染色质构象与基因功能

doi:10.16288/j.yczz.19-257

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (1): 1-17.doi: 10.16288/j.yczz.19-257

• Special Section: 3D Genome • Next Articles

Linking chromatin conformation to gene function

Qitong Huang, Qing Li, Yubo Zhang()

Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China

Received:2019-08-29 Revised:2019-10-29 Online:2020-01-20 Published:2019-11-19
Contact: Zhang Yubo E-mail:ribon_001@163.com
Supported by:
Supported by the Agricultural Science and Technology Innovation Program, the Thousand Talents Plan for Young Professionals, the Fundamental Research Funds for Central Non-profit Scientific Institution No(Y2019PT18-02);the National Natural Science Foundation of China No(31970592);the National Key R&D Program of China No(2018YFA0903201)

Abstract

Abstract:

DNA is highly compressed and packaged as chromatin within the nucleus in eukaryotes. DNA replication, DNA repair and transcription, and other biological processes are precisely regulated or determined by chromatin conformation. Activation or repression of different genes/transcription factors are tightly correlated to their chromatin conformation which contributes to cell self-maintenance, differentiation, specificity and identity. Therefore, the study of bridging chromatin conformation to gene function has became crucial for decoding genetic information and precision biology which is also a great challenge for current genomics research. Here, we review the multiple aspects of chromatin conformation, including its history, characteristics, dynamics and the impact on different dimension-chromatin architecture to gene function. Additionally, we discuss the limitation and challenges of current status of linking chromatin conformation to gene function study. We believe this is informative and foundational in combing the context between chromatin conformation and gene function as reference.

Key words: chromatin conformation, gene function, dynamic regulation

Qitong Huang, Qing Li, Yubo Zhang. Linking chromatin conformation to gene function[J]. Hereditas(Beijing), 2020, 42(1): 1-17.

