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

Cited by (271)

Items 201–271 of 271

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    Yuxiang Li, Haiyang Xu, Javed M. Chitaman, Jian Feng · 2022 · Genes
  2. Multifaceted role of CTCF in X-chromosome inactivation
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  3. Study of the N-Terminal Domain Homodimerization in Human Proteins with Zinc Finger Clusters
    Д. В. Фурсенко, Pavel G Georgiev, Artem N. Bonchuk · 2021 · Doklady Biochemistry and Biophysics
  4. Loop competition and extrusion model predicts CTCF interaction specificity
    Xi Wang, M Beer · 2021 · RePEc: Research Papers in Economics
  5. Loop competition and extrusion model predicts CTCF interaction specificity
    Wang Xi, M Beer · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  6. A domain-resolution map of in vivo DNA binding reveals the regulatory consequences of somatic mutations in zinc finger transcription factors
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  10. Positional distribution of transcription factor binding sites in the human genome
    Chun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen‐Hsiung Li · 2025 · PLoS ONE
  11. Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome Engineering
    Eugenia A. Tiukacheva, Artem V. Luzhin, Natalia A. Kruglova, Anastasia S. Shtompel, Grigorii Antonov, Anna V. Tvorogova, Yegor S Vassetzky, Sergey V. Ulianov, Sergey V. Razin · 2025 · International Journal of Molecular Sciences
  12. CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoire
    Emma L. Bush, Brigette Berke-Reynolds, Kaitlyn M. Hutchins, Xinrui Yu, Jorge A. Colón-Rosado, Fu‐Jung Chang, John Curran, Jiaxin Yang, Liangliang Sun, Jianrong Wang et al. · 2025 · Nature Communications
  13. Cooperation between architectural C2H2 proteins in CP190 recruitment to Drosophila regulatory elements
    Oksana Maksimenko, Natalia Klimenko, Ghadeer Salloum, Anastasia Umnova, Olga Kyrchanova, Larisa N. Melnikova, Pavel G Georgiev · 2025 · Epigenetics & Chromatin
  14. Epigenetics of Genes Displaying High and Preferential Expression in Myoblasts
    Kenneth C. Ehrlich, Michelle R. Lacey, Sriharsa Pradhan, Melanie Ehrlich · 2026 · Epigenomes
  15. NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture
    Wenju Sun, Nan Wu, Minhui Xia, Yilin Pan, Meishuo Liu, Shaorong Fan, Jueheng Wang, Yitian Zeng, Ligang Fan, Jie Chen et al. · 2026 · Molecular Cell
  16. Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased manner
    Tianjie Li, Jingwei Li, Leyang Wang, Haiyan Huang, Qiang Wu · 2026 · PLoS Genetics
  17. Influence of AtROS1 demethylase on transcription factors involved in tobacco plant defense
    Poonam Bharti, Sudesh Kumar Yadav, Vipin K. Hallan · 2022 · Journal of Plant Biochemistry and Biotechnology
  18. Binding of Cys2His2 transcription factors with operator DNA: functional role of linkers between Zn-fingers
    Yuri N. Chirgadze, Victor V. Ivanov · 2019 · Journal of Biomolecular Structure and Dynamics
  19. The CTCF Anatomy of Topologically Associating Domains
    Luca Nanni, Cheng Wang, Freek Manders, Laszlo A. Groh, Paula Haro, Roel Oldenkamp, Stefano Ceri, Colin Logie · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  20. ADNP Modulates SINE B2-Derived CTCF-Binding Sites during Blastocyst Formation in Mouse
    Wen Wang, Rui Gao, Dongxu Yang, Mingli Ma, Ruge Zang, Xiangxiu Wang, Chuan Chen, Jiayu Chen, Xiaochen Kou, Yanhong Zhao et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  21. Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizer
    Jane A. Skok, Catherine Do, Guimei Jiang, Giulia Cova, Christos C. Katsifis, Domenic N. Narducci, Jie Yang, Theodore Sakellaropoulos, Raphael Silveira Vidal, Priscillia Lhoumaud et al. · 2024 · Research Square
  22. Cell-Type-Specific Transposable Element Demethylation and TAD Remodeling in the Aging Mouse Brain
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  23. DNA sequence quantitatively encodes CTCF-binding affinity at genome scale
    Zihang Yin, Yefan Wang, Guojun Hou, Yuqiao Chen, Huaijin Feng, Jin Zhu, Yufan Xie, Ruoxi Wang, Zhiyu Zhang, Tao Wu et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Euplotid: A quantized geometric model of the eukaryotic cell
