综述 |
|
|
|
|
三维基因组学在动物遗传育种中的研究进展* |
陈羿何1,李欣淼1,彭巍2,雷初朝1,赵黄青1,张子敬3,刘贤4,黄永震1,**() |
1 西北农林科技大学动物科技学院 杨凌 712100 2 青海大学青海省畜牧兽医科学院 西宁 810016 3 河南省农业科学院畜牧兽医研究所 郑州 450002 4 河南省畜牧总站 郑州 450008 |
|
Research Progress of Three-dimensional Genomics in Animal Genetics and Breeding |
CHEN Yi-he1,LI Xin-miao1,PENG Wei2,LEI Chu-zhao1,ZHAO Huang-qing1,ZHANG Zi-jing3,LIU Xian4,HUANG Yong-zhen1,**() |
1 College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China 2 Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China 3 Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China 4 Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China |
引用本文:
陈羿何,李欣淼,彭巍,雷初朝,赵黄青,张子敬,刘贤,黄永震. 三维基因组学在动物遗传育种中的研究进展*[J]. 中国生物工程杂志, 2022, 42(4): 78-84.
CHEN Yi-he,LI Xin-miao,PENG Wei,LEI Chu-zhao,ZHAO Huang-qing,ZHANG Zi-jing,LIU Xian,HUANG Yong-zhen. Research Progress of Three-dimensional Genomics in Animal Genetics and Breeding. China Biotechnology, 2022, 42(4): 78-84.
链接本文:
https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.2110043
或
https://manu60.magtech.com.cn/biotech/CN/Y2022/V42/I4/78
|
[1] |
Green E D, Watson J D, Collins F S. Human Genome Project: twenty-five years of big biology. Nature, 2015, 526(7571): 29-31.
doi: 10.1038/526029a
|
[2] |
Dunham I, Kundaje A, Aldred S F, et al. An integrated encyclopedia of DNA elements in the human genome. Nature, 2012, 489 (7414): 57-74.
doi: 10.1038/nature11247
|
[3] |
Langer-Safer P R, Levine M, Ward D C. Immunological method for mapping genes on Drosophila polytene chromosomes. Proceedings of the National Academy of Sciences of the United States of America, 1982, 79(14): 4381-4385.
|
[4] |
Dekker J, Rippe K, Dekker M, et al. Capturing chromosome conformation. Science, 2002, 295(5558): 1306-1311.
pmid: 11847345
|
[5] |
Dekker J. The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nature Methods, 2006, 3 (1): 17-21.
pmid: 16369547
|
[6] |
Simonis M, Klous P, Splinter E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genetics, 2006, 38 (11): 1348-1354.
doi: 10.1038/ng1896
|
[7] |
Dostie J, Richmond T A, Arnaout R A, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Research, 2006, 16(10): 1299-1309.
pmid: 16954542
|
[8] |
Lieberman-Aiden E, van Berkum N L, Williams L, et al. 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
|
[9] |
Nagano T, Lubling Y, Stevens T J, et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 2013, 502 (7469): 59-64.
doi: 10.1038/nature12593
|
[10] |
Liu C. In situ hi-C library preparation for plants to study their three-dimensional chromatin interactions on a genome-wide scale. Methods in Molecular Biology (Clifton, N J), 2017, 1629: 155-166.
|
[11] |
Lin D, Hong P, Zhang S, et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature Genetics, 2018, 50 (5): 754-763.
doi: 10.1038/s41588-018-0111-2
pmid: 29700467
|
[12] |
Fullwood M J, Liu M H, Pan Y F, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature, 2009, 462(7269): 58-64.
doi: 10.1038/nature08497
|
[13] |
Li G L, Fullwood M J, Xu H, et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology, 2010, 11(2): R22.
doi: 10.1186/gb-2010-11-2-r22
|
[14] |
张富涵, 沈宗毅, 喻长远, 等. 三维基因组学研究进展. 生物工程学报, 2020, 36(12): 2791-2812.
|
|
Zhang F H, Shen Z Y, Yu C Y, et al. Advances in three-dimensional genomics. Chinese Journal of Biotechnology, 2020, 36(12): 2791-2812.
