Amano T, Sagai T, Tanabe H, Mizushina Y, Nakazawa H, Shiroishi T. 2009. Chromosomal dynamics at the Shh locus: Limb bud-specific differential regulation of competence and active transcription. Developmental Cell, 16, 47–57.

Armstrong E E, Taylor R W, Miller D E, Kaelin C B, Barsh G S, Hadly E A, Petrov D. 2020. Long live the king: Chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biology, 18, 1–14.

Avni R, Nave M, Barad O, Baruch K, Twardziok S O, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K. 2017. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science, 357, 93–97.

Barbieri M, Xie S Q, Triglia E T, Chiariello A M, Bianco S, Santiago I, Branco M R, Rueda D, Nicodemi M, Pombo A. 2017. Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nature Structural & Molecular Biology, 24, 515–524.

Barutcu A R, Maass P G, Lewandowski J P, Weiner C L, Rinn J L. 2018. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nature Communications, 9, 1–11.

Batra S S, Levy-Sakin M, Robinson J, Guillory J, Durinck S, Vilgalys T P, Kwok P Y, Cox L A, Seshagiri S, Song Y S. 2020. Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data. Gigascience, 9, giaa134.

Beagan J A, Phillips-Cremins J E. 2020. On the existence and functionality of topologically associating domains. Nature Genetics, 52, 8–16.

Beagrie R A, Scialdone A, Schueler M, Kraemer D C, Chotalia M, Xie S Q, Barbieri M, Santiago I, Lavitas L M, Branco M R. 2017. Complex multi-enhancer contacts captured by genome architecture mapping. Nature, 543, 519–524.

Belaghzal H, Dekker J, Gibcus J. 2017. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods, 123, 56–65.

Beliveau B J, Boettiger A N, Avendaño M S, Jungmann R, McCole R B, Joyce E F, Kim-Kiselak C, Bantignies F, Fonseka C Y, Erceg J. 2015. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nature Communications, 6, 1–13.

Bianchi A, Mozzetta C, Pegoli G, Lucini F, Valsoni S, Rosti V, Petrini C, Cortesi A, Gregoretti F, Antonelli L. 2020. Dysfunctional polycomb transcriptional repression contributes to lamin A/C-dependent muscular dystrophy. The Journal of Clinical Investigation, 130, 2408–2421.

Bickhart D M, Kolmogorov M, Tseng E, Portik D M, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan S T, Shin S. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology, 40, 711–719.

Bickhart D M, Rosen B D, Koren S, Sayre B L, Hastie A R, Chan S, Lee J, Lam E T, Liachko I, Sullivan S T. 2017. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics, 49, 643–650.

Bose D A, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger S L. 2017. RNA binding to CBP stimulates histone acetylation and transcription. Cell, 168, 135–149.

Branco M R, Pombo A. 2006. Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biology, 4, e138.

Burton J N, Adey A, Patwardhan R P, Qiu R, Kitzman J O, Shendure J. 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology, 31, 1119–1125.

Cai Y, Fu W, Cai D, Heller R, Zheng Z, Wen J, Li H, Wang X, Alshawi A, Sun Z. 2020. Ancient genomes reveal the evolutionary history and origin of cashmere-producing goats in China. Molecular Biology and Evolution, 37, 2099–2109.

Cao X, Cheng J, Huang Y, Lan X, Lei C, Chen H. 2021. Comparative enhancer map of cattle muscle genome annotated by ATAC-Seq. Frontiers in Veterinary Science, 8, 1–12.

Chen B, Gilbert L A, Cimini B A, Schnitzbauer J, Zhang W, Li G W, Park J, Blackburn E H, Weissman J S, Qi L S. 2013. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell, 155, 1479–1491.

Chen H, Levo M, Barinov L, Fujioka M, Jaynes J B, Gregor T. 2018. Dynamic interplay between enhancer–promoter topology and gene activity. Nature Genetics, 50, 1296–1303.

Chen H, Xiao J, Shao T, Wang L, Bai J, Lin X, Ding N, Qu Y, Tian Y, Chen X. 2019. Landscape of enhancer–enhancer cooperative regulation during human cardiac commitment. Molecular Therapy-Nucleic Acids, 17, 840–851.

Cho S W, Xu J, Sun R, Mumbach M R, Carter A C, Chen Y G, Yost K E, Kim J, He J, Nevins S A. 2018. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell, 173, 1398–1412.

Choi D, Goo H G, Yoo J, Kang S. 2011. Identification of RNF2-responding loci in long-range chromatin interactions using the novel 4C-ChIP-Cloning technology. Journal of Biotechnology, 151, 312–318.

