Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers

Sabari BR, Dall’Agnese A, Young RA. Biomolecular condensates in the Nucleus. Trends Biochem Sci. 2020;45:961–77. https://doi.org/10.1016/j.tibs.2020.06.007.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Misteli T. The Self-Organizing genome: principles of Genome Architecture and function. Cell. 2020;183:28–45. https://doi.org/10.1016/j.cell.2020.09.014.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. Cell Regen. 2022;11:42. https://doi.org/10.1186/s13619-022-00145-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cremer T, Cremer C, Schneider T, Baumann H, Hens L, Kirsch-Volders M. Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments. Hum Genet. 1982;62:201–9. https://doi.org/10.1007/BF00333519.

Article  CAS  PubMed  Google Scholar 

Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2:292–301. https://doi.org/10.1038/35066075.

Article  CAS  PubMed  Google Scholar 

Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, Singh H. Subnuclear compartmentalization of immunoglobulin loci during Lymphocyte Development. Science. 2002;296:158–62. https://doi.org/10.1126/science.1068768).

Article  CAS  PubMed  Google Scholar 

van Steensel B, Belmont AS. 2017 Lamina-Associated domains: links with chromosome Architecture, Heterochromatin, and Gene Repression. Cell 169, 780–91. (https://doi.org/10.1016/j.cell.2017.04.022).

Bonev B, Cavalli G. Organization and function of the 3D genome. Nat Rev Genet. 2016;17:661–78. https://doi.org/10.1038/nrg.2016.112.

Article  CAS  PubMed  Google Scholar 

Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518:331–6. https://doi.org/10.1038/nature14222.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, et al. Cell-type specialization is encoded by specific chromatin topologies. Nature. 2021;599:684–91. https://doi.org/10.1038/s41586-021-04081-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Long HS, Greenaway S, Powell G, Mallon A-M, Lindgren CM, Simon MM. Making sense of the linear genome, gene function and TADs. Epigenetics Chromatin. 2022;15(4). https://doi.org/10.1186/s13072-022-00436-9.

Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, et al. Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nat Biotechnol. 2023. https://doi.org/10.1038/s41587-022-01612-8.

Article  PubMed  PubMed Central  Google Scholar 

Forte G, Buckle A, Boyle S, Marenduzzo D, Gilbert N, Brackley CA. Transcription modulates chromatin dynamics and locus configuration sampling. Nat Struct Mol Biol. 2023;30:1275–85. https://doi.org/10.1038/s41594-023-01059-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Merkenschlager M, Odom DT. 2013 CTCF and cohesin: linking gene regulatory elements with their targets. Cell. 152, 1285–1297. (10.1016/j.cell.2013.02.029).

Rowley MJ, Corces VG. 2018 Organizational principles of 3D genome architecture. Nat Rev Genet. 19, 789–800. (10.1038/s41576-018-0060-8).

van Ruiten MS, Rowland BD. 2018 SMC Complexes: Universal DNA Looping Machines with Distinct Regulators. Trends Genet. 34, 477–487. (10.1016/j.tig.2018.03.003).

Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. 2017 Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 169, 930–944.e922. (10.1016/j.cell.2017.05.004).

Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 2017;36:3573–99.

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. 2020 CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention. Proceedings of the National Academy of Sciences. 117, 2020–2031.

Hsieh T-HS, Cattoglio C, Slobodyanyuk E, Hansen AS, Darzacq X, Tjian R. Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1. Nat Genet. 2022;54:1919–32. https://doi.org/10.1038/s41588-022-01223-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. 1993 CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 13, 7612–7624. (10.1128/mcb.13.12.7612-7624.1993).

Saldaña-Meyer R, Rodriguez-Hernaez J, Escobar T, Nishana M, Jácome-López K, Nora EP, Bruneau BG, Tsirigos A, Furlan-Magaril M, Skok J et al. ,. 2019 RNA Interactions Are Essential for CTCF-Mediated Genome Organization. Mol Cell. 76, 412–422.e415. (10.1016/j.molcel.2019.08.015)

Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT. 2021 Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell. 184, 6157–6173.e6124. (10.1016/j.cell.2021.11.012).

Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X. 2017 structural basis for the versatile and methylation-dependent binding of CTCF to DNA. Mol Cell. 66, 711–20. e713.

Zhou R, Tian K, Huang J, Duan W, Fu H, Feng Y, Wang H, Jiang Y, Li Y, Wang R. CTCF DNA-binding domain undergoes dynamic and selective protein–protein interactions. Iscience. 2022;25:105011.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vietri Rudan M, Hadjur S. Genetic tailors: CTCF and cohesin shape the genome during evolution. Trends Genet. 2015;31:651–60. https://doi.org/10.1016/j.tig.2015.09.004.

Article  CAS  PubMed  Google Scholar 

Ghirlando R, Felsenfeld G. CTCF: making the right connections. Genes Dev. 2016;30:881–91. https://doi.org/10.1101/gad.277863.116.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh T-HS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF-and cohesin-mediated chromatin looping revealed by live-cell imaging. Science. 2022;376:496–501.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aljahani A, Hua P, Karpinska MA, Quililan K, Davies JO, Oudelaar AM. 2022 analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF. Nat Commun. 13, 2139.

Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale RK. 2023 enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nat Genet. 55, 280–90.

Davidson IF, Barth R, Zaczek M, van der Torre J, Tang W, Nagasaka K, Janissen R, Kerssemakers J, Wutz G, Dekker C. 2023 CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion. Nature. 1–6.

Gu B, Comerci CJ, McCarthy DG, Saurabh S, Moerner WE, Wysocka J. 2020 Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging. Mol Cell. 80, 699–711.e697. (10.1016/j.molcel.2020.10.001).

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. ,. 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 326, 289–293. (10.1126/science.1181369)

Dekker J, Rippe K, Dekker M, Kleckner N. 2002 Capturing Chromosome Conformation. Science. 295, 1306–1311. (10.1126/science.1067799).

Eagen KP. 2018 Principles of Chromosome Architecture Revealed by Hi-C. Trends Biochem Sci. 43, 469–478. (10.1016/j.tibs.2018.03.006).

Pal K, Forcato M, Ferrari F. Hi-C analysis: from data generation to integration. Biophys Rev. 2019;11:67–78.

Article  PubMed  Google Scholar 

Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. 2021 seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin. 14, 1–17.

Andrey G, Mundlos S. 2017 The three-dimensional genome: regulating gene expression during pluripotency and development. Development. 144, 3646–3658. (10.1242/dev.148304).

MacGregor IA, Adams IR, Gilbert N. Large-scale chromatin organisation in interphase, mitosis and meiosis. Biochem J. 2019;476:2141–56.

Article  CAS  PubMed  Google Scholar 

Collas P, Liyakat Ali TM, Brunet A, Germier T. Finding friends in the crowd: three-dimensional cliques of topological genomic domains. Front Genet. 2019;10:602.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vickaryous MK, Hall BK. 2006 Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest. Biol Rev Camb Philos Soc. 81, 425–455. (10.1017/s1464793106007068).

Lovicu F, McAvoy J. 2005 Growth factor regulation of lens development. Developmental biology. 280, 1–14. (10.1016/j.ydbio.2005.01.020).

Bassnett S, Shi Y, Vrensen GF. 2011 Biological glass: structural determinants of eye lens transparency. Philos Trans R Soc Lond B Biol Sci. 366, 1250–1264. (10.1098/rstb.2010.0302).

Gunhaga L. 2011 The lens: a classical model of embryonic induction providing new insights into cell determination in early development. Philosophical Transactions of the Royal Society B: Biological Sciences. 366, 1193–1203. (10.1098/rstb.2010.0175).

