Bonev B, Cavalli G. Organization and function of the 3D genome. Nat Rev Genet. 2016;17:661–78.
Article
PubMed
CAS
Google Scholar
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–80.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell. 2012;148:458–72.
Article
PubMed
CAS
Google Scholar
Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, et al. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014;24:390–400.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhan Y, Mariani L, Barozzi I, Schulz EG, Bluthgen N, Stadler M, et al. 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; https://doi.org/10.1101/gr.212803.116.
Ibn-Salem J, Köhler S, Love MI, Chung H-R, Huang N, Hurles ME, et al. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014;15:423.
Article
PubMed
PubMed Central
Google Scholar
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161:1012–25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lupiáñez DG, Spielmann M, Mundlos S. Breaking TADs: how alterations of chromatin domains result in disease. Trends Genet. 2016;xx:1–13.
Google Scholar
Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665–80.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518:331–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gómez-Marín C, Tena JJ, Acemel RD, López-Mayorga M, Naranjo S, de la Calle-Mustienes E, et al. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proc Natl Acad Sci. 2015;112:201505463.
Article
CAS
Google Scholar
Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature. 2015; https://doi.org/10.1038/nature14450.
Hsieh T-HS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell. 2015;162(4):1–12.
Mizuguchi T, Fudenberg G, Mehta S, Belton J-M, Taneja N, Folco HD, et al. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 2014; https://doi.org/10.1038/nature13833.
Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 2015;10:1297–309.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? BioEssays. 2013;35:818–28.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003;100:11484–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kent WJ. BLAT—the BLAST-like alignment tool. Genome Res. 2002;12:656–64.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, et al. Recently mobilized transposons in the human and chimpanzee genomes. Am J Hum Genet. 2006;78:671–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution. BioEssays. 2015:n/a.
Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res. 2017;45(22):12611-12624.
Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res. 2007;17:545–55.
Article
PubMed
PubMed Central
CAS
Google Scholar
Harmston N, Ing-Simmons E, Tan G, Perry M, Merkenschlager M, Lenhard B. Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nat Commun. 2017;8:441.
Article
PubMed
PubMed Central
CAS
Google Scholar
Engström PG, Sui SJH, Drivenes Ø, Becker TS, Lenhard B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 2007;17:1898–908.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dimitrieva S, Bucher P. Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics. 2012;28:i395–401.
Article
PubMed
PubMed Central
CAS
Google Scholar
Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, et al. Genome organization drives chromosome fragility. Cell. 2017;170(3):1–15.
Redin C, Brand H, Collins RL, Kammin T, Mitchell E, Hodge JC, et al. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nat Genet. 2016; https://doi.org/10.1038/ng.3720.
Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Lassmann T, et al. A promoter-level mammalian expression atlas. Nature. 2014;507:462–70.
Article
PubMed
CAS
Google Scholar
Ibn-Salem J, Muro EM, Andrade-Navarro MA. Co-regulation of paralog genes in the three-dimensional chromatin architecture. Nucleic Acids Res. 2017;45:81–91.
Article
PubMed
CAS
Google Scholar
Schoenfelder S, Furlan-magaril M, Mifsud B, Tavares-cadete F, Sugar R, Javierre B, et al. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res. 2015;25:582-597.
Andrey G, Mundlos S. The three-dimensional genome: regulating gene expression during pluripotency and development. 2017;144:3646–3658. doi: https://doi.org/10.1242/dev.148304.
Montavon T, Thevenet L, Duboule D. Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus. Proc Natl Acad Sci U S A. 2012;109:20204–11.
Article
PubMed
PubMed Central
Google Scholar
Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, et al. Computational prediction of position effects of apparently balanced human chromosomal rearrangements. Am J Hum Genet. 2017;101:206–17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Spielmann M, Brancati F, Krawitz PM, Robinson PN, Ibrahim DM, Franke M, et al. Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. Am J Hum Genet. 2012;91:629–35.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pevzner P, Tesler G. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A. 2003;100:7672–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hou C, Li L, Qin ZS, Corces VG. Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol Cell. 2012;48:471–84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roukos V, Misteli T. The biogenesis of chromosome translocations. Nat Cell Biol. 2014;16:293–300.
Article
PubMed
CAS
Google Scholar
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, et al. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science. 2005;309:613–7.
Article
PubMed
CAS
Google Scholar
Hinsch H, Hannenhalli S. Recurring genomic breaks in independent lineages support genomic fragility. BMC Evol Biol. 2006;6:90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gordon L, Yang S, Tran-Gyamfi M, Baggott D, Christensen M, Hamilton A, et al. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res. 2007;17:1603–13.
Article
PubMed
PubMed Central
CAS
Google Scholar
Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature. 2016;538:265–269.
Hnisz D, Weintraub AS, Day DS, Valton A, Bak RO, Li CH, et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science. 2016;351:1454–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature. 2014;511:428-434.
Weischenfeldt J, Dubash T, Drainas AP, Mardin BR, Chen Y, Stütz AM, et al. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat Genet. 2016;49:65-74.
Akdemir KC, Li Y, Verhaak RG, Beroukhim R, Cambell P, Chin L, et al. Spatial Genome Organization as a framework for somatic alterations in human cancer. bioRxiv. 2017;
Acemel RD, Maeso I, Gómez-Skarmeta JL. Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals. Wiley Interdiscip Rev Dev Biol. 2017;6:e265.
Carroll SB. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell. 2008;134:25–36.
Article
PubMed
CAS
Google Scholar
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, et al. The UCSC genome browser database: update 2006. Nucleic Acids Res. 2006;34(Database issue):D590–8.
Article
PubMed
CAS
Google Scholar
Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 2009;4:1184–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wickham H, Grolemund G. R for data science: import, tidy, transform, visualize, and model data. 1st ed. Sebastopol: O’Reilly Media; 2017.
Google Scholar
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, et al. Ensembl comparative genomics resources. Database. 2016;2016 https://doi.org/10.1093/database/bav096.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods. 2015;12:115–21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lawrence M, Gentleman R, Carey V. rtracklayer: an R package for interfacing with genome browsers. Bioinformatics. 2009;25:1841–2.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9:e1003118.
Article
PubMed
PubMed Central
CAS
Google Scholar