Consortium E P. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74.

Cremer T, Cremer M. 2010. Chromosome territories. Cold Spring Harbor Perspectives in Biology, 2, a003889.

Dall’Agnese A, Caputo L, Nicoletti C, Lulio J, Schmitt A, Gatto S, Diao Y, Ye Z, Forcato M, Perera R. 2019. Transcription factor-directed re-wiring of chromatin architecture for somatic cell nuclear reprogramming toward trans-differentiation. Molecular Cell, 76, 453–472.

Davenport K M, Bickhart D M, Worley K, Murali S C, Salavati M, Clark E L, Cockett N E, Heaton M P, Smith T P, Murdoch B. 2022. An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. Gigascience, 11, giab096.

Davies J O, Oudelaar A M, Higgs D R, Hughes J R. 2017. How best to identify chromosomal interactions: A comparison of approaches. Nature Methods, 14, 125–134.

Davies J O, Telenius J M, McGowan S J, Roberts N A, Taylor S, Higgs D R, Hughes J. 2016. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nature Methods, 13, 74–80.

Davis C A, Hitz B C, Sloan C A, Chan E T, Davidson J M, Gabdank I, Hilton J A, Jain K, Baymuradov U K, Narayanan A K. 2018. The Encyclopedia of DNA elements (ENCODE): Data portal update. Nucleic Acids Research, 46, D794–D801.

Dekker J, Rippe K, Dekker M, Kleckner N. 2002. Capturing chromosome conformation. Science, 295, 1306–1311.

Deng W, Lee J, Wang H, Miller J, Reik A, Gregory P D, Dean A, Blobel G A. 2012. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell, 149, 1233–1244.

Dixon J R, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget J E, Lee A Y, Ye Z, Kim A, Rajagopal N, Xie W. 2015. Chromatin architecture reorganization during stem cell differentiation. Nature, 518, 331–336.

Dixon J R, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu J S, Ren B. 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376–380.

Dong Q, Li N, Li X, Yuan Z, Xie D, Wang X, Li J, Yu Y, Wang J, Ding B. 2018. Genome‐wide Hi‐C analysis reveals extensive hierarchical chromatin interactions in rice. The Plant Journal, 94, 1141–1156.

Dostie J, Dekker J. 2007. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols, 2, 988–1002.

Dostie J, Richmond T A, Arnaout R A, Selzer R R, Lee W L, Honan T A, Rubio E D, Krumm A, Lamb J, Nusbaum C. 2006. Chromosome conformation capture carbon copy (5C): A massively parallel solution for mapping interactions between genomic elements. Genome Research, 16, 1299–1309.

Du X, Huang G, He S, Yang Z, Sun G, Ma X, Li N, Zhang X, Sun J, Liu M. 2018. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature Genetics, 50, 796–802.

Dudchenko O, Batra S S, Omer A D, Nyquist S K, Hoeger M, Durand N C, Shamim M S, Machol I, Lander E S, Aiden A P. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356, 92–95.

Edge P, Bafna V, Bansal V. 2017. HapCUT2: Robust and accurate haplotype assembly for diverse sequencing technologies. Genome Research, 27, 801–812.

Van Eenennaam A L. 2017. Genetic modification of food animals. Current Opinion in Biotechnology, 44, 27–34.

Eres I E, Gilad Y. 2020. A TAD skeptic: Is 3D genome topology conserved? Trends in Genetics, 37, 216–223.

Fang L, Cai W, Liu S, Canela-Xandri O, Gao Y, Jiang J, Rawlik K, Li B, Schroeder S G, Rosen B D. 2020. Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle. Genome Research, 30, 790–801.

Fang R, Yu M, Li G, Chee S, Liu T, Schmitt A D, Ren B. 2016. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Research, 26, 1345.

Feng Y, Wang Y, Wang X, He X, Yang C, Naseri A, Pederson T, Zheng J, Zhang S, Xiao X. 2020. Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. Genome Biology, 21, 1–24.

Field M A, Rosen B D, Dudchenko O, Chan E K, Minoche A E, Edwards R J, Barton K, Lyons R J, Tuipulotu D E, Hayes V M. 2020. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience, 9, 1–12.

Fishman V, Battulin N, Nuriddinov M, Maslova A, Zlotina A, Strunov A, Chervyakova D, Korablev A, Serov O, Krasikova A. 2019. 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin. Nucleic Acids Research, 47, 648–665.

Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P. 2019. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biology, 17, 1–25.

Franke M, Ibrahim D M, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan W L. 2016. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature, 538, 265–269.