|
[15] |
Die stofflichen grundlagen der vererbung im organischen Reich. Nature, 1906, 75(1935): 98-99.
doi: 10.1038/075098a0
|
[16] |
Cremer T, Cremer M. Chromosome territories. Cold Spring Harbor Perspectives in Biology, 2010, 2(3): a003889.
|
[17] |
Su J H, Zheng P, Kinrot S S, et al. Genome-scale imaging of the 3D organization and transcriptional activity of chromatin. Cell, 2020, 182(6): 1641-1659.e26.
doi: 10.1016/j.cell.2020.07.032
|
[18] |
Branco M R, Pombo A. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biology, 2006, 4(5): e138.
doi: 10.1371/journal.pbio.0040138
|
[19] |
Lieberman-Aiden E, van Berkum N L, Williams L, et al. 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
|
[20] |
Dixon J R, Jung I, Selvaraj S, et al. Chromatin architecture reorganization during stem cell differentiation. Nature, 2015, 518 (7539): 331-336.
doi: 10.1038/nature14222
|
[21] |
罗扶农, 何梦楠, 唐茜子, 等. 哺乳动物染色质三维结构单元的特征及其相互关系. 农业生物技术学报, 2019, 27(8): 1485-1497.
|
|
Luo F N, He M N, Tang Q Z, et al. The characteristics and interrelation of three-dimensional structural units of chromatin in mammals. Journal of Agricultural Biotechnology, 2019, 27(8): 1485-1497.
|
[22] |
Nora E P, Lajoie B R, Schulz E G, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 2012, 485 (7398): 381-385.
doi: 10.1038/nature11049
|
[23] |
Dixon J R, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012, 485 (7398): 376-380.
doi: 10.1038/nature11082
|
[24] |
Dixon J R, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012, 485(7398):376-380.
doi: 10.1038/nature11082
|
[25] |
Kaaij L J T, van der Weide R H, Ketting R F, et al. Systemic loss and gain of chromatin architecture throughout zebrafish development. Cell Reports, 2018, 24(1): 1-10.e4.
doi: 10.1016/j.celrep.2018.06.003
|
[26] |
Zhou Z, Li M, Cheng H, et al. An intercross population study reveals genes associated with body size and plumage color in ducks. Nature Communications, 2018, 9: 2648.
doi: 10.1038/s41467-018-04868-4
|
[27] |
Dong Q L, Li N, Li X C, et al. Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice. The Plant Journal: for Cell and Molecular Biology, 2018, 94(6): 1141-1156.
doi: 10.1111/tpj.13925
|
[28] |
Wang M, Wang P, Lin M, et al. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. Nature Plants, 2018, 4 (2): 90-97.
doi: 10.1038/s41477-017-0096-3
|
[29] |
Smallwood A, Ren B. Genome organization and long-range regulation of gene expression by enhancers. Current Opinion in Cell Biology, 2013, 25(3): 387-394.
doi: 10.1016/j.ceb.2013.02.005
pmid: 23465541
|
[30] |
Sanyal A, Lajoie B R, Jain G, et al. The long-range interaction landscape of gene promoters. Nature, 2012, 489 (7414): 109-113.
doi: 10.1038/nature11279
|
[31] |
Pope B D, Ryba T, Dileep V, et al. Topologically associating domains are stable units of replication-timing regulation. Nature, 2014, 515 (7527): 402-405.
doi: 10.1038/nature13986
|
[32] |
Lupiáñez D G, Kraft K, Heinrich V, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell, 2015, 161(5): 1012-1025.
doi: S0092-8674(15)00377-3
pmid: 25959774
|
[33] |
Li L, Lyu X W, Hou C H, et al. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Molecular Cell, 2015, 58(2): 216-231.
doi: 10.1016/j.molcel.2015.02.023
pmid: 25818644
|
[34] |
Despang A, Schöpflin R, Franke M, et al. Functional dissection of the Sox9-Kcnj 2 locus identifies nonessential and instructive roles of TAD architecture. Nature Genetics, 2019, 51 (8): 1263-127
doi: 10.1038/s41588-019-0466-z
|
[35] |
答亮, 赵慕钧. 发育和癌症中染色质环结构变化. 生命的化学, 2002, 22(4): 329-331.
