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
DOI 10.1016/j.molcel.2017.05.004

Cited by (271)

Items 101–200 of 271

  1. Cys2His2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA
    Amelia J. Hodges, Nicholas O. Hudson, Bethany A. Buck‐Koehntop · 2019 · Journal of Molecular Biology
  2. Deep phylogeny of cancer drivers and compensatory mutations
    Nash D. Rochman, Yuri I. Wolf, Eugene V. Koonin · 2020 · Communications Biology
  3. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target
    Daria Kaplun, Dmitry N. Kaluzhny, Egor Prokhortchouk, Svetlana V. Zhenilo · 2023 · Acta Naturae
  4. Engineering of Zinc Finger Nucleases Through Structural Modeling Improves Genome Editing Efficiency in Cells
    Shota Katayama, Masahiro Watanabe, Yoshio Kato, Wataru Nomura, Takashi Yamamoto · 2024 · Advanced Science
  5. A tour of 3D genome with a focus on CTCF
    Diane C. Wang, William Yang Wang, Linlin Zhang, Xiangdong Wang · 2018 · Seminars in Cell and Developmental Biology
  6. Regulation of CTCF loop formation during pancreatic cell differentiation
    Xiaowen Lyu, M. Jordan Rowley, Michael J. Kulik, Stephen Dalton, Victor G. Corces · 2023 · Nature Communications
  7. Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF
    Mariangela Valletta, Rosita Russo, Ilaria Baglivo, Veronica Russo, Sara Ragucci, Annamaria Sandomenico, Emanuela Iaccarino, Menotti Ruvo, Italia De Feis, Claudia Angelini et al. · 2020 · International Journal of Molecular Sciences
  8. The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes
    L. S. Melnikova, Pavel G Georgiev, Anton K. Golovnin · 2020 · Acta Naturae
  9. Effects of DNA Methylation on TFs in Human Embryonic Stem Cells
    Ximei Luo, Tianjiao Zhang, Yixiao Zhai, Fang Wang, Shumei Zhang, Guohua Wang · 2021 · Frontiers in Genetics
  10. SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data
    Sitara Persad, Zi-Ning Choo, Christine Dien, Ignas Masilionis, Ronan Chaligné, Tal Nawy, Chrysothemis C. Brown, Itsik Pe’er, Manu N. Setty, Dana Pe’er · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  11. Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits
    Min Wang, Timothy Hancock, Amanda Jane Chamberlain, Christy J. Vander Jagt, J.E. Pryce, Benjamin G. Cocks, Michael Edward Goddard, Ben J. Hayes · 2018 · BMC Genomics
  12. The impact of the embryonic DNA methylation program on CTCF-mediated genome regulation
    Ana Monteagudo-Sánchez, Julien Richard Albert, Margherita Scarpa, D. Noordermeer, Maxim V. C. Greenberg · 2024 · Nucleic Acids Research
  13. CTCF: an R/bioconductor data package of human and mouse CTCF binding sites
    Mikhail G. Dozmorov, Wancen Mu, Eric S. Davis, Stuart A. Lee, Timothy J. Triche, Douglas H. Phanstiel, Michael I. Love · 2022 · Bioinformatics Advances
  14. Disease‐associated missense variants in ZBTB18 disrupt DNA binding and impair the development of neurons within the embryonic cerebral cortex
    Isabel Anne Hemming, Olivier Clément, Ivan Enghian Gladwyn-Ng, Hayley Daniella Cullen, Han Leng Ng, Heng B. See, Linh Ngo, Daniela Ulgiati, Kevin D. G. Pfleger, Mark Agostino et al. · 2019 · Human Mutation
  15. Repression of TERRA Expression by Subtelomeric DNA Methylation Is Dependent on NRF1 Binding
    Gabriel Le Berre, Virginie Hossard, Jean‐François Riou, Anne‐Laure Guieysse‐Peugeot · 2019 · International Journal of Molecular Sciences
  16. ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice
    Wen Wang, Rui Gao, Dongxu Yang, Mingli Ma, Ruge Zang, Xiangxiu Wang, Chuan Chen, Xiao-Chen Kou, Yan-Hong Zhao, Jia-Yu Chen et al. · 2024 · Genes & Development
  17. Structural basis of human PR/SET domain 9 (PRDM9) allele C–specific recognition of its cognate DNA sequence