Fu W, Wang R, Nanaei H A, Wang J, Hu D, Jiang Y. 2021. RGD v2. 0: A major update of the ruminant functional and evolutionary genomics database. Nucleic Acids Research, 50, D1091–D1099.

Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny L A. 2016. Formation of chromosomal domains by loop extrusion. Cell Reports, 15, 2038–2049.

Furlong E E, Levine M. 2018. Developmental enhancers and chromosome topology. Science, 361, 1341–1345.

Ganji M, Shaltiel I A, Bisht S, Kim E, Kalichava A, Haering C H, Dekker C. 2018. Real-time imaging of DNA loop extrusion by condensin. Science, 360, 102–105.

Gibcus J H, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki M T, Xie L, Paulson J R, Earnshaw W C. 2018. A pathway for mitotic chromosome formation. Science, 359, eaao6135.

Goel V Y, Hansen A S. 2020. The macro and micro of chromosome conformation capture. Wiley Interdisciplinary Reviews (Developmental Biology), 10, e395.

Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin D U, Jung I, Wu H, Zhai Y, Tang Y. 2015. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function. Cell, 162, 900–910.

Haarhuis J H, Weide R H, Blomen V A, Yáñez-Cuna J O, Amendola M, Ruiten M S, Krijger P H, Teunissen H, Medema R H, Steensel B. 2017. The cohesin release factor WAPL restricts chromatin loop extension. Cell, 169, 693–707.

Halstead M M, Kern C, Saelao P, Wang Y, Chanthavixay G, Medrano J F, Van Eenennaam A L, Korf I, Tuggle C K, Ernst C W. 2020. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics, 21, 1–16.

He K, Zhao L, Yuan Z, Canario A, Liu Q, Chen S, Guo J, Luo W, Yan H, Zhang D. 2022. Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologies. Scientific Data, 9, 482.

He M, Li Y, Tang Q, Li D, Jin L, Tian S, Che T, He S, Deng L, Gao G. 2018. Genome-wide chromatin structure changes during adipogenesis and myogenesis. International Journal of Biological Sciences, 14, 1571.

Heaton M P, Smith T P, Bickhart D M, Vander Ley B L, Kuehn L A, Oppenheimer J, Shafer W R, Schuetze F T, Stroud B, McClure J. 2021. A reference genome assembly of Simmental cattle, Bos taurus taurus. Journal of Heredity, 112, 184–191.

Heinz S, Texari L, Hayes M G, Urbanowski M, Chang M W, Givarkes N, Rialdi A, White K M, Albrecht R A, Pache L. 2018. Transcription elongation can affect genome 3D structure. Cell, 174, 1522–1536.

Hepperger C, Otten S, Hase J, Dietzel S. 2007. Preservation of large-scale chromatin structure in FISH experiments. Chromosoma, 116, 117–133.

Hildebrand E M, Dekker J. 2020. Mechanisms and functions of chromosome compartmentalization. Trends in Biochemical Sciences, 45, 385–396.

Hofmann A. 2020. 3D organization of eukaryotic and prokaryotic genomes. Ph D thesis, Combined Faculty of Natural Sciences and Mathematics of Heidelberg University, Germany.

Hsieh C L, Fei T, Chen Y, Li T, Gao Y, Wang X, Sun T, Sweeney C J, Lee G, Chen S. 2014. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proceedings of the National Academy of Sciences of the United States of America, 111, 7319–7324.

Hu S, Lv P, Yan Z, Wen B. 2019. Disruption of nuclear speckles reduces chromatin interactions in active compartments. Epigenetics & Chromatin, 12, 1–12.

Hwang Y C, Lin C F, Valladares O, Malamon J, Kuksa P P, Zheng Q, Gregory B D, Wang L. 2015. HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements. Bioinformatics, 31, 1290–1292.

Javierre B M, Burren O S, Wilder S P, Kreuzhuber R, Hill S M, Sewitz S, Cairns J, Wingett S W, Várnai C, Thiecke M J. 2016. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell, 167, 1369–1384.

Johnston M J, Nikolic A, Ninkovic N, Guilhamon P, Cavalli F, Seaman S, Zemp F J, Lee J, Abdelkareem A, Ellestad K, Murison A, Kushida M M, Coutinho F J, Ma Y, Mungall A J, Moore R, Marra M A, Taylor M D, Dirks P B, Pugh T J, et al. 2019. High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma. Genome Research, 29, 1211–1222.

Joshi O, Wang S Y, Kuznetsova T, Atlasi Y, Peng T, Fabre P J, Habibi E, Shaik J, Saeed S, Handoko L. 2015. Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency. Cell Stem Cell, 17, 748–757.

Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. 2012. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nature Biotechnology, 30, 90–98.

Kaplan N, Dekker J. 2013. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology, 31, 1143.

Karim L, Takeda H, Lin L, Druet T, Arias J A, Baurain D, Cambisano N, Davis S R, Farnir F, Grisart B. 2011. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics, 43, 405–413.

Kaul A, Bhattacharyya S, Ay F. 2020. Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2. Nature Protocols, 15, 991–1012.

Kempfer R, Pombo A. 2019. Methods for mapping 3D chromosome architecture. Nature Reviews Genetics, 21, 207–226.

Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A. 2021. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications, 12, 1–11.

Kim J H, Rege M, Valeri J, Dunagin M C, Metzger A, Titus K R, Gilgenast T G, Gong W, Beagan J A, Raj A. 2019. LADL: Light-activated dynamic looping for endogenous gene expression control. Nature Methods, 16, 633–639.

Kim J H, Titus K R, Gong W, Beagan J A, Cao Z, Phillips-Cremins J. 2018. 5C-ID: Increased resolution chromosome-conformation-capture-carbon-copy with in situ 3C and double alternating primer design. Methods, 142, 39–46.

Kim T H, Dekker J. 2018. Generation of ChIP-loop libraries. Cold Spring Harbor Protocols, 2018, doi: 10.1101/pdb.prot097857.

Kim T K, Hemberg M, Gray J M, Costa A M, Bear D M, Wu J, Harmin D A, Laptewicz M, Barbara-Haley K, Kuersten S. 2010. Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182–187.

Kim Y H, Marhon S A, Zhang Y, Steger D J, Won K J, Lazar M A. 2018. Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription. Science, 359, 1274–1277.

Van Koningsbruggen S, Gierliński M, Schofield P, Martin D, Barton G J, Ariyurek Y, den Dunnen J T, Lamond A I. 2010. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli. Molecular Biology of the Cell, 21, 3735–3748.

Kragesteen B K, Spielmann M, Paliou C, Heinrich V, Schöpflin R, Esposito A, Annunziatella C, Bianco S, Chiariello A M, Jerković I. 2018. Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. Nature Genetics, 50, 1463–1473.

Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker J D, Conte M, Gorkin D, Yu M, Li B, Dixon J R, Hu M, Nicodemi M, Zhao H, Ren B. 2021. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nature Structural & Molecular Biology, 28, 152–161.

Lai F, Orom U A, Cesaroni M, Beringer M, Taatjes D J, Blobel G A, Shiekhattar R. 2013. Activating RNAs associate with mediator to enhance chromatin architecture and transcription. Nature, 494, 497–501.

Laible G, Wei J, Wagner S. 2015. Improving livestock for agriculture–technological progress from random transgenesis to precision genome editing heralds a new era. Biotechnology Journal, 10, 109–120.

Li D, He M, Tang Q, Tian S, Zhang J, Li Y, Wang D, Jin L, Ning C, Zhu W. 2022. Comparative 3D genome architecture in vertebrates. BMC Biology, 20, 1–21.

Li F, Wang D, Song R, Cao C, Zhang Z, Wang Y, Li X, Huang J, Liu Q, Hou N, Xu B, Li X, Gao X, Jia Y, Zhao J, Wang Y. 2020. The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos. Genome Biology, 21, 203.

Li G, Fullwood M J, Xu H, Mulawadi F H, Velkov S, Vega V, Ariyaratne P N, Mohamed Y B, Ooi H S, Tennakoon C. 2010. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology, 11, R22.

Li J, Xiang Y, Zhang L, Qi X, Zheng Z, Zhou P, Tang Z, Jin Y, Zhao Q, Fu Y. 2022. Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome. BMC Biology, 20, 1–17.

Li M, Gan J, Sun Y, Xu Z, Yang J, Sun Y, Li C. 2020. Architectural proteins for the formation and maintenance of the 3D genome. Science China Life Sciences, 63, 795–810.

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen A Y, Merkurjev D, Zhang J, Ohgi K, Song X. 2013. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature, 498, 516–520.

Li W, Notani D, Rosenfeld M G. 2016. Enhancers as non-coding RNA transcription units: Recent insights and future perspectives. Nature Reviews Genetics, 17, 207.

Li X, Luo O J, Wang P, Zheng M, Wang D, Piecuch E, Zhu J J, Tian S Z, Tang Z, Li G. 2017. Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Nature Protocols, 12, 899–915.

