Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA
Hashimoto, Hideharu, Wang, Dongxue, Horton, John R., Zhang, Xing, Corces, Victor G., Cheng, Xiaodong·2017·Molecular Cell
Cited by (271)
Items 201–271 of 271
- Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation MethodsYuxiang Li, Haiyang Xu, Javed M. Chitaman, Jian Feng · 2022 · Genes
- Multifaceted role of CTCF in X-chromosome inactivationLakshmi Sowjanya Bammidi, Srimonta Gayen · 2024 · Chromosoma
- Study of the N-Terminal Domain Homodimerization in Human Proteins with Zinc Finger ClustersД. В. Фурсенко, Pavel G Georgiev, Artem N. Bonchuk · 2021 · Doklady Biochemistry and Biophysics
- Loop competition and extrusion model predicts CTCF interaction specificityXi Wang, M Beer · 2021 · RePEc: Research Papers in Economics
- Loop competition and extrusion model predicts CTCF interaction specificityWang Xi, M Beer · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- A domain-resolution map of in vivo DNA binding reveals the regulatory consequences of somatic mutations in zinc finger transcription factorsBerat Doğan, Senthilkumar Kailasam, Aldo H. Corchado, Naghmeh Nikpoor, Hamed Shateri Najafabadi · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Transcriptomic and epigenomic consequences of heterozygous loss of function mutations in AKAP11 , the first large-effect shared risk gene for bipolar disorder and schizophreniaNargess Farhangdoost, Calwing Liao, Yumin Liu, Martin Alda, Patrick A. Dion, Guy Armand Rouleau, Anouar Khayachi, Boris Chaumette · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Epstein-Barr Virus Encoded lncRNAs Control the Viral Lytic SwitchZhi‐Xuan Li, Yifei Liao, Weiyue Ding, Davide Maestri, Scott L. Grote, Gabriel A. Romero Agosto, Laura A. Murray‐Nerger, Rui Guo, Bo Zhao, Silvi Rouskin et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Selective targeting of genes regulated by zinc finger proteins in endometriosis and endometrioid adenocarcinoma by zinc niflumato complex with neocuproineIvana Špaková, Lukáš Smolko, Gabriela Sabolová, Zuzana Badovská, Katarína Kalinová, Corina T. Madreiter‐Sokolowski, Wolfgang F. Graier, Mária Mareková, Janka Vašková, Miroslava Rabajdová · 2025 · Scientific Reports
- Positional distribution of transcription factor binding sites in the human genomeChun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen‐Hsiung Li · 2025 · PLoS ONE
- Ectopic Recruitment of the CTCF N-Terminal Domain with Two Proximal Zinc-Finger Domains as a Tool for 3D Genome EngineeringEugenia 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
- CTCF couples long-range loop extrusion and diffusion to mediate a diverse Igκ repertoireEmma 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
- Cooperation between architectural C2H2 proteins in CP190 recruitment to Drosophila regulatory elementsOksana Maksimenko, Natalia Klimenko, Ghadeer Salloum, Anastasia Umnova, Olga Kyrchanova, Larisa N. Melnikova, Pavel G Georgiev · 2025 · Epigenetics & Chromatin
- Epigenetics of Genes Displaying High and Preferential Expression in MyoblastsKenneth C. Ehrlich, Michelle R. Lacey, Sriharsa Pradhan, Melanie Ehrlich · 2026 · Epigenomes
- NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architectureWenju Sun, Nan Wu, Minhui Xia, Yilin Pan, Meishuo Liu, Shaorong Fan, Jueheng Wang, Yitian Zeng, Ligang Fan, Jie Chen et al. · 2026 · Molecular Cell
- Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased mannerTianjie Li, Jingwei Li, Leyang Wang, Haiyan Huang, Qiang Wu · 2026 · PLoS Genetics
- Influence of AtROS1 demethylase on transcription factors involved in tobacco plant defensePoonam Bharti, Sudesh Kumar Yadav, Vipin K. Hallan · 2022 · Journal of Plant Biochemistry and Biotechnology
- Binding of Cys2His2 transcription factors with operator DNA: functional role of linkers between Zn-fingersYuri N. Chirgadze, Victor V. Ivanov · 2019 · Journal of Biomolecular Structure and Dynamics
- The CTCF Anatomy of Topologically Associating DomainsLuca Nanni, Cheng Wang, Freek Manders, Laszlo A. Groh, Paula Haro, Roel Oldenkamp, Stefano Ceri, Colin Logie · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- ADNP Modulates SINE B2-Derived CTCF-Binding Sites during Blastocyst Formation in MouseWen 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)
- Brain and cancer associated binding domain mutations provide insight into CTCF’s relationship with chromatin and its ability to act as a chromatin organizerJane 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