    Diego Borges-Rivera · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  25. The Effect of rs77275268 on Gene Expression at the Transcriptional Hub at 6q25.1
    Sarah Mackie · 2020 · Otago University Research Archive (University of Otago)
  26. Cancer methylomes characterization enabled by Rocker-meth
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  27. CTCF zinc finger mutations produce cellular phenotypes explained by structure-function relationships
    Charles G. Bailey, Shailendra K. Gupta, Cynthia Metierre, Punkaja Amarasekara, Patrick O’Young, Wunna Kyaw, Tatyana Laletin, Habib Francis, Crystal Semaan, Krishna Singh et al. · 2021 · Research Square
  28. A Non-Canonical Linker between Zinc Fingers 10 and 11 of Miz-1 Promotes Conformational Exchange: Implications for the Mechanism of Recognition of the Consensus DNA Sequence
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  29. Faculty Opinions recommendation of RNA Interactions Are Essential for CTCF-Mediated Genome Organization.
    Cigall Kadoch · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  30. The rescue of epigenomic abnormalities in ICF1 patient iPSCs following DNMT3B correction is incomplete at a residual fraction of H3K4me3-enriched regions
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  31. DNA binding domain undergoes dynamic and selective protein–protein interactions to facilitate CTCF insulation
    Zhou Rong, Kai Tian, Huang Jie, Wenjia Duan, Hongye Fu, Ying Feng, Hui Wang, Yongpeng Jiang, Li Yuanjun, Rui Wang et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Identification of a Novel Mutation in CTCF in a Family with MRD21
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  33. Data from Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy
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  34. Additional file 1 of The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates
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  35. Using Free Energy-Based Modeling to Predict Chromatin Loops in the Human Genome
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  36. Structural insights into the recognition of purine‐pyrimidine dinucleotide repeats by zinc finger protein ZBTB43
    Yang Yang, Shuting Zhang, Li Xu, Yan Pan, Yumi Xuan, Yuanzhong Kai, Xuemin Chen · 2024 · FEBS Journal
  37. DNA methylation insulates genic regions from CTCF loops near nuclear speckles
    Shelby A Roseman, Allison P. Siegenfeld, Ceejay Lee, Nicholas Z. Lue, Amanda L. Waterbury, Brian B. Liau · 2024 · eLife
  38. C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility data
    Panos Firbas, Carolina de Souza Thimoteo Gonçalves, Gonzalo G. de Polavieja · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  39. Epigenetic machinery
    Ramón Cacabelos, Iván Tellado, Natalia Cacabelos, Olaia A. Martínez-Iglesias, Vinogran Naidoo · 2025 · Elsevier eBooks
  40. DNA methylation insulates genic regions from CTCF loops near nuclear speckles
    Shelby A Roseman, Allison P. Siegenfeld, Ceejay Lee, Nicholas Z. Lue, Amanda L. Waterbury, Brian B. Liau · 2025 · eLife
  41. Additional file 4 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
    Judith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Li, Chunliang · 2024 · Figshare
  42. Additional file 3 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
    Judith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Li, Chunliang · 2024 · Figshare
  43. Additional file 1 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
    Zhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
  44. Additional file 4 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
    Sofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
  45. Additional file 2 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
    Zhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
  46. Additional file 2 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
    Judith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
  47. Additional file 5 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
    Judith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
  48. Additional file 2 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
    Sofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
