细胞终末分化过程中三维基因组结构与功能调控的分子机制
收稿日期: 2019-09-05
修回日期: 2019-12-13
网络出版日期: 2019-12-25
基金资助
国家重点研发计划干细胞及转化研究专项编号(2016YFA0100603);中国医学科学院医学与健康科技创新工程协同创新团队项目编号(2016-I2M-3-002);国家自然科学基金面上项目资助编号(81670108)
Molecular mechanism of the 3D genome structure and function regulation during cell terminal differentiation
Received date: 2019-09-05
Revised date: 2019-12-13
Online published: 2019-12-25
Supported by
Supported by the National Key Research and Development Program for Stem Cells and Transformation Research No(2016YFA0100603);Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Engineering Collaborative Innovation Team Project No(2016-I2M-3-002);General Program of the National Natural Science Foundation of China No(81670108)
杨科, 薛征, 吕湘 . 细胞终末分化过程中三维基因组结构与功能调控的分子机制[J]. 遗传, 2020 , 42(1) : 32 -44 . DOI: 10.16288/j.yczz.19-270
The eukaryotic chromatin is folded into highly complex three-dimensional (3D) structures, which plays an important role in the precise regulation of gene expression and normal physiological function. During differentiation and terminal maturation, cells usually undergo dramatic morphology and gene expression changes, accompanied by significant changes in the 3D structure of the genome. In this review, we provide a comprehensive view of the spatial hierarchical organization of the genome, including chromosome territories, A/B compartment, topologically associating domains (TADs) and looping, focusing on recent progresses in the dynamic 3D genomic structural changes and functional regulation during cell differentiation and terminal maturation. In the end, we summarize the unsolved issues as well as prospects of the 3D genome research in cell differentiation and maturation.
| [1] | Li GL, Ruan YJ, Gu RS, Du SM . Emergence of 3D genomics. Chin Sci Bull, 2014,59(13):1165-1172. |
| [1] | 李国亮, 阮一骏, 谷瑞升, 杜生明 . 起航三维基因组学研究. 科学通报, 2014,59(13):1165-1172. |
| [2] | Dekker J, Rippe K, Dekker M, Kleckner N . Capturing chromosome conformation. Science, 2002,295(5558):1306-1311. |
| [3] | Zhao Z, Tavoosidana G, Sj?linder M, G?nd?r A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, Ohlsson R . Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet, 2006,38(11):1341-1347. |
| [4] | Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W,. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet, 2006,38(11):1348-1354. |
| [5] | Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J . Comprehensive mapping of long- range interactions reveals folding principles of the human genome. Science, 2009,326(5950):289-293. |
| [6] | Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J . Chromosome Conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res, 2006,16(10):1299-1309. |
| [7] | Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y . An oestrogen-receptor-alpha-bound human chromatin interactome. Nature, 2009,462(7269):58-64. |
| [8] | Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs DR. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet, 2014,46(2):205-212. |
| [9] | Zheng H, Xie W . The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol, 2019,20(9):535-550. |
| [10] | Cremer T, Cremer M . Chromosome territories. Cold Spring Harb Perspect Biol, 2010,2(3):a003889. |
| [11] | Macville M, Veldman T, Padilla-Nash H, Wangsa D, O'Brien P, Schr?ck E, Ried T. Spectral karyotyping, a 24-colour FISH technique for the identification of chromosomal rearrangements. Histochem Cell Biol, 1997,108(4-5):299-305. |
| [12] | Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell, 2012,148(5):908-921. |
| [13] | Boyle S, Rodesch MJ, Halvensleben HA, Jeddeloh JA, Bickmore WA . Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res, 2011,19(7):901-909. |
| [14] | Heard E, Bickmore W . The ins and outs of gene regulation and chromosome territory organisation. Curr Opin Cell Biol, 2007,19(3):311-316. |
| [15] | Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo YY, Wei CL, Ruan YJ, Bieker JJ, Fraser P . Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet, 2010,42(1):53-61. |
| [16] | Morey C, Da Silva NR, Perry P, Bickmore WA . Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development, 2007,134(5):909-919. |
| [17] | Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, Müller S, Eils R, Cremer C, Speicher MR, Cremer T . Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol, 2005,3(5):e157. |