Figures/Tables 4

References 133

[1]	Kornberg RD . Chromatin structure: A repeating unit of histones and DNA. Science, 1974,184(4139):868-871. doi: 10.1126/science.184.4139.868 pmid: 4825889
[2]	Guertin MJ, Lis JT . Mechanisms by which transcription factors gain access to target sequence elements in chromatin. Curr Opin Genet Dev, 2013,23(2):116-123. doi: 10.1016/j.gde.2012.11.008
[3]	Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA . The accessible chromatin landscape of the human genome. Nature, 2012,489(7414):75-82. doi: 10.1038/nature11232
[4]	Finch JT, Klug A . Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA, 1976,73(6):1897-1901. doi: 10.1073/pnas.73.6.1897 pmid: 1064861
[5]	Boveri T . Die blastomerenkerne von ascaris megalocephala und die theorie der chromosomenindividualität. Arch Zellforsch, 1909,3:181-268.
[6]	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. doi: 10.1126/science.1181369 pmid: 19815776
[7]	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. doi: 10.1038/nature11082
[8]	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. doi: 10.1038/nature11049
[9]	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. doi: 10.1016/j.cell.2014.11.021
[10]	Zhang YB . 3D Genomics and precision biology. Chin J Biochem Mol Biol, 2018,34(4):351-363.
	张玉波 . 三维基因组学与精准生物学. 中国生物化学与分子生物学报, 2018,34(4):351-363.
[11]	Risca VI, Greenleaf WJ . Unraveling the 3D genome: Genomics tools for multiscale exploration. Trends Genet, 2015,31(7):357-372. doi: 10.1016/j.tig.2015.03.010 pmid: 25887733
[12]	Ning CY, He MN, Tang QZ, Zhu Q, Li MZ, Li DY . Advances in mammalian three-dimensional genome by using Hi-C technology approach. Hereditas(Beijing), 2019,41(3):215-233.
	宁椿游, 何梦楠, 唐茜子, 朱庆, 李明洲, 李地艳 . 基于Hi-C技术哺乳动物三维基因组研究进展. 遗传, 2019,41(03):215-233.
[13]	Ke Y, Xu Y, Chen X, Feng S, Liu Z, Sun Y, Yao X, Li F, Zhu W, Gao L, Chen H, Du Z, Xie W, Xu X, Huang X, Liu J . 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell, 2017,170(2):367-381. doi: 10.1016/j.cell.2017.06.029 pmid: 28709003
[14]	Barutcu AR, Lajoie BR, Mccord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol, 2015,16(1):214. doi: 10.1186/s13059-015-0768-0 pmid: 26415882
[15]	Taberlay PC, Achinger-Kawecka J, Lun AT, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O'Donoghue SI, Clark SJ. Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res, 2016,26(6):719-731. doi: 10.1101/gr.201517.115 pmid: 27053337
[16]	Brown KE . Chromatin folding and gene expression: New tools to reveal the spatial organization of genes. Chromosome Res, 2003,11(5):423-433. doi: 10.1023/A:1024966424909
[17]	Almassalha LM, Tiwari A, Ruhoff PT, Stypula-Cyrus Y, Cherkezyan L, Matsuda H, Dela Cruz MA, Chandler JE, White C, Maneval C, Subramanian H, Szleifer I, Roy HK, Backman V . The global relationship between chromatin physical topology, fractal structure, and gene expression. Sci Rep, 2017,7:41061. doi: 10.1038/srep41061 pmid: 28117353
[18]	Hübner MR, Eckersley-Maslin MA, Spector DL . Chromatin organization and transcriptional regulation. Curr Opin Genet Dev, 2013,23(2):89-95. doi: 10.1016/j.gde.2012.11.006
[19]	Peng C, Li GL, Zhang YH, Ruan YJ . Reconstruction of three-dimensional structures of chromatin and its biological implications. Sci Sin Vitae, 2014,44(8):794-802. doi: 10.1360/052014-108
	彭城, 李国亮, 张红雨, 阮一骏 . 染色质三维结构重建及其生物学意义. 中国科学: 生命科学, 2014,44(8):794-802. doi: 10.1360/052014-108
[20]	Oudet P, Gross-Bellard M, Chambon P . Electron microscopic and biochemical evidence that chromatin structure is a repeating unit. Cell, 1975,4(4):281-300. doi: 10.1016/0092-8674(75)90149-x pmid: 1122558
[21]	Olins AL, Olins DE . Spheroid chromatin units (v bodies). Science. 1974,183(4122):330-332. doi: 10.1126/science.183.4122.330 pmid: 4128918
[22]	Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ . Crystal structure of the nucleosome core particle at 2.8 a resolution. Nature, 1997,389(6648):251-260. doi: 10.1038/38444 pmid: 9305837
[23]	Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD . Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet, 2004,36(8):900-905. doi: 10.1038/ng1400 pmid: 15247917
[24]	Sekinger EA, Moqtaderi Z, Struhl K . Intrinsic Histone- DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell, 2005,18(6):735-748. doi: 10.1016/j.molcel.2005.05.003 pmid: 15949447