Li Y, Gao G, Lin Y, Hu S, Luo Y, Wang G, Jin L, Wang Q, Wang J, Tang Q. 2020. Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome. GigaScience, 9, giaa114.

Lieberman-Aiden E, Berkum N L, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B R, Sabo P J, Dorschner M O. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289–293.

Lievens A, Petrillo M, Querci M, Patak A. 2015. Genetically modified animals: Options and issues for traceability and enforcement. Trends in Food Science & Technology, 44, 159–176.

Lilja K C, Zhang N, Magli A, Gunduz V, Bowman C J, Arpke R W, Darabi R, Kyba M, Perlingeiro R, Dynlacht B D. 2017. Pax7 remodels the chromatin landscape in skeletal muscle stem cells. PLoS ONE, 12, e0176190.

Lin X, Liu Y, Liu S, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H. 2022. Nested epistasis enhancer networks for robust genome regulation. Science, 377, 1077–1085.

Lindblad-Toh K, Garber M, Zuk O, Lin M F, Parker B J, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478, 476–482.

Liu R, Li X, Zhang X, Ren R, Sun Y, Tian X, Zhang Q, Zhao S, Yu M, Cao J. 2022. Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle. Genomics, 114, 110482.

Liu S, Gao Y, Canela-Xandri O, Wang S, Yu Y, Cai W, Li B, Xiang R, Chamberlain A J, Pairo-Castineira E. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics, 54, 1438–1447.

Liu S, Yu Y, Zhang S, Cole J B, Tenesa A, Wang T, McDaneld T G, Ma L, Liu G E, Fang L. 2020. Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. BMC Biology, 18, 1–16.

Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders M J, Ruzzante L, Feron R, Waterhouse R M, Wu Y. 2022. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nature Communications, 13, 1–22.

Lupiáñez D G, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz J M, Laxova R. 2015. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell, 161, 1012–1025.

Ma H, Tu L C, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. 2016. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nature Biotechnology, 34, 528–530.

Maass P G, Barutcu A R, Weiner C L, Rinn J L. 2018. Inter-chromosomal contact properties in live-cell imaging and in Hi-C. Molecular Cell, 69, 1039–1045.

Magli A, Baik J, Pota P, Cordero C O, Kwak I Y, Garry D J, Love P E, Dynlacht B D, Perlingeiro R C. 2019. Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nature Communications, 10, 1–17.

Marti-Marimon M, Vialaneix N, Lahbib-Mansais Y, Zytnicki M, Camut S, Robelin D, Yerle-Bouissou M, Foissac S. 2021. Major reorganization of chromosome conformation during muscle development in pig. Frontiers in Genetics, 12, 748239.

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok S O, Wicker T, Radchuk V, Dockter C, Hedley P E, Russell J. 2017. A chromosome conformation capture ordered sequence of the barley genome. Nature, 544, 427–433.

Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe N. 2017. GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. PLoS ONE, 12, e0174744.

Morgan S L, Mariano N C, Bermudez A, Arruda N L, Wu F, Luo Y, Shankar G, Jia L, Chen H. 2017. Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping. Nature Communications, 8, 1–9.

Mousavi K, Zare H, Dell’Orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager G L, Sartorelli V. 2013. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Molecular Cell, 51, 606–617.

Mumbach M R, Rubin A J, Flynn R A, Dai C, Khavari P A, Greenleaf W J, Chang H Y. 2016. HiChIP: Efficient and sensitive analysis of protein-directed genome architecture. Nature Methods, 13, 919–922.

Nagano T, Lubling Y, Stevens T J, Schoenfelder S, Yaffe E, Dean W, Laue E D, Tanay A, Fraser P. 2013. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature, 502, 59–64.

Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, Cohen N M, Wingett S, Fraser P, Tanay A. 2017. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature, 547, 61–67.

Nagano T, Lubling Y, Yaffe E, Wingett S W, Dean W, Tanay A, Fraser P. 2015. Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell. Nature Protocols, 10, 1986–2003.

Naumova N, Smith E M, Zhan Y, Dekker J. 2012. Analysis of long-range chromatin interactions using chromosome conformation capture. Methods, 58, 192–203.

Naval-Sanchez M, Nguyen Q, McWilliam S, Porto-Neto L R, Tellam R, Vuocolo T, Reverter A, Perez-Enciso M, Brauning R, Clarke S. 2018. Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds. Nature Communications, 9, 1–13.

Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G. 2010. Initial genomics of the human nucleolus. PLoS Genetics, 6, e1000889.