| [18] | Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P . Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 2013,502(7469):59-64. |
| [19] | Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, de Ridder J, Berns A, Wessels LF, van Lohuizen M, van Steensel B . Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell, 2013,154(4):914-927. |
| [20] | Tanabe H, Müller S, Neusser M, von Hase J, Calcagno E, Cremer M, Solovei I, Cremer C, Cremer T. Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci USA, 2002,99(7):4424-4429. |
| [21] | Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr?f S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell, 2010,38(4):603-613. |
| [22] | Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A . Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation. Blood, 2010,116(13):2356-2364. |
| [23] | Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P . Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet, 2004,36(10):1065-1071. |
| [24] | Papantonis A, Cook PR . Transcription factories: genome organization and gene regulation. Chem Rev, 2013,113(11):8683-8705. |
| [25] | Zhou GL, Xin L, Song W, Di LJ, Liu G, Wu XS, Liu DP, Liang CC . Active chromatin hub of the mouse alpha- globin locus forms in a transcription factory of clustered housekeeping genes. Mol Cell Biol, 2006,26(13):5096-5105. |
| [26] | Faro-Trindade I, Cook PR . Transcription factories: structures conserved during differentiation and evolution. Biochem Soc Trans, 2006,34(Pt 6):1133-1137. |
| [27] | Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA . Chromatin organization by an interplay of loop extrusion and compartmental segregation. Proc Natl Acad Sci USA, 2018,115(29):E6697-E6706. |
| [28] | Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B . Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012,485(7398):376-380. |
| [29] | Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 2012,485(7398):381-385. |
| [30] | 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(3):458-472. |
| [31] | Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S . Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J, 2013,32(24):3119-3129. |
| [32] | Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J . Organization of the mitotic chromosome. Science, 2013,342(6161):948-953. |
| [33] | Smallwood A, Ren B . Genome organization and long- range regulation of gene expression by enhancers. Curr Opin Cell Biol, 2013,25(3):387-394. |
| [34] | Hou C, Li L, Qin ZS, Corces VG . Gene density, transcription, and insulators contribute to the partition of the drosophila genome into physical domains. Mol Cell, 2012,48(3):471-484. |
| [35] | Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van IJcken WF, Grosveld FG, Ren B, Wendt KS. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci USA, 2014,111(3):996-1001. |
| [36] | Phillips JE, Corces VG . CTCF: master weaver of the genome. Cell, 2009,137(7):1194-1211. |
| [37] | Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL. Cohesin loss eliminates all loop domains. Cell, 2017,171(2):305-320 e324. |
| [38] | 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(5): 930-944.e922. |
| [39] | 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(7678):51-56. |
| [40] | Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O'Shaughnessy- Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MGS, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature, 2017,544(7648):59-64. |
| [41] | Bintu B, Mateo LJ, Su JH, Sinnott-Armstrong NA, Parker M, Kinrot S, Yamaya K, Boettiger AN, Zhuang XW. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science, 2018,362(6413): eaau1783. |
| [42] | Szabo Q, Jost D, Chang JM, Cattoni DI, Papadopoulos GL, Bonev B, Sexton T, Gurgo J, Jacquier C, Nollmann M, Bantignies F, Cavalli G. TADs are 3D structural units of higher-order chromosome organization in Drosophila. Sci Adv, 2018, 4(2): eaar8082. |
| [43] | Noordermeer D, de Laat W . Joining the loops: beta-globin gene regulation. IUBMB Life, 2008,60(12):824-833. |
| [44] | Bulger M, Groudine M . Looping versus linking: toward a model for long-distance gene activation. Genes Dev, 1999,13(19):2465-2477. |
| [45] | Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P . Long-range chromatin regulatory interactions in vivo. Nat Genet, 2002,32(4):623-626. |
| [46] | Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y . Extensive promoter- centered chromatin interactions provide a topological basis for transcription regulation. Cell, 2012,148(1-2):84-98. |