[25]	Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL . Global nucleosome occupancy in yeast. Genome Biol, 2004,5(9):1-11. doi: 10.1016/j.jinorgbio.2019.110769 pmid: 31326773
[26]	Saragosti S, Moyne G, Yaniv M . Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell, 1980,20(1):65-73. doi: 10.1016/0092-8674(80)90235-4 pmid: 6248237
[27]	Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C . Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science, 2009,325(5940):626-628. doi: 10.1126/science.1172926 pmid: 19644123
[28]	Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R . Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol, 2009,16(9):996-1001. doi: 10.1038/nsmb.1658 pmid: 19684599
[29]	Schwartz S, Meshorer E, Ast G . Chromatin organization marks exon-intron structure. Nat Struct Mol Biol, 2009,16(9):990-995. doi: 10.1038/nsmb.1659 pmid: 19684600
[30]	Mavrich TN, Jiang C, Ioshikhes IP, Li XY, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF . Nucleosome organization in the Drosophila genome. Nature, 2008,358(7193):358-362. doi: 10.1038/nature06929 pmid: 18408708
[31]	Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C . A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet, 2007,39(10):1235-1244. doi: 10.1038/ng2117 pmid: 17873876
[32]	Leimgruber E, Seguín-Estévez Q, Dunand-Sauthier I, Rybtsova N, Schmid CD, Ambrosini G, Bucher P, Reith W . Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site. Nucleic Acids Res, 2009,37(8):2514-2528. doi: 10.1093/nar/gkp116 pmid: 19264803
[33]	Segal E, Widom J . What controls nucleosome positions? Trends Genet, 2009,25(8):335-343. doi: 10.1016/j.tig.2009.06.002
[34]	Schwartz S, Ast G . Chromatin density and splicing destiny: On the cross-talk between chromatin structure and splicing. Embo J, 2014,29(10):1629-1636. doi: 10.1038/emboj.2010.71 pmid: 20407423
[35]	Spies N, Nielsen CB, Padgett RA, Burge CB . Biased chromatin signatures around polyadenylation sites and exons. Mol Cell, 2009,36(2):245-254. doi: 10.1016/j.molcel.2009.10.008 pmid: 19854133
[36]	Laybourn PJ, Kadonaga JT . Role of nucleosomal cores and histone h1 in regulation of transcription by RNA polymerase II. Science, 1991,254(5029):238-245. doi: 10.1126/science.1718039 pmid: 1718039
[37]	Jiang C, Pugh BF . Nucleosome positioning and gene regulation: Advances through genomics. Nat Rev Genet, 2009,10(3):161-172. doi: 10.1038/nrg2522 pmid: 19204718
[38]	Widom J, Klug A . Structure of the 3000Å chromatin filament: X-ray diffraction from oriented samples. Cell, 1985,43(1):207-213. doi: 10.1016/0092-8674(85)90025-x pmid: 4075395
[39]	Woodcock CL, Frado LL, Rattner JB . The higher-order structure of chromatin: Evidence for a helical ribbon arrangement. . Cell Biol, 1984,99(1):42-52. doi: 10.1083/jcb.99.1.42 pmid: 6736132
[40]	Benedetta D, Thomas S, Alexandra K, Sylwia D, Schroeder RR, Richmond TJ . Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science, 2004,306(5701):1571-1573. doi: 10.1126/science.1103124 pmid: 15567867
[41]	Song F, Chen P, Sun D, Wang M, Dong L, Liang D, Xu RM, Zhu P, Li G . Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science, 2014,344(6182):376-380. doi: 10.1126/science.1251413 pmid: 24763583
[42]	Li W, Chen P, Yu J, Dong L, Liang D, Feng J, Yan J, Wang PY, Li Q, Zhang Z, Li M, Li G . FACT remodels the tetranucleosomal unit of chromatin fibers for gene transcription. Mol Cell, 2016,64(1):120-133. doi: 10.1016/j.molcel.2016.08.024 pmid: 27666592
[43]	Ohno M, Ando T, Priest DG, Kumar V, Yoshida Y, Taniguchi Y. Sub-nucleosomal genome structure reveals distinct nucleosome folding motifs. Cell, 2019, 176(3): 520- 534.e25. doi: 10.1016/j.cell.2018.12.014 pmid: 30661750
[44]	Rabl C. Über zelltheilung. Morph Jb, 1885,10:214-330.
[45]	Cremer T, Cremer M . Chromosome territories. Cold Spring Harb Perspect Biol, 2010,2(3):a003889. doi: 10.1101/cshperspect.a003889 pmid: 20300217
[46]	International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature, 2004,431(7011):931-945. doi: 10.1038/nature03001 pmid: 15496913
[47]	The ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA elements) project. Science, 2004,306(5696):636-640. doi: 10.1126/science.1105136 pmid: 15499007
[48]	Dekker J, Rippe K, Dekker M, Kleckner N . Capturing chromosome conformation. Science, 2002,295(5558):1306-1311. doi: 10.1126/science.1067799 pmid: 11847345