    Patel, Anamika, Zhang, Xing, Blumenthal, Robert M., Cheng, Xiaodong · 2017 · Journal of Biological Chemistry
  18. Structural insights into DNA loop extrusion by SMC protein complexes
    Sumanjit Datta, Léa Lecomte, Christian H. Haering · 2020 · Current Opinion in Structural Biology
  19. Competitive regulation by transcription factors and DNA methylation in the bovine SIRT5 promoter: Roles of E2F4 and KLF6
    Jieyun Hong, Xiaoyu Wang, Chugang Mei, Linsen Zan · 2018 · Gene
  20. Expansion of the genotypic and phenotypic spectrum of CTCF ‐related disorder guides clinical management: 43 new subjects and a comprehensive literature review
    Hannah Gabriela Valverde de Morales, Hsiao‐Lin V. Wang, Kathryn B. Garber, Xiaodong Cheng, Victor G. Corces, Hong Li · 2022 · American Journal of Medical Genetics Part A
  21. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer
    Mahmoud Adel Bassal · 2023 · Biomolecules
  22. Mechanism of REST/NRSF regulation of clustered protocadherin α genes
    Yuanxiao Tang, Zhilian Jia, Honglin Xu, Lin‐Tai Da, Qiang Wu · 2021 · Nucleic Acids Research
  23. On the dependent recognition of some long zinc finger proteins
    Zheng Zuo, Timothy Billings, Michael Walker, Petko M. Petkov, Polly Morrell Fordyce, Gary D. Stormo · 2023 · Nucleic Acids Research
  24. ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network
    Chongil Yi, Yuka Kitamura, So Maezawa, Satoshi H. Namekawa, Bradley Robert Cairns · 2025 · Nature Structural & Molecular Biology
  25. Biallelic variants in ZNF142 lead to a syndromic neurodevelopmental disorder
    Maria Bejerholm Christensen, Amanda M. Levy, Nazanin A. Mohammadi, Marcello Niceta, Rauan B. Kaiyrzhanov, Maria Lisa Dentici, Chadi Al Alam, Viola Alesi, Valérie Benoît, Kailash P. Bhatia et al. · 2022 · Clinical Genetics
  26. SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells
    Daijing Sun, Yueyan Zhu, Wenzhu Peng, Shenghui Zheng, Jie Weng, Shulong Dong, Jiaqi Li, Qi Chen, Chuanhui Ge, Liyong Liao et al. · 2024 · Genome biology
  27. Insights into the Links between MYC and 3D Chromatin Structure and Epigenetics Regulation: Implications for Cancer Therapy
    Fatemeh Amjadi‐Moheb, Alireza Paniri, Haleh Akhavan‐Niaki · 2021 · Cancer Research
  28. Definition of clinical gene tests
    CSGT group, Duojiao Wu, Yunfeng Cheng, Xiangdong Wang · 2019 · Cell Biology and Toxicology
  29. Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia
    Ren Ren, John R. Horton, Qin Chen, Jie Yang, Bin Liu, Yun Huang, Robert Blumenthal, Xing Zhang, Xiaodong Cheng · 2023 · Journal of Biological Chemistry
  30. Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer
    Sarah Preston‐Alp, Lisa Beatrice Caruso, Chenhe Su, Kelsey Keith, Samantha S. Soldan, Davide Maestri, Jozef Madžo, Andrew V. Kossenkov, Giorgia Napoletani, Benjamin E. Gewurz et al. · 2023 · mBio
  31. CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation
    Md Tajmul, Dharmendra Nath Bhatt, Luminiţa Ruje, Emma Price, Yon Ju Ji, Dmitri I. Loukinov, Vladimir B. Teif, Victor V. Lobanenkov, Elena M. Pugacheva · 2025 · Nucleic Acids Research
  32. DNA Methylation and Transcription Factors Competitively Regulate SIRT4 Promoter Activity in Bovine Adipocytes: Roles of NRF1 and CMYB
    Jieyun Hong, Xiaoyu Wang, Chugang Mei, Hongbao Wang, Linsen Zan · 2018 · DNA and Cell Biology
  33. A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences
    Evgenia N. Nikolova, Robyn L. Stanfield, H. Jane Dyson, Peter E. Wright · 2020 · Biochemistry
  34. Charting differentially methylated regions in cancer with Rocker-meth
