哺乳动物染色质三维结构单元的特征及其相互关系

doi:10.3969/j.issn.1674-7968.2019.08.017

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Abstract In the nucleus of mammals, chromatins are folded into various three-dimensional structural units, such as chromosome territories, chromatin compartments, topologically associating domains, and chromatin loops, etc. These structural units play key roles in the regulation of gene expression, cell differentiation and disease development. Previous studies suggested that these structural units represented three dimensional conformations of chromatin at different levels, and distributed hierarchically in mammalian cell nuclei. In recent years, with the rapid development of new technologies of chromatin conformation capture, it has been found that these structural units may not be a simple hierarchical architecture in the nucleus. In this review, we summarize the recently developed technologies of chromatin conformation capture,detailly describe the features and functions of different three-dimensional structural units of chromatin folding.Particularly, we focused on the interrelation among different chromatin structural units. This review provides a valuable reference for subsequent studies.

Key words： Mammal Chromatin three-dimensional structural units Hi-C technology Chromatin spatial conformation

Received: 04 December 2018

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Corresponding Authors: * , longjin@sicau.edu.cn

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	LUO Fu-Nong
	HE Meng-Nan
	TANG Qian-Zi
	LI Yan
	LI Ming-Zhou
	JIN Long

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LUO Fu-Nong,HE Meng-Nan,TANG Qian-Zi, et al. The Characteristics and Interrelation of Three-dimensional Structural Units of Chromatin in Mammals[J]. 农业生物技术学报, 2019, 27(8): 1485-1497.

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http://journal05.magtech.org.cn/Jwk_ny/EN/10.3969/j.issn.1674-7968.2019.08.017 OR http://journal05.magtech.org.cn/Jwk_ny/EN/Y2019/V27/I8/1485