| [47] | Sanyal A, Lajoie BR, Jain G, Dekker J . The long-range interaction landscape of gene promoters. Nature, 2012,489(7414):109-113. |
| [48] | Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Gr?ntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R . Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell, 2013,155(7):1507-1520. |
| [49] | Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B . A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature, 2013,503(7475):290-294. |
| [50] | Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J . Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell, 2013,154(4):801-813. |
| [51] | Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR, Jr., Calof AL, Lander AD, Groudine MT, Yokomori K. Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. . Biol Chem, 2011,286(20):17870-17878. |
| [52] | Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL,. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci USA, 2015,112(47):E6456-E6465. |
| [53] | Busslinger GA, Stocsits RR, van der Lelij P, Axelsson E, Tedeschi A, Galjart N, Peters JM,. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl. Nature, 2017,544(7651):503-507. |
| [54] | Palstra RJ, Simonis M, Klous P, Brasset E, Eijkelkamp B, de Laat W. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One, 2008,3(2):e1661. |
| [55] | Mitchell JA, Fraser P . Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev, 2008,22(1):20-25. |
| [56] | Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA . Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell, 2012,149(6):1233-1244. |
| [57] | Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT . Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. Proc Natl Acad Sci USA, 2019,116(39):19431-19439. |
| [58] | Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate. Cell, 2017,171(1):103-119 e118. |
| [59] | Hu GQ, Cui KR, Fang DF, Hirose S, Wang X, Wangsa D, Jin WF, Ried T, Liu PT, Zhu JF, Rothenberg EV, Zhao KJ. Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells. Immunity, 2018, 48(2): 227-242.e228. |
| [60] | Bunting KL, Soong TD, Singh R, Jiang Y, Béguelin W, Poloway DW, Swed BL, Hatzi K, Reisacher W, Teater M, Elemento O, Melnick AM . Multi-tiered reorganization of the genome during b cell affinity maturation anchored by a germinal center-specific locus control region. Immunity, 2016,45(3):497-512. |
| [61] | Kieffer-Kwon KR, Nimura K, Rao SSP, Xu JL, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R,. Myc regulates chromatin decompaction and nuclear architecture during B cell activation. Mol Cell, 2017,67(4):566-578 e510. |
| [62] | Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP . Static and Dynamic DNA loops form AP-1-Bound activation hubs during macrophage development. Mol Cell, 2017,67(6):1037-1048 e1036. |
| [63] | Magli A, Baik J, Pota P, Cordero CO, Kwak IY, Garry DJ, Love PE, Dynlacht BD, Perlingeiro RCR . Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nat Commun, 2019,10(1):2316. |
| [64] | Monahan K, Horta A, Lomvardas S . LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. Nature, 2019,565(7740):448-453. |
| [65] | Bonev B, Mendelson Cohen N, Szabo Q, Fritsch L, Papadopoulos GL, Lubling Y, Xu X, Lv X, Hugnot JP, Tanay A, Cavalli G. Multiscale 3D genome rewiring during mouse neural development. Cell, 2017,171(3): 557-572. e524. |
| [66] | Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA . Lineage-specific dynamic and pre-established enhancer- promoter contacts cooperate in terminal differentiation. Nat Genet, 2017,49(10):1522-1528. |
| [67] | Ediger BN, Lim HW, Juliana C, Groff DN, Williams LT, Dominguez G, Liu JH, Taylor BL, Walp ER, Kameswaran V, Yang J, Liu C, Hunter CS, Kaestner KH, Naji A, Li C, Sander M, Stein R, Sussel L, Won KJ, May CL, Stoffers DA . LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells. . Clin Invest, 2017,127(1):215-229. |
| [68] | Carpenter AC, Bosselut R . Decision checkpoints in the thymus. Nat Immunol, 2010,11(8):666-673. |
| [69] | Solovei I, Wang AS, Thanisch K, Schmidt CS, Krebs S, Zwerger M, Cohen TV, Devys D, Foisner R, Peichl L, Herrmann H, Blum H, Engelkamp D, Stewart CL, Leonhardt H, Joffe B . LBR and lamin A/C sequentially tether peripheral heterochromatin and inversely regulate differentiation. Cell, 2013,152(3):584-598. |
