Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA
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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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This selective sensitivity to 5mC can be explained by the biophysical properties of CTCF's 11 zinc fingers, which make it sensitive to methylation of specific cytosines in its binding motif.
“This selective 5mC sensitivity can be explained by the different biophysical property of CTCF’s 11 zinc fingers leading to its sensitivity to specific cytosine within its binding motif being methylated (31).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [31]
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LATS kinase–mediated CTCF phosphorylation and selective loss of genomic binding
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Structures of CTCF–DNA complexes including all 11 zinc fingers
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Self-citationCTCF binding modulates UV damage formation to promote mutation hot spots in melanoma
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- Authors
- Hashimoto, H., Wang, D., Horton, J. R., Zhang, X., Corces, V. G., & Cheng, X.
- Affiliations
- Emory University (US)
- The University of Texas MD Anderson Cancer Center (US)
- Corresponding author
- Cheng, Xiaodong
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2017-06
- Volume
- 66
- Issue
- 5
- Pages
- 711-720.e3
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC5542067
- OpenAlex
- W2614347829
- Cited by
- 268
- References
- 49
- Citations by year
- 2026: 21 · 2025: 28 · 2024: 36 · 2023: 27 · 2022: 29 · 2021: 31 · 2020: 37 · 2019: 30 · 2018: 24 · 2017: 5
- FWCI
- 10.72
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH (GM049245-23)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- CTCF, zinc finger DNA-binding domain, cytosine methylation, sequence specificity, consensus sequence, hydrogen bonding, chromatin organization, protein-DNA interactions
- MeSH terms
- CCCTC-Binding Factor, Binding Sites, Cloning, Molecular, DNA, Humans, Hydrogen Bonding, Models, Molecular, Nucleic Acid Conformation, Protein Binding, Repressor Proteins, Structure-Activity Relationship, Zinc Fingers, Crystallography, X-Ray, Trinucleotide Repeats, DNA Methylation, 5-Methylcytosine, Protein Stability
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