Cvekl A, Zhang X. Signaling and Gene Regulatory Networks in mammalian Lens Development. Trends Genet. 2017;33:677–702. https://doi.org/10.1016/j.tig.2017.08.001).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cvekl A, Eliscovich C. 2021 Crystallin gene expression: Insights from studies of transcriptional bursting. Experimental Eye Research. 207, 108564. (10.1016/j.exer.2021.108564).

Vrensen GF, Graw J, De Wolf A. 1991 Nuclear breakdown during terminal differentiation of primary lens fibres in mice: a transmission electron microscopic study. Exp Eye Res. 52, 647–659. (10.1016/0014-4835(91)90017-9).

Chaffee BR, Shang F, Chang M-L, Clement TM, Eddy EM, Wagner BD, Nakahara M, Nagata S, Robinson ML, Taylor A. 2014 Nuclear removal during terminal lens fiber cell differentiation requires CDK1 activity: appropriating mitosis-related nuclear disassembly. Development. 141, 3388–3398. (10.1242/dev.106005).

He S, Limi S, McGreal RS, Xie Q, Brennan LA, Kantorow WL, Kokavec J, Majumdar R, Hou H Jr, Edelmann W et al. 2016 Chromatin remodeling enzyme Snf2h regulates embryonic lens differentiation and denucleation. Development. 143, 1937–1947. (10.1242/dev.135285).

Lyu L, Whitcomb EA, Jiang S, Chang ML, Gu Y, Duncan MK, Cvekl A, Wang WL, Limi S, Reneker LW et al. 2016 Unfolded-protein response-associated stabilization of p27(Cdkn1b) interferes with lens fiber cell denucleation, leading to cataract. Faseb j. 30, 1087–1095. (10.1096/fj.15-278036).

Limi S, Senecal A, Coleman R, Lopez-Jones M, Guo P, Polumbo C, Singer RH, Skoultchi AI, Cvekl A. 2018 Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. Journal of Biological Chemistry. 293, 13176–13190. (10.1074/jbc.RA118.001927).

Martynova E, Zhao Y, Xie Q, Zheng D, Cvekl A. Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3. Open Biology. 2019;9:190220.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun J, Rockowitz S, Chauss D, Wang P, Kantorow M, Zheng D, Cvekl A. Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators. Mol Vis. 2015;21:955–73.

CAS  PubMed  PubMed Central  Google Scholar 

Hamai Y, Fukui HN, Kuwabara T. 1974 Morphology of hereditary mouse cataract. Exp Eye Res. 18, 537–546. (10.1016/0014-4835(74)90060-8).

Pendergrass W, Penn P, Possin D, Wolf N. 2005 Accumulation of DNA, nuclear and mitochondrial debris, and ROS at sites of age-related cortical cataract in mice. Invest Ophthalmol Vis Sci. 46, 4661–4670. (10.1167/iovs.05-0808).

Pendergrass WR, Penn PE, Possin DE, Wolf NS. 2006 Cellular debris and ROS in age-related cortical cataract are caused by inappropriate involution of the surface epithelial cells into the lens cortex. Mol Vis. 12, 712–24.

Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM et al. ,. 2023 Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. 83, 2624–2640. (10.1016/j.molcel.2023.06.018)

Norrie JL, Lupo MS, Xu B, Al Diri I, Valentine M, Putnam D, Griffiths L, Zhang J, Johnson D, Easton J et al. ,. 2019 Nucleome Dynamics during Retinal Development. Neuron. 104, 512–528.e511. (10.1016/j.neuron.2019.08.002)

Marchal C, Singh N, Batz Z, Advani J, Jaeger C, Corso-Díaz X, Swaroop A. 2022 High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci. Nat Commun. 13, 5827. (10.1038/s41467-022-33427-1).

Li M, Huang H, Wang B, Jiang S, Guo H, Zhu L, Wu S, Liu J, Wang L, Lan X. Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity. Nat Commun. 2022;13:1293.

Article  CAS  PubMed  PubMed Central  Google Scholar 

McGreal-Estrada RS, Wolf LV, Cvekl A. 2018 Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus. Biol Open. 7, (10.1242/bio.036897).

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