[49]	Marieke S, Petra K, Erik S, Yuri M, Rob W, Elzo DW, Bas VS, Wouter DL . Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet, 2006,38(11):1348-1354. doi: 10.1038/ng1896 pmid: 17033623
[50]	Zhao Z, Tavoosidana G, Sjölinder M, Göndör 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. doi: 10.1038/ng1891 pmid: 17033624
[51]	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. doi: 10.1101/gr.5571506 pmid: 16954542
[52]	Fullwood MJ, Liu MH, Pan YF, Liu J, Han X, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EGY, Huang PYH, Welboren WJ, Han YY, Ooi HS, Ariyaratne PN, Vega VB, Luo AQ, Tan PY, Choy PY, Wansa KDSA, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li HX, Desai KV, Thomsen JS, Lee YK, Karuturi RKM, Herve T, Bourque BG, Stunnenberg HG, Ruan I, Cacheux-Rataboul V, Sung WK, Liu DT, Wei CL, Cheung E, Ruan YJ. An oestrogen receptor α-bound human chromatin interactome. Nature, 2009,462(7269):58-64. doi: 10.1038/nature08497 pmid: 19890323
[53]	Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z . Fine- scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods, 2015,12(1):71-78. doi: 10.1038/nmeth.3205 pmid: 25437436
[54]	Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo YQ, 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. doi: 10.1038/ng.496 pmid: 20010836
[55]	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. doi: 10.1038/nature12593
[56]	Lin D, Hong P, Zhang S, Xu W, Jamal M, Yan K, Lei Y, Li L, Ruan Y, Fu ZF, Li G, Cao G . Digestion- ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nat Genet, 2018,50(5):754-763 doi: 10.1038/s41588-018-0111-2 pmid: 29700467
[57]	Koehler D, Zakhartchenko V, Froenicke L, Stone G, Stanyon R, Wolf E, Cremer T, Brero A . Changes of higher order chromatin arrangements during major genome activation in bovine preimplantation embryos. Exp Cell Res, 2009,315(12):2053-2063. doi: 10.1016/j.yexcr.2009.02.016 pmid: 19254712
[58]	Cremer M, Grasser F, Lanctôt C, Müller S, Neusser M, Zinner R, Solovei I, Cremer T . Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. Methods Mol Biol, 2008,463(463):205-239. doi: 10.1007/978-1-59745-406-3_15 pmid: 18951171
[59]	Takizawa T, Meaburn KJ, Misteli T . The meaning of gene positioning. Cell, 2008,135(1):9-13. doi: 10.1016/j.cell.2008.09.026 pmid: 18854147
[60]	Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B . Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell, 2009,137(2):356-368. doi: 10.1016/j.cell.2009.01.052 pmid: 19379699
[61]	Ryba T, Hiratani I, Lu JJ, Itoh M, Kulik M, Zhang JF, Schulz TC, Robins AJ, Dalton S, Gilbert DM . Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res, 2010,20(6):761-770. doi: 10.1101/gr.099655.109 pmid: 20430782
[62]	Dixon JR, Inkyung J, Siddarth S, Yin S, Antosiewicz- Bourget JE, Ah Young L, Zhen Y, Audrey K, Nisha R, Wei X, Diao Y, Liang J, Zhao HM, Lobanenkov VV, Ecker JR, Thomson J, Ren B . Chromatin architecture reorganization during stem cell differentiation. Nature, 2015,518(7539):331-336. doi: 10.1038/nature14222 pmid: 25693564
[63]	Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi S, Hiratani I . Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization. Nat Genet, 2019,51(9):1356-1368. doi: 10.1038/s41588-019-0474-z pmid: 31406346
[64]	Dekker J, Heard E . Structural and functional diversity of Topologically Associating Domains. Febs Lett, 2015,589(20PartA):2877-2884. doi: 10.1016/j.febslet.2015.08.044 pmid: 26348399
[65]	Dixon J, Gorkin D, Ren B . Chromatin domains: The unit of chromosome organization. Mol Cell, 2016,62(5):668-680. doi: 10.1016/j.molcel.2016.05.018 pmid: 27259200
[66]	Battulin N, Fishman VS, Mazur AM, Pomaznoy M, Khabarova AA, Afonnikov DA, Prokhortchouk EB, Serov OL . Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach. Genome Biol, 2015,16(1):77. doi: 10.1186/s13059-015-0642-0 pmid: 25886366
[67]	Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, ardison RC, Kahveci T, Ren B, Gilbert DM. Topologically associating domains are stable units of replication-timing regulation. Nature, 2014,515(7527):402-405. doi: 10.1038/nature13986
[68]	Ke Y, Xu Y, Chen X, Feng S, Liu Z, Sun Y, Yao X, Li F, Zhu W, Gao L, Chen H, Du Z, Xie W, Xu X, Huang X, Liu J . 3D chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis. Cell, 2017,170(2):367-381. doi: 10.1016/j.cell.2017.06.029 pmid: 28709003
