Jerković I, Szabo Q, Bantignies F, Cavalli G. Higher-order chromosomal structures mediate genome function. J Mol Biol. 2020;432:676–81. https://doi.org/10.1016/J.JMB.2019.10.014.

Article  PubMed  Google Scholar 

Furlong EEM, Levine M. Developmental enhancers and chromosome topology. Science. 2018;361:1341–5. https://doi.org/10.1126/SCIENCE.AAU0320.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sikorska N, Sexton T. Defining functionally relevant spatial chromatin domains: it is a TAD complicated. J Mol Biol. 2020;432:653–64. https://doi.org/10.1016/J.JMB.2019.12.006.

Article  CAS  PubMed  Google Scholar 

Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol. 2019;20:535–50. https://doi.org/10.1038/S41580-019-0132-4.

Article  CAS  PubMed  Google Scholar 

Kantidze OL, Razin SV. Weak interactions in higher-order chromatin organization. Nucleic Acids Res. 2020;48:4615–26. https://doi.org/10.1093/NAR/GKAA261.

Article  Google Scholar 

Szabo Q, Donjon A, Jerković I, Papadopoulos GL, Cheutin T, Bonev B, Nora EP, Bruneau BG, Bantignies F, Cavalli G. Regulation of single-cell genome organization into TADs and chromatin nanodomains. Nat Genet. 2020;52:1151–7. https://doi.org/10.1038/S41588-020-00716-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kyrchanova OV, Bylino OV, Georgiev PG. Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila. Front Genet. 2022;13. https://doi.org/10.3389/FGENE.2022.1081088.

Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF as an example of DNA-Binding transcription factors containing clusters of C2H2-Type Zinc Fingers. Acta Naturae. 2021;13:31–46. https://doi.org/10.32607/ACTANATURAE.11206.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Arzate-Mejıá RG, Recillas-Targa F, Corces VG. Developing in 3D: the role of CTCF in cell differentiation. Development. 2018;145. https://doi.org/10.1242/DEV.137729.

Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X. Structural basis for the versatile and methylation-dependent binding of CTCF to DNA. Mol Cell. 2017;66:711–e7203. https://doi.org/10.1016/J.MOLCEL.2017.05.004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters J. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 2017;36:3573–99. https://doi.org/10.15252/EMBJ.201798004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017;551:51–6. https://doi.org/10.1038/NATURE24281.

Article  PubMed  PubMed Central  Google Scholar 

Haarhuis JHI, van der Weide RH, Blomen VA, Yáñez-Cuna JO, Amendola M, van Ruiten MS, Krijger PHL, Teunissen H, Medema RH, van Steensel B, Brummelkamp TR, de Wit E, Rowland BD. The Cohesin release factor WAPL restricts chromatin Loop Extension. Cell. 2017;169:693–e70714. https://doi.org/10.1016/J.CELL.2017.04.013.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol. 2020;21. https://doi.org/10.1186/S13059-019-1894-X.

Anania C, Acemel RD, Jedamzick J, Bolondi A, Cova G, Brieske N, Kühn R, Wittler L, Real FM, Lupiáñez DG. In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation. Nat Genet. 2022;54:1026–36. https://doi.org/10.1038/S41588-022-01117-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hanssen LLP, Kassouf MT, Oudelaar AM, Biggs D, Preece C, Downes DJ, Gosden M, Sharpe JA, Sloane-Stanley JA, Hughes JR, Davies B, Higgs DR. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat Cell Biol. 2017;19:952–61. https://doi.org/10.1038/NCB3573.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vos ESM, Valdes-Quezada C, Huang Y, Allahyar A, Verstegen MJAM, Felder AK, van der Vegt F, Uijttewaal ECH, Krijger PHL, de Laat W. Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression. Mol Cell. 2021;81:3082–e30956. https://doi.org/10.1016/J.MOLCEL.2021.06.008.

Article  CAS  PubMed  Google Scholar 

Li Y, Haarhuis JHI, Sedeño Cacciatore Á, Oldenkamp R, van Ruiten MS, Willems L, Teunissen H, Muir KW, de Wit E, Rowland BD, Panne D. The structural basis for cohesin-CTCF-anchored loops. Nature. 2020;578:472–6. https://doi.org/10.1038/S41586-019-1910-Z.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen H, Tian Y, Shu W, Bo X, Wang S. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-Binding sites in the Human Genome. PLoS ONE. 2012;7:e41374. https://doi.org/10.1371/journal.pone.0041374.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pugacheva EM, Kubo N, Loukinov D, Tajmul M, Kang S, Kovalchuk AL, Strunnikov AV, Zentner GE, Ren B, Lobanenkov VV. CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proc Natl Acad Sci U S A. 2020;117:2020–31. https://doi.org/10.1073/pnas.1911708117.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell. 2017;169:930–e94422. https://doi.org/10.1016/j.cell.2017.05.004.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Narendra V, Bulajié M, Dekker J, Mazzoni EO, Reinberg D. CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes Dev. 2016;30:2657–62. https://doi.org/10.1101/GAD.288324.116.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol. 2015;33:555–62. https://doi.org/10.1038/NBT.3128.

Article  CAS  PubMed  Google Scholar 

Persikov AV, Singh M. De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res. 2014;42:97–108. https://doi.org/10.1093/NAR/GKT890.

Article  CAS  PubMed  Google Scholar 

Baxley RM, Bullard JD, Klein MW, Fell AG, Morales-Rosado JA, Duan T, Geyer PK. Deciphering the DNA code for the function of the Drosophila polydactyl zinc finger protein suppressor of hairy-wing. Nucleic Acids Res. 2017;45:4463–78. https://doi.org/10.1093/NAR/GKX040.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc Natl Acad Sci U S A. 2012;109:17507–12. https://doi.org/10.1073/PNAS.1111941109/DCSUPPLEMENTAL/SAPP.PDF.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonchuk A, Maksimenko O, Kyrchanova O, Ivlieva T, Mogila V, Deshpande G, Wolle D, Schedl P, Georgiev P. Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster. BMC Biol. 2015;13:63. https://doi.org/10.1186/s12915-015-0168-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonchuk A, Kamalyan S, Mariasina S, Boyko K, Popov V, Maksimenko O, Georgiev P. N-terminal domain of the architectural protein CTCF has similar structural organization and ability to self-association in bilaterian organisms. Sci Rep. 2020;10:1–11. https://doi.org/10.1038/s41598-020-59459-5.

Article  CAS  Google Scholar 

Eagen KP, Aiden EL, Kornberg RD. Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Proc Natl Acad Sci U S A. 2017;114:8764–9. https://doi.org/10.1073/PNAS.1701291114.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Q, Sun Q, Czajkowsky DM, Shao Z. Sub-kb Hi-C in D. Melanogaster reveals conserved characteristics of TADs between insect and mammalian cells. Nat Commun. 2018;9. https://doi.org/10.1038/S41467-017-02526-9.

Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell. 2012;148:458–72. https://doi.org/10.1016/J.CELL.2012.01.010.

Article  CAS  PubMed  Google Scholar 

Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res. 2016;26:70–84. https://doi.org/10.1101/GR.196006.115.

Article  PubMed  PubMed Central  Google Scholar 

Fudenberg G, Nora EP. Embryogenesis without CTCF in flies and vertebrates. Nat Struct Mol Biol. 2021;28:774–6. https://doi.org/10.1038/S41594-021-00662-X.