    Matteo Benelli, Gian Marco Franceschini, Alberto Magi, Dario Romagnoli, Chiara Biagioni, Ilenia Migliaccio, Luca Malorni, Francesca Demichelis · 2021 · Communications Biology
  35. Role of DNA De-methylation intermediate ‘5-hydroxymethylcytosine’ in ovarian cancer management: A comprehensive review
    Deepa Bisht, Arisha Arora, Manisha Sachan · 2022 · Biomedicine & Pharmacotherapy
  36. CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy
    Matthew T. Mawhinney, Runcong Liu, Fang Lu, Jasna Maksimoska, Kevin DAmico, Ronen Marmorstein, Paul M. Lieberman, Brigita Urbanc · 2018 · Journal of Molecular Biology
  37. Coordinate regulation by transcription factors and DNA methylation in the core promoter region of SIRT6 in bovine adipocytes
    Jieyun Hong, Chugang Mei, Shijun Li, Hongbao Wang, Chunping Zhao, Linsen Zan · 2018 · Archives of Biochemistry and Biophysics
  38. Alterations in 5hmC Level and Genomic Distribution in Aging-Related Epigenetic Drift in Human Adipose Stem Cells
    Joanna Borkowska, Anna Domaszewska-Szostek, Paulina Kołodziej, Zofia Wicik, Jacek Połosak, Буяновская Ольга Анатольевна, Łukasz Charzewski, Marek Stańczyk, Bartlomiej Henryk Noszczyk, Monika Puzianowska‐Kuźnicka · 2020 · Epigenomics
  39. 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 · bioRxiv
  40. Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation
    Hadeel Khamis, Sergei Rudnizky, Philippa Melamed, Ariel Kaplan · 2021 · Nucleic Acids Research
  41. Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation
    Yijun Tian, Alex C. Soupir, Qian Liu, Lang Wu, Chiang‐Ching Huang, Jong Y. Park, Liang Wang · 2021 · Human Molecular Genetics
  42. Proteins That Read DNA Methylation
    Ke Liu, Takashi Shimbo, Xiaosheng Song, Paul A. Wade, Jinrong Min · 2022 · Advances in experimental medicine and biology
  43. Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-à-brac - zinc finger protein ZBTB10
    Suman Wang, Ziyan Xu, Meili Li, Mengqi Lv, Siyuan Shen, Yunyu Shi, Fudong Li · 2023 · Journal of Biological Chemistry
  44. DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding
    Stacey L. Thomas, Ting-Hai Xu, Brittany L. Carpenter, Steven E. Pierce, Bradley M. Dickson, Minmin Liu, Gangning Liang, Peter A. Jones · 2023 · Nucleic Acids Research
  45. RNA interactions with CTCF are essential for its proper function
    Ricardo Saldaña-Meyer, Javier Rodriguez-Hernaez, Mayilaadumveettil Nishana, Karina Jácome-López, Elphège Pierre Nora, Benoit G. Bruneau, Mayra Furlan-Magaril, Jane A. Skok, Danny Reinberg · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
    Mayilaadumveettil Nishana, Caryn J. Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphège Pierre Nora, Sana Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  47. CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion
    I. Davidson, R. Barth, M. Zaczek, J. van der Torre, Wen Tang, Kota Nagasaka, R. Janissen, J. Kerssemakers, G. Wutz, C. Dekker et al. · 2022 · bioRxiv
  48. Genome folding by cohesin
    Shutao Qi, Zhubing Shi, Hongtao Yu · 2025 · Current Opinion in Genetics & Development
  49. Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering
    Gundeep Kaur, Ren Ren, Michal Hammel, John R. Horton, Jie Yang, Yu J Cao, Chenxi He, Fei Lan, Xianjiang Lan, Gerd A. Blobel et al. · 2023 · Nucleic Acids Research
  50. The mitoepigenome responds to stress, suggesting novel mito-nuclear interactions in vertebrates
    John J. Lees, Fábio Pértille, Pia Katrine Løtvedt, Per Jensen, Carlos Guerrero‐Bosagna · 2023 · BMC Genomics
  51. CpG island turnover events predict evolutionary changes in enhancer activity