[69]	Wang CY, Jégu T, Chu HP, Oh HJ, Lee JT . SMCHD1 merges chromosome compartments and assists formation of Super-Structures on the inactive x. Cell, 2018,174(2):406-421. doi: 10.1016/j.cell.2018.05.007 pmid: 29887375
[70]	Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J . Structural organization of the inactive X chromosome in the mouse. Nature, 2016,535(7613):575-579. doi: 10.1038/nature18589 pmid: 27437574
[71]	Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S . Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell, 2015,161(5):1012-1025. doi: 10.1016/j.cell.2015.04.004 pmid: 25959774
[72]	Li W, Gong K, Li Q, Alber F, Zhou XJ . Hi-Corrector: A fast, scalable and memory-efficient package for normalizing large-scale Hi-C data. Bioinformatics, 2015,31(6):960-962. doi: 10.1093/bioinformatics/btu747 pmid: 25391400
[73]	Lupiáñez DG, Spielmann M, Mundlos S . Breaking TADs: How alterations of chromatin domains result in disease. Trends Genet, 2016,32(4):225-237. doi: 10.1016/j.tig.2016.01.003 pmid: 26862051
[74]	Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA . Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science, 2016,351(6280):1454-1458. doi: 10.1126/science.aad9024 pmid: 26940867
[75]	Zhan Y, Mariani L, Barozzi I, Schulz EG, Blüthgen N, Stadler M, Tiana G, Giorgetti L . Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res, 2017,27(3):479-490. doi: 10.1101/gr.212803.116 pmid: 28057745
[76]	Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F . Functional and topological characteristics of mammalian regulatory domains. Genome Res, 2014,24(3):390-400. doi: 10.1101/gr.163519.113
[77]	Yin S, Feng Y, Mccleary DF, Zhen Y, Lee E, Samantha K, Ulrich W, Jesse D, Leonard L, Lobanenkov VV, Ren B . A map of the cis-regulatory sequences in the mouse genome. Nature, 2012,488(7409):116-120. doi: 10.1038/nature11243
[78]	Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M . Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell, 2015,162(5):1051-1065. doi: 10.1016/j.cell.2015.07.048 pmid: 26300125
[79]	Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET . Population variation and genetic control of modular chromatin architecture in humans. Cell, 2015,162(5):1039-1050. doi: 10.1016/j.cell.2015.08.001 pmid: 26300124
[80]	Fritz AJ, Ghule PN, Boyd JR, Tye CE, Page NA, Hong D, Shirley DJ, Weinheimer AS, Barutcu AR, Gerrard DL, Frietze S, van Wijnen AJ, Zaidi SK, Imbalzano AN, Lian JB, Stein JL, Stein GS. Intranuclear and higher- order chromatin organization of the major histone gene cluster in breast cancer. . Cell Physiol, 2018,233(2):278-1290. doi: 10.1002/jcp.25996 pmid: 28504305
[81]	Sanyal A, Lajoie BR, Jian G, Dekker J . The long-range interaction landscape of gene promoters. Nature, 2012,489(7414):109-113. doi: 10.1038/nature11279
[82]	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. doi: 10.1038/nature12644
[83]	Austenaa L, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman BM, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G,. Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination. Mol Cell, 2015,60(3):460-474. doi: 10.1016/j.molcel.2015.09.018 pmid: 26593720
[84]	Despang A, Schöpflin R, Franke M, Ali S, Jerković I, Paliou C, Chan WL, Timmermann B, Wittler L, Vingron M, Mundlos S, Ibrahim DM . Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture. Nat Genet, 2019,51(8):1263-1271. doi: 10.1038/s41588-019-0466-z pmid: 31358994
[85]	Bornfleth H, Edelmann P, Zink D, Cremer T, Cremer C . Quantitative motion analysis of subchromosomal foci in living cells using Four-Dimensional microscopy. Biophys J, 1999,77(5):2871-2886. doi: 10.1016/S0006-3495(99)77119-5 pmid: 10545385
[86]	Tang Z, Luo OJ, Nbsp O, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y . CTCF-Mediated human 3D genome architecture reveals chromatin topology for transcription. Cell, 2015,163(7):1611-1627. doi: 10.1016/j.cell.2015.11.024 pmid: 26686651
[87]	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. doi: 10.1016/j.cell.2014.11.021
[88]	Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E, Mulawadi FH, Sung WK, Nicolis S, Ahituv N, Ruan Y, Wei CL . Chromatin connectivity maps reveal dynamic promoter- enhancer long-range associations. Nature, 2013,504(7479):306-310. doi: 10.1038/nature12716
[89]	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):84-98. doi: 10.1016/j.cell.2011.12.014 pmid: 22265404
