Horton; Xing Zhang; Victor G. Corces; Xiaodong Cheng

doi:10.1016/j.molcel.2017.05.004

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces, Xiaodong Cheng

Research output: Contribution to journal › Article › peer-review

154 Scopus citations

Abstract

The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3–7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.

Original language	English (US)
Pages (from-to)	711-720.e3
Journal	Molecular cell
Volume	66
Issue number	5
DOIs	https://doi.org/10.1016/j.molcel.2017.05.004
State	Published - Jun 1 2017

Keywords

C2H2 zinc-finger arrays
CTCF
DNA methylation
DNA-binding adaptability to sequence variations
epigenetics
protein-DNA recognition

ASJC Scopus subject areas

Molecular Biology
Cell Biology

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10.1016/j.molcel.2017.05.004

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title = "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA",

abstract = "The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3–7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.",

keywords = "C2H2 zinc-finger arrays, CTCF, DNA methylation, DNA-binding adaptability to sequence variations, epigenetics, protein-DNA recognition",

author = "Hideharu Hashimoto and Dongxue Wang and Horton, {John R.} and Xing Zhang and Corces, {Victor G.} and Xiaodong Cheng",

note = "Funding Information: We thank B. Baker of New England Biolabs for synthesizing the oligos; Yiwei Liu for initial work on CTCF; Yusuf Olatunde Olanrewaju, John Shanks, and Alison Setili for help with protein purifications; Robert M. Blumenthal for comments; and Lanlan Shen for discussion. The Department of Biochemistry of Emory University School of Medicine supported the use of SER-CAT beamlines. This work was supported by a grant from the NIH (GM049245-23) to X.Z. and X.C. Publisher Copyright: {\textcopyright} 2017 Elsevier Inc.",

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doi = "10.1016/j.molcel.2017.05.004",

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AU - Horton, John R.

AU - Zhang, Xing

AU - Corces, Victor G.

AU - Cheng, Xiaodong

N1 - Funding Information: We thank B. Baker of New England Biolabs for synthesizing the oligos; Yiwei Liu for initial work on CTCF; Yusuf Olatunde Olanrewaju, John Shanks, and Alison Setili for help with protein purifications; Robert M. Blumenthal for comments; and Lanlan Shen for discussion. The Department of Biochemistry of Emory University School of Medicine supported the use of SER-CAT beamlines. This work was supported by a grant from the NIH (GM049245-23) to X.Z. and X.C. Publisher Copyright: © 2017 Elsevier Inc.

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N2 - The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3–7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.

AB - The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3–7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein. These interactions compensate for deviations from the consensus sequence, allowing CTCF to adapt to sequence variations. CTCF is sensitive to cytosine methylation at position 2, but insensitive at position 12 of the 15-bp core sequence. These differences can be rationalized structurally. Although included in crystallizations, ZF10 and ZF11 are not visible, while ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to overall binding stability.

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KW - protein-DNA recognition

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Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

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