[1] Bi X, Cheng Y J, Hu B, et al.2017. Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery[J]. Genome Research, 27(7): 1162-1173.
[2] Bolzer A, Kreth G, Solovei I, et al.2005. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes[J]. PLoS Biology, 3(5): e157.
[3] Bouwman B A, de Laat W.2015. Getting the genome in shape: The formation of loops, domains and compartments[J]. Genome Biology, 16: 154.
[4] Boyle S, Gilchrist S, Bridger J M, et al.2001. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells[J]. Human Molecular Genetics, 10(3): 211-219.
[5] Branco M R, Pombo A.2006. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations[J]. PLoS Biology, 4(5): e138.
[6] Carninci P, Kasukawa T, Katayama S, et al.2005. The transcriptional landscape of the mammalian genome[J]. Science, 309(5740): 1559-1563.
[7] Cesana M, Cacchiarelli D, Legnini I, et al.2011. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA[J]. Cell, 147(2): 358-369.
[8] Chimpanzee S, Analysis C.2005. Initial sequence of the chimpanzee genome and comparison with the human genome[J]. Nature, 437(7055): 69-87.
[9] Consortium E P.2012. An integrated encyclopedia of DNA elements in the human genome[J]. Nature, 489(7414): 57-74.
[10] Crane E, Bian Q, McCord R P, et al.2015. Condensin-driven remodelling of X chromosome topology during dosage compensation[J]. Nature, 523(7559): 240-244.
[11] Cremer T, Kurz A, Zirbel R, et al.1993. Role of chromosome territories in the functional compartmentalization of the cell nucleus[J]. Cold Spring Harbor Symposia on Quantitative Biology, 58: 777-792.
[12] Cremer T, Cremer C.2006a. Rise, fall and resurrection of chromosome territories: A historical perspective. PartⅠ. The rise of chromosome territories[J]. European Journal of Histochemistry, 50(3): 161-176.
[13] Cremer T, Cremer C.2006b. Rise, fall and resurrection of chromosome territories: A historical perspective. PartⅡ. Fall and resurrection of chromosome territories during the 1950s to 1980s. PartⅢ. Chromosome territories and the functional nuclear architecture: Experiments and models from the 1990s to the present[J]. European Journal of Histochemistry, 50(4): 223-272.
[14] Cremer T, Cremer M.2010. Chromosome territories[J]. Cold Spring Harbor Perspectives in Biology, 2(3): a003889.
[15] Croft J A, Bridger J M, Boyle S, et al.1999. Differences in the localization and morphology of chromosomes in the human nucleus[J]. Journal of Cell Biology, 145(6): 1119-1131.
[16] Dali R, Blanchette M.2017. A critical assessment of topologically associating domain prediction tools[J]. Nucleic Acids Research, 45(6): 2994-3005.
[17] Davies J O, Oudelaar A M, Higgs D R, et al.2017. How best to identify chromosomal interactions: A comparison of approaches[J]. Nature Methods, 14(2): 125-134.
[18] Dekker J, Rippe K, Dekker M, et al.2002. Capturing chromosome conformation[J]. Science, 295(5558): 1306-1311.
[19] Dekker J, Heard E.2015. Structural and functional diversity of topologically associating domains[J]. FEBS Letters, 589(20 Pt A): 2877-2884.
[20] Dekker J, Mirny L.2016. The 3D Genome as moderator of chromosomal communication[J]. Cell, 164(6): 1110-1121.
[21] Dekker J, Belmont A S, Guttman M, et al.2017. The 4D nucleome project[J]. Nature, 549(7671): 219-226.
[22] Dixon J R, Selvaraj S, Yue F, et al.2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions[J]. Nature, 485(7398): 376-380.
[23] Dixon J R, Jung I, Selvaraj S, et al.2015. Chromatin architecture reorganization during stem cell differentiation[J]. Nature, 518(7539): 331-336.
[24] Dixon J R, Gorkin D U, Ren B.2016. Chromatin domains: The unit of chromosome organization[J]. Molecular Cell, 62(5): 668-680.
[25] Dong P, Tu X, Chu P Y, et al.2017. 3D chromatin architecture of large plant genomes determined by local A/B compartments[J]. Molecular Plant, 10(12): 1497-1509.
[26] Dong Q, Li N, Li X, et al.2018. Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice[J]. Plant Journal, 94(6): 1141-1156.
[27] Dostie J, Richmond T A, Arnaout R A, et al.2006. Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements[J]. Genome Research, 16(10): 1299-1309.
[28] Dryden N H, Broome L R, Dudbridge F, et al.2014. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C[J]. Genome Research, 24(11): 1854-1868.