| [70] | Spilianakis CG, Flavell RA . Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol, 2004,5(10):1017-1027. |
| [71] | Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA . Interchromosomal associations between alternatively expressed loci. Nature, 2005,435(7042):637-645. |
| [72] | Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows GA, Fraser P, Luscombe NM, Osborne CS,. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet, 2015,47(6):598-606. |
| [73] | Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 2014,159(7):1665-1680. |
| [74] | Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, de Laat W. The beta-globin nuclear compartment in development and erythroid differentiation. Nat Genet, 2003,35(2):190-194. |
| [75] | Zhai YN, Xu Q, Guo Y, Wu Q . Characterization of a cluster of CTCF-binding sites in a protocadherin regulatory region. Hereditas(Beijing), 2016,38(4):323-336. |
| [75] | 翟亚男, 许泉, 郭亚, 吴强 . 原钙粘蛋白基因簇调控区域中成簇的CTCF结合位点分析. 遗传, 2016,38(4):323-336. |
| [76] | Ong CT, Corces VG . CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet, 2014,15(4):234-246. |
| [77] | Ghirlando R, Felsenfeld G . CTCF: making the right connections. Genes Dev, 2016,30(8):881-891. |
| [78] | Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT . Jpx RNA activates xist by evicting CTCF. Cell, 2013,153(7):1537-1551. |
| [79] | Hansen AS, Hsieh THS, Cattoglio C, Pustova I, Salda?a- Meyer R, Reinberg D, Darzacq X, Tjian R. Distinct classes of chromatin loops revealed by deletion of an RNA-Binding region in CTCF. Mol Cell, 2019, 76(3): 395-411.e313. |
| [80] | Salda?a-Meyer R, Rodriguez-Hernaez J, Escobar T, Nishana M, Jácome-López K, Nora EP, Bruneau BG, Tsirigos A, Furlan-Magaril M, Skok J, Reinberg D. RNA interactions are essential for CTCF-Mediated genome organization. Mol Cell, 2019, 76(3): 412-422.e415. |
| [81] | Stadhouders R, Thongjuea S, Andrieu-Soler C, Palstra RJ, Bryne JC, van den Heuvel A, Stevens M, de Boer E, Kockx C, van der Sloot A, van den Hout M, van Ijcken W, Eick D, Lenhard B, Grosveld F, Soler E. Dynamic long- range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO J, 2012,31(4):986-999. |
| [82] | Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S . CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, 2011,479(7371):74-79. |
| [83] | Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA. YY1 is a Structural Regulator of enhancer- promoter loops. Cell, 2017, 171(7): 1573-1588. e1528. |
| [84] | Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP . Genome-wide map of regulatory interactions in the human genome. Genome Res, 2014,24(12):1905-1917. |
| [85] | Ye BY, Shen WL, Wang D, Li P, Zhang Z, Shi ML, Zhang Y, Zhang FX, Zhao ZH . ZNF143 is involved in CTCF- mediated chromatin interactions by cooperation with cohesin and other partners. Mol Biol (Mosk), 2016,50(3):496-503. |
| [86] | Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, Reik A, Gregory PD, Rivella S, Dean A, Blobel GA . Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell, 2014,158(4):849-860. |
| [87] | Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, Markenscoff-Papadimitriou E, Evans ZA, Kheradpour P, Mountoufaris G, Carey C, Barnea G, Kellis M, Lomvardas S . An epigenetic signature for monoallelic olfactory receptor expression. Cell, 2011,145(4):555-570. |
| [88] | Monahan K, Lomvardas S . Monoallelic expression of olfactory receptors. Annu Rev Cell Dev Biol, 2015,31:721-740. |
| [89] | Flyamer IM, Gassler J, Imakaev M, Brand?o HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana- Konwalski K . Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature, 2017,544(7648):110-114. |
| [90] | Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, Huang SC, Sanborn AL, Machol I, Shamim M, Seberg AP, Lander ES, Chadwick BP, Aiden EL . Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. Proc Natl Acad Sci USA, 2016,113(31):E4504-E4512. |
| [91] | Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-order inter-chromosomal hubs shape 3D Genome organization in the nucleus. Cell, 2018, 174(3): 744-757.e724. |
| [92] | Zheng M, Tian SZ, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu JJ, Li Z, Wong CH, Ngan CY, Wang P, Ruan X, Wei CL, Ruan Y . Multiplex chromatin interactions with single-molecule precision. Nature, 2019,566(7745):558-562. |
/
| 〈 |
|
〉 |
www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:
