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Three-dimensional Genomic Organization of Genes’ Function in Eukaryotes

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Evolutionary Biology

Abstract

It is well known that in prokaryotes, genes are organized in transcription units called operons. Since each operon includes genes which are related to the same pathway, a relation between genomic proximity and functionality can be easily observed. In eukaryotes, usually there are no operons; however, in the last few decades, there have been growing evidence that the organization of eukaryotic genes is not random: Evolution shapes gene organization in eukaryotes in a way that will improve the organism’s fitness. In this chapter, we will review how previous studies in the field employed sophisticated experiments and analysis tools to decipher the way genes are organized in eukaryotic genomes.

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References

  • Ay F, Bailey TL, Noble WS (2014a) Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res 2014a Feb 5; gr. 160374.113

    Google Scholar 

  • Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert J-P et al (2014b) Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression. Genome Res 24(6):974–988

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Babaei S, Akhtar W, de Jong J, Reinders M, de Ridder J (2015) 3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes. Nat Commun 27(6):6381

    Article  Google Scholar 

  • Bártová E, Kozubek S (2006) Nuclear architecture in the light of gene expression and cell differentiation studies. Biol Cell 98(6):323–336

    Article  PubMed  Google Scholar 

  • Batada NN, Hurst LD (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39(8):945–949

    Article  CAS  PubMed  Google Scholar 

  • Belmont AS (2001) Visualizing chromosome dynamics with GFP. Trends Cell Biol 11(6):250–257

    Article  CAS  PubMed  Google Scholar 

  • Ben-Elazar S, Yakhini Z, Yanai I (2013) Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome. Nucleic Acids Res 41(4):2191–2201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bickmore WA, Teague P (2002) Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. Chromosome Res 10(8):707–715

    Article  CAS  PubMed  Google Scholar 

  • Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J et al (2002) A global analysis of Caenorhabditis elegans operons. Nature 417(6891):851–854

    Article  CAS  PubMed  Google Scholar 

  • Bronshtein I, Kepten E, Kanter I, Berezin S, Lindner M, Redwood AB et al (2015) Loss of lamin a function increases chromatin dynamics in the nuclear interior. Nat Commun 24(6):8044

    Article  Google Scholar 

  • Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P et al (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291(5507):1289–1292

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Dokholyan NV (2006) The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet 22(8):416–419

    Article  CAS  PubMed  Google Scholar 

  • Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho Y-J et al (2011) Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147(1):107–119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26(2):183–186

    Article  CAS  PubMed  Google Scholar 

  • Cook PR (2002) Predicting three-dimensional genome structure from transcriptional activity. Nat Genet 32(3):347–352

    Article  CAS  PubMed  Google Scholar 

  • Corces MR, Corces VG (2016) The three-dimensional cancer genome. Curr Opin Genet Dev 36:1–7

    Google Scholar 

  • Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS et al (2010) The genetic landscape of a cell. Science 327(5964):425–431

    Article  CAS  PubMed  Google Scholar 

  • Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J (2012) Normalization of a chromosomal contact map. BMC Genom 13(1):436

    Article  CAS  Google Scholar 

  • Cremer T, Cremer M, Dietzel S, Müller S, Solovei I, Fakan S (2006) Chromosome territories—a functional nuclear landscape. Curr Opin Cell Biol 18(3):307–316

    Article  CAS  PubMed  Google Scholar 

  • Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306–1311

    Article  CAS  PubMed  Google Scholar 

  • Diament A, Tuller T (2015) Improving 3D genome reconstructions using orthologous and functional constraints. PLoS Comput Biol 11(5):e1004298

    Article  PubMed  PubMed Central  Google Scholar 

  • Diament A, Pinter RY, Tuller T (2014) Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function. Nat Commun 5:5876

    Google Scholar 

  • Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y et al (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY et al (2015) Chromatin architecture reorganization during stem cell differentiation. Nature 518(7539):331–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA et al (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16(10):1299–1309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doyle B, Fudenberg G, Imakaev M, Mirny LA (2014) Chromatin loops as allosteric modulators of enhancer-promoter interactions. PLoS Comput Biol 10(10):e1003867

    Article  PubMed  PubMed Central  Google Scholar 

  • Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C et al (2010) A three-dimensional model of the yeast genome. Nature 465(7296):363–367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Field B, Osbourn AE (2008) Metabolic diversification—independent assembly of operon-like gene clusters in different plants. Science 320(5875):543–547