Nguyen Q H, Tellam R L, Naval-Sanchez M, Porto-Neto L R, Barendse W, Reverter A, Hayes B, Kijas J, Dalrymple B P. 2018. Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics data. GigaScience, 7, gix136.

Nora E P, Lajoie B R, Schulz E G, Giorgetti L, Okamoto I, Servant N, Piolot T, Berkum N L, Meisig J, Sedat J. 2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature, 485, 381–385.

O’Sullivan J M, Hendy M D, Pichugina T, Wake G C, Langowski J. 2013. The statistical-mechanics of chromosome conformation capture. Nucleus, 4, 390–398.

Padeken J, Heun P. 2014. Nucleolus and nuclear periphery: Velcro for heterochromatin. Current opinion in Cell Biology, 28, 54–60.

Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L. 2021. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Molecular Ecology Resources, 21, 2093–2108.

Pombo A, Dillon N. 2015. Three-dimensional genome architecture: Players and mechanisms. Nature Reviews Molecular Cell Biology, 16, 245–257.

Pontvianne F, Carpentier M C, Durut N, Pavlištová V, Jaške K, Schořová Š, Parrinello H, Rohmer M, Pikaard C S, Fojtová M. 2016. Identification of nucleolus-associated chromatin domains reveals a role for the nucleolus in 3D organization of the A. thaliana genome. Cell Reports, 16, 1574–1587.

Prowse-Wilkins C P, Wang J, Xiang R, Garner J B, Goddard M E, Chamberlain A J. 2021. Putative causal variants are enriched in annotated functional regions from six bovine tissues. Frontiers in Genetics, 12, 1–17.

Quinodoz S A, Ollikainen N, Tabak B, Palla A, Schmidt J M, Detmar E, Lai M M, Shishkin A A, Bhat P, Takei Y. 2018. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell, 174, 744–757.

Raap A, Marijnen J, Vrolijk J, Ploeg M. 1986. Denaturation, renaturation, and loss of DNA during in situ hybridization procedures. Cytometry: The Journal of the International Society for Analytical Cytology, 7, 235–242.

Rao S S, Huntley M H, Durand N C, Stamenova E K, Bochkov I D, Robinson J T, Sanborn A L, Machol I, Omer A D, Lander E S. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159, 1665–1680.

Raymond O, Gouzy J, Just J, Badouin H, Verdenaud M, Lemainque A, Vergne P, Moja S, Choisne N, Pont C. 2018. The rosa genome provides new insights into the domestication of modern roses. Nature Genetics, 50, 772–777.

Razin S V, Ulianov S V. 2017. Gene functioning and storage within a folded genome. Cellular & Molecular Biology Letters, 22, 1–15.

Redin C, Brand H, Collins R L, Kammin T, Mitchell E, Hodge J C, Hanscom C, Pillalamarri V, Seabra C M, Abbott M A. 2017. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nature Genetics, 49, 36–45.

Ren G, Jin W, Cui K, Rodrigez J, Hu G, Zhang Z, Larson D R, Zhao K. 2017. CTCF-mediated enhancer-promoter interaction is a critical regulator of cell-to-cell variation of gene expression. Molecular Cell, 67, 1049–1058.

Rowley M J, Corces V G. 2018. Organizational principles of 3D genome architecture. Nature Reviews Genetics, 19, 789–800.

Rowley M J, Nichols M H, Lyu X, Ando-Kuri M, Rivera I, Hermetz K, Wang P, Ruan Y, Corces V G. 2017. Evolutionarily conserved principles predict 3D chromatin organization. Molecular Cell, 67, 837–852.

Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T. 2005. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development, 132, 797–803.

De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi B K, Muller H, Ragoussis J, Wei C L, Natoli G. 2010. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biology, 8, e1000384.

Schaukowitch K, Joo J Y, Liu X, Watts J K, Martinez C, Kim T K. 2014. Enhancer RNA facilitates NELF release from immediate early genes. Molecular Cell, 56, 29–42.

Schmid M W, Grob S, Grossniklaus U. 2015. HiCdat: A fast and easy-to-use Hi-C data analysis tool. BMC Bioinformatics, 16, 1–6.

Schoenfelder S, Fraser P. 2019. Long-range enhancer–promoter contacts in gene expression control. Nature Reviews Genetics, 20, 437–455.

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca N A, Huber W, Haering C H, Mirny L. 2017. Two independent modes of chromatin organization revealed by cohesin removal. Nature, 551, 51–56.

Scionti I, Hayashi S, Mouradian S, Girard E, Lima J E, Morel V, Simonet T, Wurmser M, Maire P, Ancelin K. 2017. LSD1 controls timely MyoD expression via MyoD core enhancer transcription. Cell Reports, 18, 1996–2006.