[29] Filippova D, Patro R, Duggal G, et al.2014. Identification of alternative topological domains in chromatin[J]. Algorithms for Molecular Biology, 9: 14.
[30] Forcato M, Nicoletti C, Pal K, et al.2017. Comparison of computational methods for Hi-C data analysis[J]. Nature Methods, 14(7): 679-685.
[31] Fritz A J, Barutcu A R, Martin-Buley L, et al.2016. Chromosomes at work: Organization of chromosome territories in the interphase nucleus[J]. Journal of Cellular Biochemistry, 117(1): 9-19.
[32] Fudenberg G, Imakaev M, Lu C, et al.2016. Formation of chromosomal domains by loop extrusion[J]. Cell Reports, 15(9): 2038-2049.
[33] Fullwood M J, Liu M H, Pan Y F, et al.2009. An oestrogen-receptor-alpha-bound human chromatin interactome[J]. Nature, 462(7269): 58-64.
[34] Ganji M, Shaltiel I A, Bisht S, et al.2018. Real-time imaging of DNA loop extrusion by condensin[J]. Science, 360(6384): 102-105.
[35] Gassler J, Brandao H B, Imakaev M, et al.2017. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture[J]. EMBO Journal, 36(24): 3600-3618.
[36] Haarhuis J H I, van der Weide R H, Blomen V A, et al.2017. The cohesin release factor WAPL restricts chromatin loop extension[J]. Cell, 169(4): 693-707 e614.
[37] Handoko L, Xu H, Li G, et al.2011. CTCF-mediated functional chromatin interactome in pluripotent cells[J]. Nature Genetics, 43(7): 630-638.
[38] Hong S, Kim D.2017. Computational characterization of chromatin domain boundary-associated genomic elements[J]. Nucleic Acids Research, 45(18): 10403-10414.
[39] Hsieh T H, Weiner A, Lajoie B, et al.2015. Mapping nucleosome resolution chromosome folding in yeast by Micro-C[J]. Cell, 162(1): 108-119.
[40] Ibn-Salem J, Muro E M, Andrade-Navarro M A.2017. Co-regulation of paralog genes in the three-dimensional chromatin architecture[J]. Nucleic Acids Research, 45(1): 81-91.
[41] Kaikkonen M U, Niskanen H, Romanoski C E, et al.2014. Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization[J]. Nucleic Acids Research, 42(20): 12570-12584.
[42] Kalhor R, Tjong H, Jayathilaka N, et al.2011. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling[J]. Nature Biotechnology, 30(1): 90-98.
[43] Ke Y, Xu Y, Chen X, et al.2017. 3D Chromatin structures of mature gametes and structural reprogramming during mammalian embryogenesis[J]. Cell, 170(2): 367-381 e320.
[44] Lander E S, Linton L M, Birren B, et al.2001. Initial sequencing and analysis of the human genome[J]. Nature, 409(6822): 860-921.
[45] Le Dily F, Bau D, Pohl A, et al.2014. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation[J]. Genes & Development, 28(19): 2151-2162.
[46] Le T B, Imakaev M V, Mirny L A, et al.2013. High-resolution mapping of the spatial organization of a bacterial chromosome[J]. Science, 342(6159): 731-734.
[47] Lieberman-Aiden E, van Berkum N L, Williams L, et al.2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome[J]. Science, 326(5950): 289-293.
[48] Lupianez D G, Kraft K, Heinrich V, et al.2015. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions[J]. Cell, 161(5): 1012-1025.
[49] Lupianez D G, Spielmann M, Mundlos S.2016. Breaking TADs: How alterations of chromatin domains result in disease[J]. Trends in Genetics, 32(4): 225-237.
[50] Martin P, McGovern A, Orozco G, et al.2015. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci[J]. Nat Commun, 6: 10069.
[51] Mizuguchi T, Fudenberg G, Mehta S, et al.2014. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe[J]. Nature, 516(7531): 432-435.
[52] Nagano T, Lubling Y, Stevens T J, et al.2013. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure[J]. Nature, 502(7469): 59-64.
[53] Nagano T, Lubling Y, Varnai C, et al.2017. Cell-cycle dynamics of chromosomal organization at single-cell resolution[J]. Nature, 547(7661): 61-67.
[54] Nora E P, Lajoie B R, Schulz E G, et al.2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre[J]. Nature, 485(7398): 381-385.
[55] Nora E P, Goloborodko A, Valton A L, et al.2017. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization[J]. Cell, 169(5): 930-944. e22.
[56] Parada L A, Roix J J, Misteli T.2003. An uncertainty principle in chromosome positioning[J]. Trends in Cell Biology, 13(8): 393-396.
[57] Phillips-Cremins J E, Sauria M E, Sanyal A, et al.2013. Architectural protein subclasses shape 3D organization of genomes during lineage commitment[J]. Cell, 153(6): 1281-1295.
[58] Pinkel D, Landegent J, Collins C, et al.1988. Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 and translocations of chromosome 4[J]. Proceedings of the National Academy of Sciences of the USA, 85(23): 9138-9142.
[59] Pope B D, Ryba T, Dileep V, et al.2014. Topologically associating domains are stable units of replication-timing regulation[J]. Nature, 515(7527): 402-405.
[60] Rao S S, Huntley M H, Durand N C, et al.2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping[J]. Cell, 159(7): 1665-1680.
[61] Rao S S P, Huang S C, Glenn St Hilaire B, et al.2017. Cohesin loss eliminates all loop domains[J]. Cell, 171(2): 305-320 e324.
[62] Roukos V, Misteli T.2014. The biogenesis of chromosome translocations[J]. Nature Cell Biology, 16(4): 293-300.
[63] Rowley M J, Nichols M H, Lyu X, et al.2017. Evolutionarily conserved principles predict 3D chromatin organization[J]. Molecular Cell, 67(5): 837-852 e837.
[64] Sanborn A L, Rao S S, Huang S C, et al.2015. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes[J]. Proceedings of the National Academy of Sciences of the USA, 112(47): E6456-6465.
[65] Sazer S, Schiessel H.2018. The biology and polymer physics underlying large-scale chromosome organization[J]. Traffic, 19(2): 87-104.
[66] Schmitt A D, Hu M, Jung I, et al.2016. A compendium of chromatin contact maps reveals spatially active regions in the human genome[J]. Cell Reports, 17(8): 2042-2059.
[67] Schwarzer W, Abdennur N, Goloborodko A, et al.2017. Two independent modes of chromatin organization revealed by cohesin removal[J]. Nature, 551(7678): 51-56.
[68] Sexton T, Yaffe E, Kenigsberg E, et al.2012. Three-dimensional folding and functional organization principles of the Drosophila genome[J]. Cell, 148(3): 458-472.
[69] Simonis M, Klous P, Splinter E, et al.2006. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)[J]. Nature Genetics, 38(11): 1348-1354.
[70] Sofueva S, Yaffe E, Chan W C, et al.2013. Cohesin-mediated interactions organize chromosomal domain architecture[J]. EMBO Journal, 32(24): 3119-3129.
[71] Solovei I, Cavallo A, Schermelleh L, et al.2002. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH)[J]. Experimental Cell Research, 276(1): 10-23.
[72] Sun H B, Shen J, Yokota H.2000. Size-dependent positioning of human chromosomes in interphase nuclei[J]. Biophysical Journal, 79(1): 184-190.
[73] Trussart M, Yus E, Martinez S, et al.2017. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae[J]. Nature Communications, 8: 14665.
[74] van Steensel B, Belmont A S.2017. Lamina-associated domains: Links with chromosome architecture, heterochromatin, and gene repression[J]. Cell, 169(5): 780-791.
[75] Wang C, Liu C, Roqueiro D, et al.2015a. Genome-wide analysis of local chromatin packing in Arabidopsis thaliana[J]. Genome Research, 25(2): 246-256.
[76] Wang J, Meng X, Chen H, et al.2016. Exploring the mechanisms of genome-wide long-range interactions: Interpreting chromosome organization[J]. Briefings in Functional Genomics, 15(5): 385-395.
[77] Wang X T, Dong P F, Zhang H Y, et al.2015b. Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes[J]. Nucleic Acids Research, 43(15): 7237-7246.
[78] Waterston R H, Lindblad-Toh K, Birney E, et al.2002. Initial sequencing and comparative analysis of the mouse genome[J]. Nature, 420(6915): 520-562.
[79] Wei Z, Gao F, Kim S, et al.2013. Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency[J]. Cell Stem Cell, 13(1): 36-47.
[80] Wutz G, Varnai C, Nagasaka K, et al.2017. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins[J]. EMBO Journal, 36(24): 3573-3599.
[81] Yu M, Ren B.2017. The three-dimensional organization of mammalian genomes[J]. Annual Review of Cell and Developmental Biology, 33: 265-289.
[82] Zhao Z, Tavoosidana G, Sjolinder M, et al.2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions[J]. Nature Genetics, 38(11): 1341-1347.
[83] Zuin J, Dixon J R, van der Reijden M I, et al.2014. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells[J]. Proceedings of the National Academy of Sciences of the USA, 111(3): 996-1001.