- Cell-Type-Specific Transposable Element Demethylation and TAD Remodeling in the Aging Mouse BrainQiurui Zeng, Wei Tian, Amit Klein, Anna Bartlett, Hanqing Liu, Joseph R. Nery, Rosa Castanon, Julia K. Osteen, Nicholas D. Johnson, Wenliang Wang et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- DNA sequence quantitatively encodes CTCF-binding affinity at genome scaleZihang 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)
- Euplotid: A quantized geometric model of the eukaryotic cellDiego Borges-Rivera · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- The Effect of rs77275268 on Gene Expression at the Transcriptional Hub at 6q25.1Sarah Mackie · 2020 · Otago University Research Archive (University of Otago)
- Cancer methylomes characterization enabled by Rocker-methMatteo Benelli, Gian Marco Franceschini, Alberto Magi, Dario Romagnoli, Chiara Biagioni, Ilenia Migliaccio, Luca Malorni, Angelo Di Leo, Francesca Demichelis · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- CTCF zinc finger mutations produce cellular phenotypes explained by structure-function relationshipsCharles 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
- 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 SequenceOlivier Boisvert, Danny Létourneau, Patrick Delattre, Cynthia Tremblay, Émilie Jolibois, Martin Montagne, Pierre Lavigne · 2021 · SSRN Electronic Journal
- 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
- The rescue of epigenomic abnormalities in ICF1 patient iPSCs following DNMT3B correction is incomplete at a residual fraction of H3K4me3-enriched regionsVarsha Poondi Krishnan, Barbara Morone, Shir Toubiana, Monika Krzak, Maria Strazzullo, Claudia Angelini, Sara Selig, Maria Rosaria Matarazzo · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- DNA binding domain undergoes dynamic and selective protein–protein interactions to facilitate CTCF insulationZhou 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)
- Identification of a Novel Mutation in CTCF in a Family with MRD21Yimeng Qiao, Baiyun Chen, Yanqiang Han, Yangong Wang, Jin Zhang, Yu Su, Ye Cheng, Ting Wang, Jian Ding, Simin Ye et al. · 2022 · Research Square
- Data from Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer TherapyFatemeh Amjadi‐Moheb, Alireza Paniri, Haleh Akhavan‐Niaki · 2023
- Additional file 1 of The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebratesJohn J. Lees, Fábio Pértille, Pia Katrine Løtvedt, Jensen, Per, Carlos Guerrero‐Bosagna · 2023 · Figshare
- Using Free Energy-Based Modeling to Predict Chromatin Loops in the Human GenomeWayne Dawson, Michał Łaźniewski, Dariusz Plewczyński · 2024 · Elsevier eBooks
- Structural insights into the recognition of purine‐pyrimidine dinucleotide repeats by zinc finger protein ZBTB43Yang Yang, Shuting Zhang, Li Xu, Yan Pan, Yumi Xuan, Yuanzhong Kai, Xuemin Chen · 2024 · FEBS Journal
- DNA methylation insulates genic regions from CTCF loops near nuclear specklesShelby A Roseman, Allison P. Siegenfeld, Ceejay Lee, Nicholas Z. Lue, Amanda L. Waterbury, Brian B. Liau · 2024 · eLife
- C.La.P.: Enhancing transformer-based genomic signal modeling by integrating DNA sequences and chromatin accessibility dataPanos Firbas, Carolina de Souza Thimoteo Gonçalves, Gonzalo G. de Polavieja · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Epigenetic machineryRamón Cacabelos, Iván Tellado, Natalia Cacabelos, Olaia A. Martínez-Iglesias, Vinogran Naidoo · 2025 · Elsevier eBooks
- DNA methylation insulates genic regions from CTCF loops near nuclear specklesShelby A Roseman, Allison P. Siegenfeld, Ceejay Lee, Nicholas Z. Lue, Amanda L. Waterbury, Brian B. Liau · 2025 · eLife
- Additional file 4 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulationJudith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Li, Chunliang · 2024 · Figshare
- Additional file 3 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulationJudith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Li, Chunliang · 2024 · Figshare
- Additional file 1 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selectionZhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
- Additional file 4 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionalitySofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
- Additional file 2 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selectionZhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