    Acadia A. Kocher, Emily V. Dutrow, Severin Uebbing, Kristina Yim, María F. Rosales Larios, Marybeth Baumgartner, Timothy Nottoli, James P. Noonan · 2024 · Genome biology
  52. Factors that determine cell type–specific CTCF binding in health and disease
    Catherine Do, Jane A. Skok · 2024 · Current Opinion in Genetics & Development
  53. CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity
    Manthan Patel, Divyesh Patel, Subhamoy Datta, Umashankar Singh · 2020 · BMC Genetics
  54. 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 · BMC Genomics
  55. DNA-binding proteins from MBD through ZF to BEN: recognition of cytosine methylation status by one arginine with two conformations
    Xing Zhang, Robert Blumenthal, Xiaodong Cheng · 2024 · Nucleic Acids Research
  56. Multimeric transcription factor BCL11A utilizes two zinc-finger tandem arrays to bind clustered short sequence motifs
    John R. Horton, Meigen Yu, Jujun Zhou, Melody L. Tran, Rithvi R Anakal, Yue Lu, Robert Blumenthal, Xiaotian Zhang, Yun Huang, Xing Zhang et al. · 2025 · Nature Communications
  57. Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing
    Xiong Xiong, Hengye Chen, Qifan Zhang, Yangying Liu, Chenhuan Xu · 2024 · Nucleic Acids Research
  58. Natural Antisense Transcript PEBP1P3 Regulates the RNA Expression, DNA Methylation and Histone Modification of CD45 Gene
    Zhongjing Su, Guangyu Liu, Bin Zhang, Ze Lin, Dongyang Huang · 2021 · Genes
  59. The Effect of CDK6 Expression on DNA Methylation and DNMT3B Regulation
    Gerwin Heller, Sofie Nebenfuehr, Florian Bellutti, Huriye Ünal, Markus Zojer, Lisa Scheiblecker, Veronika Sexl, Karoline Kollmann · 2020 · iScience
  60. ZBTB11 dysfunction: spectrum of brain abnormalities, biochemical signature and cellular consequences
    Dulika Sumathipala, Petter Strømme, Zohreh Fattahi, Torben Lüders, Ying Sheng, Kimia Kahrizi, Ingunn Holm Einarsen, Jennifer L. Sloan, Hossein Najmabadi, Lambert van den Heuvel et al. · 2022 · Brain
  61. The geometric influence on the Cys2His2 zinc finger domain and functional plasticity
    April L. Mueller, Carles Corbi‐Verge, David O. Giganti, David M. Ichikawa, Jeffrey M. Spencer, Mark R. MacRae, Michael Garton, Philip M. Kim, Marcus B. Noyes · 2020 · Nucleic Acids Research
  62. The aberrant epigenome of DNMT3B -mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
    Varsha Poondi Krishnan, Barbara Morone, Shir Toubiana, Monika Krzak, Salvatore Fioriniello, Floriana Della Ragione, Maria Strazzullo, Claudia Angelini, Sara Selig, Maria Rosaria Matarazzo · 2023 · Genome Research
  63. Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain
    Qiurui Zeng, Wenliang Wang, Wei Tian, Amit Klein, Anna Bartlett, Hanqing Liu, Joseph R. Nery, Rosa Castanon, Julia K. Osteen, Nicholas D. Johnson et al. · 2026 · Cell
  64. Pushing the TAD boundary: Decoding insulator codes of clustered CTCF sites in 3D genomes
    Haiyan Huang, Qiang Wu · 2024 · BioEssays
  65. CCCTC-binding factor N-terminal domain regulates clustered protocadherin gene expression by enhancing cohesin processivity
    Yijun Zhang, Qiang Wu · 2025 · Journal of Biological Chemistry
  66. DNA recognition patterns of the multi-zinc-finger protein CTCF: a mutagenesis study
    Jingjing Guo, Li Ni, Jiexiong Han, Fei Pei, Tianyu Wang, Duo Lü, Jian‐Dong Jiang · 2018 · Acta Pharmaceutica Sinica B
  67. Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation
    Benjamin Lebeau, Kaiqiong Zhao, Maïka Jangal, Tiejun Zhao, Maria Guerra, Celia M.T. Greenwood, Michael Witcher · 2022 · Nucleic Acids Research
  68. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality
    Sofia Kamalyan, Olga Kyrchanova, Natalia S. Klimenko, Valentin Babosha, Yulia Vasileva, Elena Belova, Д. В. Фурсенко, Oksana G Maksimenko, Pavel G Georgiev · 2024 · Epigenetics & Chromatin