    Article  CAS  PubMed  Google Scholar 

  • Forment JV, Kaidi A, Jackson SP (2012) Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer 12(10):663–670

    Article  CAS  PubMed  Google Scholar 

  • Fullwood MJ, Ruan Y (2009) ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem 107(1):30–39

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang S-M, Macfarlan TS et al (2015) Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. Genome Biol 16:289

    Article  PubMed  PubMed Central  Google Scholar 

  • Girvan M, Newman MEJ (2002) Community structure in social and biological networks. PNAS 99(12):7821–7826

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR et al (2015) Genetic control of chromatin states in humans involves local and distal chromosomal interactions. Cell 162(5):1051–1065

    Google Scholar 

  • Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W et al (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453(7197):948–951

    Article  CAS  PubMed  Google Scholar 

  • Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon K-R, Jankovic M et al (2012) DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 484(7392):69–74

    CAS  PubMed  PubMed Central  Google Scholar 

  • Homouz D, Kudlicki AS (2013) The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes. PLoS ONE 8(1):e54699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hsieh T-HS, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ (2015) Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell 162(1):108–119

    Google Scholar 

  • Hurst LD, Pál C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5(4):299–310

    Article  CAS  PubMed  Google Scholar 

  • Huvet M, Nicolay S, Touchon M, Audit B, d’Aubenton-Carafa Y, Arneodo A et al (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17(9):000–000

    Google Scholar 

  • Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR et al (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9(10):999–1003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Imakaev MV, Fudenberg G, Mirny LA (2015) Modeling chromosomes: Beyond pretty pictures. FEBS Lett 589(20, Part A):3031–3036

    Google Scholar 

  • Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L (2012) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotech 30(1):90–98

    Article  CAS  Google Scholar 

  • Karathia H, Kingsford C, Girvan M, Hannenhalli S (2015) A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. BioRxiv 027045

    Google Scholar 

  • Katainen R, Dave K, Pitkänen E, Palin K, Kivioja T, Välimäki N et al (2015) CTCF/cohesin-binding sites are frequently mutated in cancer. Nat Genet 47(7):818–821

    Google Scholar 

  • Kim T-M, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res 23(2):217–227

    Google Scholar 

  • Kim SH, McQueen PG, Lichtman MK, Shevach EM, Parada LA, Misteli T (2004) Spatial genome organization during T-cell differentiation. Cytogenet Genome Res 105(2–4):292–301

    Article  CAS  PubMed  Google Scholar 

  • Kosak ST, Groudine M (2004) Gene order and dynamic domains. Science 306(5696):644–647

    Article  CAS  PubMed  Google Scholar 

  • Kosak ST, Skok JA, Medina KL, Riblet R, Beau MML, Fisher AG et al (2002) Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296(5565):158–162

    Article  CAS  PubMed  Google Scholar 

  • Kruse K, Sewitz S, Babu MM (2013) A complex network framework for unbiased statistical analyses of DNA–DNA contact maps. Nucl Acids Res 41(2):701–710

    Article  CAS  PubMed  Google Scholar 

  • Langer-Safer PR, Levine M, Ward DC (1982) Immunological method for mapping genes on Drosophila polytene chromosomes. Proc Natl Acad Sci USA 79(14):4381–4385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee JM, Sonnhammer ELL (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13(5):875–882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31(2):180–183

    Article  CAS  PubMed  Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E et al (2015) Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161(5):1012–1025

    Article  PubMed  PubMed Central  Google Scholar 

  • Marcotte EM, Pellegrini M, Ng H-L, Rice DW, Yeates TO, Eisenberg D (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285(5428):751–753

    Article  CAS  PubMed  Google Scholar 

  • Martin J, Lercher AOU (2003) A unification of mosaic structures in the human genome. Hum Mol Genet 12(19):2411–2415

    Article  Google Scholar 

  • Meaburn KJ, Misteli T, Soutoglou E (2007) Spatial genome organization in the formation of chromosomal translocations. Semin Cancer Biol 17(1):80–90

    Article  CAS  PubMed  Google Scholar 

  • Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L et al (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47(6):598–606

    Article  CAS  PubMed  Google Scholar 

  • Miller MA, Cutter AD, Yamamoto I, Ward S, Greenstein D (2004) Clustered organization of reproductive genes in the C. elegans genome. Curr Biol 14(14):1284–1290