[90]	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. doi: 10.1016/j.cell.2014.05.050
[91]	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. doi: 10.1016/j.cell.2012.03.051
[92]	Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, Mclane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, Yuan GC, Young RA, George RE . BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature, 2019,572(7771):676-680. doi: 10.1038/s41586-019-1472-0 pmid: 31391581
[93]	Peng YL, Zhang YB . Enhancer and super-enhancer: Positive regulators in gene transcription. Anim Mod Exp Med, 2018,1(03):169-179. doi: 10.1002/ame2.12032 pmid: 30891562
[94]	Luo Z, Rhie SK, Lay FD, Farnham PJ . A prostate cancer risk element functions as a repressive loop that regulates HOXA13. Cell Rep, 2017,21(6):1411-1417. doi: 10.1016/j.celrep.2017.10.048 pmid: 29117547
[95]	de Laat W, Duboule D . Topology of mammalian developmental enhancers and their regulatory landscapes. Nature, 2013,502(7472):499-506. doi: 10.1038/nature12753
[96]	Palstra RJ, Tolhuis B, Splinter E, Nijmeijer R, Grosveld F, De Laat W . The β-globin nuclear compartment in development and erythroid differentiation. Nat Genet, 2003,35(2):190-194. doi: 10.1038/ng1244 pmid: 14517543
[97]	Vernimmen D, De Gobbi M, Sloane-Stanley JA, Wood WG, Higgs DR . Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. Embo J, 2014,26(8):2041-2051. doi: 10.1038/sj.emboj.7601654 pmid: 17380126
[98]	van De Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Öz Y, Bouwman BAM, Verstegen MJAM, De Wit E, Tanay A, De Laat W . Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods, 2012,9(10):969-972. doi: 10.1038/NMETH.2173
[99]	Cooper DN, Krawczak M . Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum Genet, 1989,83(2):181-188. doi: 10.1007/bf00286715 pmid: 2777259
[100]	Deng DJ . DNA methylation and demethylation: current status and future per-spective. Hereditas(Beijing), 2014,36(5):403-410. doi: 10.3724/SP.J.1005.2014.0403
	邓大君 . DNA甲基化和去甲基化的研究现状及思考. 遗传, 2014,36(5):403-410. doi: 10.3724/SP.J.1005.2014.0403
[101]	Lorincz MC, Dickerson DR, Schmitt M, Groudine M . Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol, 2004,11(11):1068-1075. doi: 10.1038/nsmb840 pmid: 15467727
[102]	Lin XQ, Su JZ, Chen KF, Rodriguez B, Li W . Sparse conserved under-methylated CpGs are associated with high-order chromatin structure. Genome Biol, 2017,18(1):163. doi: 10.1186/s13059-017-1296-x pmid: 28859663
[103]	Gudjonsson JE, Krueger G . A role for epigenetics in psoriasis: methylated cytosine-guanine sites differentiate lesional from nonlesional skin and from normal skin. . Invest Dermatol, 2012,132(1):506-508. doi: 10.1038/jid.2011.364 pmid: 22327261
[104]	Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE . Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature, 2016,529(7584):110-114. doi: 10.1038/nature16490 pmid: 26700815
[105]	Witkowski L, Foulkes WD . In Brief: Picturing the complex world of chromatin remodelling families. . Pathol, 2016,237(4):403-406. doi: 10.1002/path.4585 pmid: 26174723
[106]	Gangaraju VK, Bartholomew B . Mechanisms of ATP dependent chromatin remodeling. Mutat Res, 2007,618(1-2):3-17. doi: 10.1016/j.mrfmmm.2006.08.015 pmid: 17306844
[107]	Li MJ, Xia X, Tian YY, Jia Q, Liu XY, Lu Y, Li M, Li XM, Chen ZC . Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Nature, 2019,567(7748):409-413. doi: 10.1038/s41586-019-1029-2 pmid: 30867599
[108]	Yan LJ, Wu H, Li XM, Gao N, Chen ZC . Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling. Nat Struct Mol Biol, 2019,26:258-266. doi: 10.1038/s41594-019-0199-9 pmid: 30872815
[109]	Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C . ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science, 2004,303(5656):343-348. doi: 10.1126/science.1090701 pmid: 14645854
[110]	Mersfelder EL, Parthun MR . The tale beyond the tail: Histone core domain modifications and the regulation of chromatin structure. Nucleic Acids Res, 2006,34(9):2653-2662. doi: 10.1093/nar/gkl338 pmid: 16714444
[111]	Zhang R, Erler J, Langowski J . Histone acetylation regulates chromatin accessibility: Role of H4K16 in inter-nucleosome interaction. Biophys J, 2017,112(3):450-459. doi: 10.1016/j.bpj.2016.11.015 pmid: 27931745