  49. Additional file 1 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
    Sofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
  50. Additional file 2 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
    Sun, Daijing, Yueyan Zhu, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
  51. Additional file 3 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
    Zhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
  52. Additional file 3 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
    Sun, Daijing, Yueyan Zhu, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
  53. Additional file 1 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
    Sun, Daijing, Zhu, Yueyan, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
  54. Additional file 1 of Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1–2
    Irene M. Kaplow, Abhimanyu Banerjee, Chuan Sheng Foo · 2022 · Figshare
  55. Additional file 3 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
    Sofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
  56. Additional file 1 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulation
    Judith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
  57. An H4K20me3-CTCF switch at stable TAD boundaries enforces reversible cell state transitions
    Kaiser Atai, Mithun Mitra, Eliana Bohn, Richard Hu, Adriana Z. Corvalan, David Jelínek, Laurent Voisin, Aaron Ambrus, Kirthana Sarathy, William Mason Sparks et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  58. An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activity
    Sarion R. Bowers, Peter N. Cockerill · 2026 · PLoS ONE
  59. Pathology of Methylation, Demethylation, and Methylated DNA Binding Machinery
    О. А. Земляная, V. V. Strelnikov, Dmitry V. Zaletaev · 2026 · Molecular Biology
  60. DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cells
    Julie Segueni · 2024 · theses.fr (ABES)
  61. Molecular Mimics: How Viral Genomes Dupe Their Host by Usurping CTCF to Establish Infection
    Clairine I. S. Larsen, Rhiannon R. Abrahams, Kinjal Majumder · 2026 · Viruses
  62. Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs
    Jisun Lee, Jujun Zhou, John R. Horton, Meigen Yu, Munachi Daniella Muoghalu, Faizan Ahmed Khan, Xiaotian Zhang, Yun Huang, Robert Blumenthal, Xiaodong Cheng et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  63. Dynamic CTCF bridges drive genome organization
    Colleen C. Caldwell, Matilde Sá, Bram J. Hoogland, Andrea Ridolfi, Natal F. Zaghal, Chase P. Broedersz, Andreas S. Biebricher, Gijs J. L. Wuite · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. Disruption of CTCF binding by germline non-coding variants in CDKN2B suppress CDKN2A expression and predispose to melanoma
    Jessica L. Scales, Jayne A. Barbour, Alisa M. Goldstein, Rebecca Hennessey, Mai Xu, Abigail J Dennis, Sophie Papiernik, Jung Kim, Sudipto Das, Haocheng Yang et al. · 2026 · medRxiv
  65. CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals
    Valmik Ranparia, Geoffrey Fudenberg, Mark Chaisson · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  66. DNA methylation and histone modifications in tumor hypoxia
    Shruti Ganesh Dhamdhere, Parik Kakani, Sanjeev Shukla · 2026 · Methods in enzymology on CD-ROM/Methods in enzymology
  67. Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles
    Oberon Dixon-Luinenburg, Ayesha Bajwa, Mitchell Robert Vollger, Andrew Stergachis, Aaron Streets, Nilah M. Ioannidis · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  68. RNAPII and XPC remodel the 3D genome for UV repair
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  69. Genome-wide rotational and translational phasing of nucleosomes with human transcription factors
    Haining Chen, Jordan Krebs, Olivia W. Lang, Jiayi Hu, Devin C Mellini, Judith W. Hyle, Chunliang Li, William Lai, B. Franklin Pugh · 2026 · Molecular Cell
  70. Comprehensive landscape of potential CTCF-binding sites across the complete telomere-to-telomere human genome
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  71. A Genotype–Phenotype Analysis of Four Chinese Children Carrying Distinct Pathogenic Variants in the CTCF Gene
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