- Additional file 2 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulationJudith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
- Additional file 5 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulationJudith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
- Additional file 2 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionalitySofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
- Additional file 1 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionalitySofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
- Additional file 2 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cellsSun, Daijing, Yueyan Zhu, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
- Additional file 3 of Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selectionZhilian Jia, Jingwei Li, Xiao Ge, Wu, Yonghu, Guo, Ya, Wu, Qiang · 2020 · Figshare
- Additional file 3 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cellsSun, Daijing, Yueyan Zhu, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
- Additional file 1 of SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cellsSun, Daijing, Zhu, Yueyan, Peng, Wenzhu, Zheng, Shenghui, Jie Weng, Shulong Dong, Li, Jiaqi, Chen, Qi, Chuanhui Ge, Liao, Liyong et al. · 2024 · Figshare
- Additional file 1 of Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1–2Irene M. Kaplow, Abhimanyu Banerjee, Chuan Sheng Foo · 2022 · Figshare
- Additional file 3 of The N-terminal dimerization domains of human and Drosophila CTCF have similar functionalitySofia Kamalyan, Olga Kyrchanova, Klimenko, Natalia, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Maksimenko, Oksana, Pavel G Georgiev · 2024 · Figshare
- Additional file 1 of Auxin-inducible degron 2 system deciphers functions of CTCF domains in transcriptional regulationJudith W. Hyle, Mohamed Nadhir Djekidel, Williams, Justin, Shaela Wright, Shao, Ying, Xu, Beisi, Chunliang Li · 2024 · Figshare
- An H4K20me3-CTCF switch at stable TAD boundaries enforces reversible cell state transitionsKaiser 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)
- An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activitySarion R. Bowers, Peter N. Cockerill · 2026 · PLoS ONE
- Pathology of Methylation, Demethylation, and Methylated DNA Binding MachineryО. А. Земляная, V. V. Strelnikov, Dmitry V. Zaletaev · 2026 · Molecular Biology
- DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cellsJulie Segueni · 2024 · theses.fr (ABES)
- Molecular Mimics: How Viral Genomes Dupe Their Host by Usurping CTCF to Establish InfectionClairine I. S. Larsen, Rhiannon R. Abrahams, Kinjal Majumder · 2026 · Viruses
- Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifsJisun 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)
- Dynamic CTCF bridges drive genome organizationColleen 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)
- Disruption of CTCF binding by germline non-coding variants in CDKN2B suppress CDKN2A expression and predispose to melanomaJessica 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
- CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individualsValmik Ranparia, Geoffrey Fudenberg, Mark Chaisson · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- DNA methylation and histone modifications in tumor hypoxiaShruti Ganesh Dhamdhere, Parik Kakani, Sanjeev Shukla · 2026 · Methods in enzymology on CD-ROM/Methods in enzymology
- Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and allelesOberon Dixon-Luinenburg, Ayesha Bajwa, Mitchell Robert Vollger, Andrew Stergachis, Aaron Streets, Nilah M. Ioannidis · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- RNAPII and XPC remodel the 3D genome for UV repairVeysel Oğulcan Kaya, Mustafa Malkoç, Lucian-Alexandru Todirica, Ogün Adebalı, Hanspeter Naegeli, Michelle N. Yancoskie · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factorsHaining Chen, Jordan Krebs, Olivia W. Lang, Jiayi Hu, Devin C Mellini, Judith W. Hyle, Chunliang Li, William Lai, B. Franklin Pugh · 2026 · Molecular Cell
- Comprehensive landscape of potential CTCF-binding sites across the complete telomere-to-telomere human genomeEleftherios Bochalis, Ilias Georgakopoulos‐Soares · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
- A Genotype–Phenotype Analysis of Four Chinese Children Carrying Distinct Pathogenic Variants in the CTCF GeneJuan Du, Muhan Li, Aimin Liang, Mingyan Hei, Xiaotun Ren · 2026 · Genes