Selvaraj S, Dixon J R, Bansal V, Ren B. 2013. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nature Biotechnology, 31, 1111.

Servant N, Varoquaux N, Lajoie B R, Viara E, Chen C J, Vert J P, Heard E, Dekker J, Barillot E. 2015. HiC-Pro: An optimized and flexible pipeline for Hi-C data processing. Genome Biology, 16, 1–11.

Session A M, Uno Y, Kwon T, Chapman J A, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M. 2016. Genome evolution in the allotetraploid frog Xenopus laevis. Nature, 538, 336–343.

Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng C H, Koulena N, Cronin C, Karp C, Liaw E J. 2018. Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Cell, 174, 363–376.

Shao D, Yang Y, Shi S, Tong H. 2022. Three-dimensional organization of chicken genome provides insights into genetic adaptation to extreme environments. Genes, 13, 2317.

Sigova A A, Abraham B J, Ji X, Molinie B, Hannett N M, Guo Y E, Jangi M, Giallourakis C C, Sharp P A, Young R A. 2015. Transcription factor trapping by RNA in gene regulatory elements. Science, 350, 978–981.

Sima J, Chakraborty A, Dileep V, Michalski M, Klein K N, Holcomb N P, Turner J L, Paulsen M T, Rivera-Mulia J C, Trevilla-Garcia C. 2019. Identifying cis elements for spatiotemporal control of mammalian DNA replication. Cell, 176, 816–830.

Smemo S, Tena J J, Kim K H, Gamazon E R, Sakabe N J, Gómez-Marín C, Aneas I, Credidio F L, Sobreira D R, Wasserman N F. 2014. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature, 507, 371–375.

Song D, Qian Y, Meng M, Dong X, Lv W, Huo T. 2021. Chromosome-level genome assembly of the burbot (Lota lota) using nanopore and Hi-C technologies. Frontiers in Genetics, 12, 747552.

Spitz F. 2016. Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles. Seminars in Cell & Developmental Biology, 57, 57–67.

Stadhouders R, Filion G J, Graf T. 2019. Transcription factors and 3D genome conformation in cell-fate decisions. Nature, 569, 345–354.

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y. 2018. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nature Genetics, 50, 238–249.

Stevens T J, Lando D, Basu S, Atkinson L P, Cao Y, Lee S F, Leeb M, Wohlfahrt K J, Boucher W, O’Shaughnessy-Kirwan A. 2017. 3D structures of individual mammalian genomes studied by single-cell Hi-C. Nature, 544, 59–64.

Stunnenberg H G, Abrignani S, Adams D, Almeida M, Altucci L, Amin V, Amit I, Antonarakis S E, Aparicio S, Arima T. 2016. The international human epigenome consortium: A blueprint for scientific collaboration and discovery. Cell, 167, 1145–1149.

Symmons O, Uslu V, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. 2014. Functional and topological characteristics of mammalian regulatory domains. Genome Research, 24, 390–400.

Tan L, Xing D, Chang C H, Li H, Xie X S. 2018. Three-dimensional genome structures of single diploid human cells. Science, 361, 924–928.

Teh B T, Lim K, Yong C H, Ng C, Rao S R, Rajasegaran V, Lim W K, Ong C K, Chan K, Cheng V. 2017. The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics, 49, 1633–1641.

Tian H, Yang Y, Liu S, Quan H, Gao Y Q. 2020. Toward an understanding of the relation between gene regulation and 3D genome organization. Quantitative Biology, 8, 295–311.

Tian H F, Hu Q M, Li Z. 2021. A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data. Genes Genomes Genetics, 11, jkaa032.

Tian X, Li R, Fu W, Li Y, Wang X, Li M, Du D, Tang Q, Cai Y, Long Y. 2020. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Science China Life Sciences, 63, 750–763.

Tsai P F, Dell’Orso S, Rodriguez J, Vivanco K O, Ko K D, Jiang K, Juan A H, Sarshad A A, Vian L, Tran M. 2018. A muscle-specific enhancer RNA mediates cohesin recruitment and regulates transcription in trans. Molecular Cell, 71, 129–141.

Wang H, Han M, Qi L S. 2021. Engineering 3D genome organization. Nature Reviews Genetics, 22, 343–360.

Wang M, Hancock T P, MacLeod I M, Pryce J E, Cocks B G, Hayes B J. 2017. Putative enhancer sites in the bovine genome are enriched with variants affecting complex traits. Genetics Selection Evolution, 49, 1–16.