  69. Recruitment of CTCF to an Fto enhancer is responsible for transgenerational inheritance of obesity
    Yoon Hee Jung, Hsiao‐Lin V. Wang, Daniel Ruíz, Fiorella Carla Grandi, Brianna J. Bixler, Hannah Linsenbaum, Jian‐Feng Xiang, Samantha Forestier, Andrew M. Shafik, Peng Jin et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  70. Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification
    Aled Parry, Christel Krueger, Tim Lohoff, Steven Wingett, Stefan Schoenfelder, Wolf Reik · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Increasingly efficient chromatin binding of cohesin and CTCF supports chromatin architecture formation during zebrafish embryogenesis
    Jonas Coßmann, Pavel I. Kos, Vassiliki Varamogianni‐Mamatsi, Devin S. Assenheimer, Tobias A. Bischof, Timo Kuhn, Thomas Vomhof, Argyris Papantonis, Luca Giorgetti, J. Christof M. Gebhardt · 2025 · Nature Communications
  72. Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
    Michael J. Camerino, William K. Chang, Aleš Cvekl · 2024 · Epigenetics & Chromatin
  73. Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation
    Heng Zhou, Xiaoling He, Yue Xiong, Yixuan Gong, Yuanyuan Zhang, Shuangli Li, Rui Hu, Ying Li, Xu Dong Zhang, Xin Zhou et al. · 2025 · Nature Communications
  74. Quantitative analysis of ZFY and CTCF reveals dependent recognition of tandem zinc finger proteins
    Zheng Zuo, Timothy Billings, Michael Walker, Petko M. Petkov, Gary D. Stormo, Polly Morrell Fordyce · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  75. A negatively charged region within carboxy-terminal domain maintains proper CTCF DNA binding
    Lian Liu, Yuanxiao Tang, Yan Zhang, Qiang Wu · 2024 · iScience
  76. Methylation Data Analysis and Interpretation
    Yuehua Zhu, Weiguang Mao, Rezwan Hosseini, Maria D. Chikina · 2025 · Annual Review of Biomedical Data Science
  77. Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus
    Yonghu Wu, Zhilian Jia, Xiao Ge, Qiang Wu · 2020 · Science China Life Sciences
  78. Differential 3D genome architecture and imprinted gene expression: cause or consequence?
    Benoît Moindrot, Yui Imaizumi, Robert Feil · 2024 · Biochemical Society Transactions
  79. CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression
    Daniela Samaniego-Castruita, Isabella Han, Roxroy C. Morgan, S. Carpenter, Bryce Williams, Abhijit Chakraborty, Ishwar Radhakrishnan, Ferhat Ay, Samuel A. Myers, Anjana Rao et al. · 2026 · Proceedings of the National Academy of Sciences of the United States of America
  80. Biallelic loss-of-function variants in ZNF142 are associated with a robust DNA methylation signature affecting a limited number of genomic loci
    Mathis Hildonen, Andrea Ciolfi, Marco Ferilli, Camilla Cappelletti, Chadi Al Alam, David J. Amor, Tahsin Stefan Barakat, Valérie Benoît, Ohad S. Birk, Bert Louis Callewaert et al. · 2025 · European Journal of Human Genetics
  81. CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
    Kimberly Lucero, Sungwook Han, Pin‐Yao Huang, Xiang Qiu, Esteban O. Mazzoni, Danny Reinberg · 2025 · Science Advances
  82. A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes
    Ran Tang, Yiqun Li, Fang Han, Zhenzhi Li, Xiaoyu Lin, Haoxiu Sun, Xiaoqing Zhang, Qinghua Jiang, Huan Nie, Yu Li · 2022 · Frontiers in Oncology
  83. 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
  84. Srd5a1is Differentially Regulated and Methylated During Prepubertal Development in the Ovary and Hypothalamus
    Ben Bar-Sadeh, Lilach Pnueli, Sarai Keestra, Gillian R. Bentley, Philippa Melamed · 2023 · Journal of the Endocrine Society