|
|
Da L, Zhao M J. Changes in chromatin ring structure in development and cancer. Chemistry of Life, 2002, 22(4): 329-331.
|
[36] |
Rao S S P, Huntley M H, Durand N C, et al. 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
|
[37] |
Zhao Y, Hou Y, Xu Y, et al. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications, 2021, 12: 2217.
doi: 10.1038/s41467-021-22448-x
|
[38] |
Li F F, Wang D Y, Song R G, et al. The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos. Genome Biology, 2020, 21: 203.
doi: 10.1186/s13059-020-02095-z
|
[39] |
Tian X M, Li R, Fu W W, et al. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Science China Life Sciences, 2020, 63(5): 750-763.
doi: 10.1007/s11427-019-9551-7
|
[40] |
Jin L, Tang Q, Hu S, et al. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nature Communications, 2021, 12: 3715.
doi: 10.1038/s41467-021-23560-8
|
[41] |
Ou J T. DNA molecular markers and animalsbreeding. Journal of Southwest University for Nationalities(Natural Sciens Edition), 2002, 28(4):524-529.
|
[42] |
夏文财, 鲁绍雄. 牛遗传图谱的研究进展. 吉林畜牧兽医, 2008, 29(5): 14-16.
|
|
Xia W C, Lu S X. Progress of research on genetic map of cattle. Jilin Animal Husbandry and Veterinary Medicine, 2008, 29(5): 14-16.
|
[43] |
Lee D, Cho M, Hong W Y, et al. Evolutionary analyses of hanwoo (Korean cattle)-specific single-nucleotide polymorphisms and genes using whole-genome resequencing data of a hanwoo population. Molecules and Cells, 2016, 39(9): 692-698.
doi: 10.14348/molcells.2016.0148
|
[44] |
Sasago N, Abe T, Sakuma H, et al. Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle. Animal Science Journal, 2017, 88(1): 33-44.
doi: 10.1111/asj.12595
pmid: 27112906
|
[45] |
Kim S J, Ka S, Ha J W, et al. Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama. BMC Genomics, 2017, 18(1): 371.
doi: 10.1186/s12864-017-3742-2
|
[46] |
曹修凯, 程杰, 王晓刚, 等. 动物染色质三维基因组及转录调控研究进展. 中国牛业科学, 2020, 46(3): 25-31, 83.
|
|
Cao X K, Cheng J, Wang X G, et al. Proceedings of 3D genome of animal chromatin and its transcriptional regulation. China Cattle Science, 2020, 46(3): 25-31, 83.
|
[47] |
Crawford A M, Dodds K G, Ede A J, et al. An autosomal genetic linkage map of the sheep genome. Genetics, 1995, 140(2): 703-724.
doi: 10.1093/genetics/140.2.703
pmid: 7498748
|
[48] |
de Gortari M J, Freking B A, Cuthbertson R P, et al. A second-generation linkage map of the sheep genome. Mammalian Genome, 1998, 9(3): 204-209.
pmid: 9501303
|
[49] |
Bickhart D M, Rosen B D, Koren S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics, 2017, 49(4): 643-650.
doi: 10.1038/ng.3802
pmid: 28263316
|
[50] |
Li X, Yang J, Shen M, et al. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nature Communications, 2020, 11: 2815.
doi: 10.1038/s41467-020-16485-1
|
[51] |
Du Z H, Zheng H, Huang B, et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature, 2017, 547(7662): 232-235.
doi: 10.1038/nature23263
|
[52] |
Chen M, Zhu Q S, Li C, et al. Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos. Nature Communications, 2020, 11(1): 1813.
doi: 10.1038/s41467-020-15607-z
pmid: 32286279
|
[53] |
Yang H B, Luan Y, Liu T T, et al. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature, 2020, 588(7837): 337-343.
doi: 10.1038/s41586-020-2962-9
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|