[112]	Wang C, Fu M, Pestell RG . Histone acetylation/ deacetylation as a regulator of cell cycle gene expression. Methods Mol Biol, 2004,241(241):207-216. doi: 10.1016/j.ejcb.2009.11.006 pmid: 20004495
[113]	Dion MF, Altschuler SJ, Wu LF, Rando OJ . Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci USA, 2005,102(15):5501-5506. doi: 10.1073/pnas.0500136102 pmid: 15795371
[114]	Carmen AA, Milne L, Grunstein M . Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. . Biol Chem, 2002,277(7):4778-4781. doi: 10.1074/jbc.M110532200 pmid: 11714726
[115]	Nielsen PR, Nietlispach D, Mott HR, Callaghan J, Bannister A, Kouzarides T, Murzin AG, Murzina NV, Laue ED . Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature, 2002,416(6876):103-107. doi: 10.1038/nature722 pmid: 11882902
[116]	Zhao YQ, Jordan IK, Lunyak VV . Epigenetics components of aging in the central nervous system. Neurotherapeutics, 2013,10(4):647-663. doi: 10.1007/s13311-013-0229-y
[117]	Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD . Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell, 2013,155(1):107-120. doi: 10.1016/j.cell.2013.08.061
[118]	Fan JY, Gordon F, Luger K, Hansen JC, Tremethick DJ . The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nat Struct Biol, 2002,9(3):172-176. doi: 10.1038/nsb767 pmid: 11850638
[119]	Fan JY, Rangasamy D, Luger K, Tremethick DJ . H2A.Z alters the nucleosome surface to promote HP1alpha- mediated chromatin fiber folding. Mol Cell, 2004,16(4):655-661. doi: 10.1016/j.molcel.2004.10.023 pmid: 15546624
[120]	Feng Z, Chen XD, Zhang MD, Zhang MJ . Formation of biological condensates via phase separation: Characteristics, analytical methods, and physiological implications. . Biol Chem, 2019, ( 40), doi: 10.1074/jbc.rev119. 007895. doi: 10.1074/jbc.REV119.007895 pmid: 31444270
[121]	Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH . Phase separation drives heterochromatin domain formation. Nature, 2017,547(7662):241-245. doi: 10.1038/nature22989 pmid: 28636597
[122]	Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ . Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature, 2017,547(7662):236-240. doi: 10.1038/nature22822 pmid: 28636604
[123]	Larson AG, Narlikar GJ . The role of phase separation in heterochromatin formation, function, and regulation. Biochemistry, 2018,57(17):2540-2548. doi: 10.1021/acs.biochem.8b00401 pmid: 29644850
[124]	Shin Y, Chang Y, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP . Liquid nuclear condensates mechanically sense and restructure the genome. Cell, 2019,175(6):1481-1491. doi: 10.1016/j.cell.2018.10.057 pmid: 30500535
[125]	Forcato M, Nicoletti C, Pal K, Livi CM, Ferrari F, Bicciato S . Comparison of computational methods for Hi-C data analysis. Nat Methods, 2017,14(7):679-685. doi: 10.1038/nmeth.4325 pmid: 28604721
[126]	Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM . Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat Genet, 2019,51:1272-1282. doi: 10.1038/s41588-019-0462-3 pmid: 31308546
[127]	Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O’Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science, 2017, 357(6349): eaag0025. doi: 10.1126/science.357.6349.422 pmid: 28751612
[128]	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):u1783. doi: 10.1126/science.aau1783 pmid: 30361340
[129]	Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY . HiChIP: Efficient and sensitive analysis of protein-directed genome architecture. Nat Methods, 2016,13(11):919-922. doi: 10.1038/nmeth.3999 pmid: 27643841
[130]	Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN . Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature, 2019,568(7750):49-54. doi: 10.1038/s41586-019-1035-4 pmid: 30886393
[131]	Zhang Y, An L, Xu J, Zhang B, Zheng WJ, Hu M, Tang JJ, Yue F . Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus. Nat Commun, 2018,9(1):750. doi: 10.1038/s41467-018-03113-2 pmid: 29467363
[132]	Li WR, Wong WH, Jiang R . DeepTACT: Predicting 3D chromatin contacts via bootstrapping deep learning. Nucleic Acids Res, 2019,47(10):e60. doi: 10.1093/nar/gkz167 pmid: 30869141
[133]	Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature, 2017,549(7671):219-226. doi: 10.1038/nature23884 pmid: 28905911

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Linking chromatin conformation to gene function

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