  85. Encoding, Regression, and Classification of Transcription Factors’ Specificity and Methylation Effects
    Zheng Zuo · 2021 · OBM Genetics
  86. Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation
    Mingqi Zhou, Nancy H. Nabilsi, Anqi Wang, Marie‐Pierre L. Gauthier, Kevin O. Murray, Hassan Azari, William S. Owens, Jeremy R. B. Newman, Francisco J. Pardo-Palacios, Ana Conesa et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  87. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics
    Corriene E. Sept, Y. Esther Tak, Christian G. Cerda-Smith, Haley M. Hutchinson, Viraat Y. Goel, Marco Blanchette, Mital S. Bhakta, Anders S. Hansen, J. Keith Joung, Sarah E. Johnstone et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  88. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene
    Karim Karimi, Merel O. Mol, Sadegheh Haghshenas, Raissa Relator, Michael A. Levy, Jennifer Kerkhof, Haley McConkey, Alice S. Brooks, Evelien Zonneveld‐Huijssoon, Erica H. Gerkes et al. · 2023 · Genetics in Medicine
  89. Comprehensive metabolomic and epigenomic characterization of microsatellite stable BRAF-mutated colorectal cancer
    Aurora Taira, Mervi Aavikko, Riku Katainen, Eevi Kaasinen, Niko Välimäki, Janne Ravantti, Ari P. Ristimaki, Toni T. Seppälä, Laura Renkonen‐Sinisalo, Anna Lepistö et al. · 2025 · Oncogene
  90. The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteins
    Alan G. Herbert · 2025 · Open Biology
  91. Regulation of loop extrusion on the interphase genome
    Hyogyung Shin, Yoori Kim · 2023 · Critical Reviews in Biochemistry and Molecular Biology
  92. Protein Hyperacylation Links Mitochondrial Dysfunction with Nuclear Organization
    John A. Smestad, Micah J. McCauley, Matthew Amato, Yuning Xiong, Juan Liu, Yi-Cheng Sin, Jake Ellingson, Yue Chen, Fatimah J. Al Khazal, Brandon A. Wilbanks et al. · 2020 · SSRN Electronic Journal
  93. Transgenerational inheritance of BPA-induced obesity correlates with transmission of new CTCF sites in the Fto gene
    Victor G. Corces, Yoon Hee Jung, Brianna J. Bixler, Daniel Ruíz, Hsiao‐Lin V. Wang, Hannah Linsenbaum, Jian‐Feng Xiang, Andrew M. Shafik, Peng Jin · 2020 · Research Square
  94. Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchors
    Manuel Osorio‐Valeriano, Alexander C. Stone, Masahiro Nagano, Bonnie G. Su, Laura Caccianini, Anders S. Hansen, Lucas Farnung, Seychelle M. Vos · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  95. Structural insights into ZBTB20 action at the AFP promoter.
    Lingna Yang, H. Xie, Xiaoqing Wan, Mengfeng Li, Meng-Qi Lv, Yi Duan, Yun-Yu Shi, Wei-Ping J. Zhang, Fu-Dong Li · 2025 · Structure
  96. The myoblast methylome: multiple types of associations with chromatin and transcription
    Sagnik Sen, Michelle R. Lacey, Carl Baribault, V. K. Chaithanya Ponnaluri, Pierre Olivier Esteve, Kenneth C. Ehrlich, Mia Meletta, Sriharsa Pradhan, Melanie Ehrlich · 2025 · Epigenetics
  97. Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs
    Chenyu Li, Mei Ge, Keren Long, Ziyin Han, Mingzhou Li, Zhiyan Zhang, Lusheng Huang · 2025 · Nature Communications
  98. Fine mapping regulatory variants by characterizing native CpG methylation with nanopore long-read sequencing
    Yijun Tian, Shannon K. McDonnell, Lang Wu, Nicholas Bradley Larson, Liang Wang · 2025 · Human Genetics and Genomics Advances
  99. Unraveling the interplay of DNA methylation and chromosome organization
    Yuhe Pei, Guoqiang Li · 2025 · Biochemical Society Transactions
  100. Is developmental synchrony enabled by CTCF residence time?
    Hsiao‐Lin V. Wang, Victor G. Corces · 2021 · Developmental Cell