Wang R, Chen F, Chen Q, Wan X, Shi M, Chen A K, Ma Z, Li G, Wang M, Ying Y. 2022. MyoD is a 3D genome structure organizer for muscle cell identity. Nature Communications, 13, 1–17.

Wang S, Su J H, Beliveau B J, Bintu B, Moffitt J R, Wu C, Zhuang X. 2016. Spatial organization of chromatin domains and compartments in single chromosomes. Science, 353, 598–602.

Van De Werken H J, De Vree P J, Splinter E, Holwerda S J, Klous P, De Wit E, De Laat W. 2012. 4C technology: Protocols and data analysis. Methods in Enzymology, 513, 89–112.

Wingett S, Ewels P, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P, Andrews S. 2015. HiCUP: Pipeline for mapping and processing Hi-C data. F1000Research, 4, 1310.

Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello A M. 2021. Cell-type specialization is encoded by specific chromatin topologies. Nature, 599, 684–691.

Xiang R, Berg I, MacLeod I M, Hayes B J, Prowse-Wilkins C P, Wang M, Bolormaa S, Liu Z, Rochfort S J, Reich C M. 2019. Quantifying the contribution of sequence variants with regulatory and evolutionary significance to 34 bovine complex traits. Proceedings of the National Academy of Sciences of the United States of America, 116, 19398–19408.

Xie T, Zheng J F, Liu S, Peng C, Zhou Y M, Yang Q Y, Zhang H Y. 2015. De novo plant genome assembly based on chromatin interactions: A case study of Arabidopsis thaliana. Molecular Plant, 8, 489–492.

Ye H, Rong Z, Lin Y. 2017. Live cell imaging of genomic loci using dCas9-SunTag system and a bright fluorescent protein. Protein & Cell, 8, 853–855.

Yekefenhazi D, He Q, Wang X, Han W, Song C, Li W. 2022. Chromosome-level genome assembly of Nibea coibor using PacBio HiFi reads and Hi-C technologies. Scientific Data, 9, 670.

Zeng Q, Zhou Z, He Q, Li L, Pu F, Yan M, Xu P. 2023. Chromosome-level haplotype-resolved genome assembly for Takifugu ocellatus using PacBio and Hi-C technologies. Scientific Data, 10, 22.

Zhang J, Liu P, He M, Wang Y, Kui H, Jin L, Li D, Li M. 2022. Reorganization of 3D genome architecture across wild boar and Bama pig adipose tissues. Journal of Animal Science and Biotechnology, 13, 1011–1027.

Zhang L, Li X, Ma B, Gao Q, Du H, Han Y, Li Y, Cao Y, Qi M, Zhu Y. 2017. The tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance. Molecular Plant, 10, 1224–1237.

Zhang N, Mendieta-Esteban J, Magli A, Lilja K C, Perlingeiro R C, Marti-Renom M A, Tsirigos A, Dynlacht B D. 2020. Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology. Nature Communications, 11, 1–18.

Zhang X, Lin C, Li H, Liu S, Wang Q, Yang S, Shi M, Sahu S K, Zhu Y, Wang J. 2022. Chromosome-level genome assembly of the green peafowl (Pavo muticus). Genome Biology and Evolution, 14, evac015.

Zhao Y, Hou Y, Xu Y, Luan Y, Zhou H, Qi X, Hu M, Wang D, Wang Z, Fu Y, Li J, Zhang S, Chen J, Han J, Li X, Zhao S. 2021. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications, 12, 2217.

Zhao Y, Wang L, Ren S, Wang L, Blackburn P R, McNulty M S, Gao X, Qiao M, Vessella R L, Kohli M. 2016. Activation of P-TEFb by androgen receptor-regulated enhancer RNAs in castration-resistant prostate cancer. Cell Reports, 15, 599–610.

Zhao Y, Zhou J, He L, Li Y, Yuan J, Sun K, Chen X, Bao X, Esteban M A, Sun H. 2019. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nature Communications, 10, 1–17.

Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu K S, Singh U. 2006. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nature Genetics, 38, 1341–1347.

Zheng H, Xie W. 2019. The role of 3D genome organization in development and cell differentiation. Nature Reviews Molecular Cell Biology, 20, 535–550.

Zheng M, Tian S Z, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu J J, Li Z. 2019. Multiplex chromatin interactions with single-molecule precision. Nature, 566, 558–562.

Zhi M, Zhang J, Tang Q, Yu D, Gao S, Gao D, Liu P, Guo J, Hai T, Gao J. 2021. Generation and characterization of stable pig pregastrulation epiblast stem cell lines. Cell Research, 32, 383–400.