    Article  CAS  PubMed  Google Scholar 

  • Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128(4):787–800

    Article  CAS  PubMed  Google Scholar 

  • Mitra K, Carvunis A-R, Ramesh SK, Ideker T (2013) Integrative approaches for finding modular structure in biological networks. Nat Rev Genet 14(10):719–732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mizuguchi T, Fudenberg G, Mehta S, Belton J-M, Taneja N, Folco HD et al (2014) Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature 516(7531):432–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W et al (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502(7469):59–64

    Article  CAS  PubMed  Google Scholar 

  • Nagano T, Várnai C, Schoenfelder S, Javierre B-M, Wingett SW, Fraser P (2015) Comparison of Hi-C results using in-solution versus in-nucleus ligation. Genome Biol 16:175

    Article  PubMed  PubMed Central  Google Scholar 

  • Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oliveira TY, Resch W, Jankovic M, Casellas R, Nussenzweig MC, Klein IA (2012) Translocation capture sequencing: a method for high throughput mapping of chromosomal rearrangements. J Immunol Methods 375(1–2):176–181

    Article  CAS  PubMed  Google Scholar 

  • Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E et al (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36(10):1065–1071

    Article  CAS  PubMed  Google Scholar 

  • Osbourn AE, Field B (2009) Operons. Cell Mol Life Sci 66(23):3755–3775

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pál C, Hurst LD (2003) Evidence for co-evolution of gene order and recombination rate. Nat Genet 33(3):392–395

    Article  PubMed  Google Scholar 

  • Petkov PM, Graber JH, Churchill GA, DiPetrillo K, King BL, Paigen K (2007) Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Biol 5(5):e127

    Article  PubMed  PubMed Central  Google Scholar 

  • Poyatos JF, Hurst LD (2007) The determinants of gene order conservation in yeasts. Genome Biol 8(11):R233

    Article  PubMed  PubMed Central  Google Scholar 

  • Pritykin Y, Singh M (2013) Simple topological features reflect dynamics and modularity in protein interaction networks. PLoS Comput Biol 9(10):e1003243

    Article  PubMed  PubMed Central  Google Scholar 

  • Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT et al (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680

    Article  CAS  PubMed  Google Scholar 

  • Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási A-L (2002) Hierarchical organization of modularity in metabolic networks. Science 297(5586):1551–1555

    Article  CAS  PubMed  Google Scholar 

  • Rousseau M, Fraser J, Ferraiuolo MA, Dostie J, Blanchette M (2011) Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. BMC Bioinformatics 25(12):414

    Article  Google Scholar 

  • Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418(6901):975–979

    CAS  PubMed  Google Scholar 

  • Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J (2000) Operons in Escherichia coli: genomic analyses and predictions. Proc Natl Acad Sci US A 97(12):6652–6657

    Article  CAS  Google Scholar 

  • Sanborn AL, Rao SSP, Huang S-C, Durand NC, Huntley MH, Jewett AI et al (2015) Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. PNAS 112(47):E6456–E6465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schmidt T, Schwarzacher T, Heslop-Harrison JS (1994) Physical mapping of rRNA genes by fluorescent in-situ hybridization and structural analysis of 5S rRNA genes and intergenic spacer sequences in sugar beet (Beta vulgaris). Theoret Appl Genet 88(6–7):629–636

    Article  CAS  Google Scholar 

  • Schuster-Böckler B, Lehner B (2012) Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488(7412):504–507

    Article  PubMed  Google Scholar 

  • Sémon M, Duret L (2006) Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol 23(9):1715–1723

    Article  PubMed  Google Scholar 

  • Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M et al (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148(3):458–472

    Article  CAS  PubMed  Google Scholar 

  • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38(11):1348–1354

    Article  CAS  PubMed  Google Scholar 

  • Singer GAC, Lloyd AT, Huminiecki LB, Wolfe KH (2005) Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol 22(3):767–775

    Article  CAS  PubMed  Google Scholar 

  • Slot JC, Rokas A (2010) Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. PNAS 107(22):10136–10141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Speicher MR, Ballard SG, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12(4):368–375

    Article  CAS  PubMed  Google Scholar 

  • Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJG, Zhu Y et al (2011) The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes Dev 25(13):1371–1383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sproul D, Gilbert N, Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 6(10):775–781

    Article  CAS  PubMed  Google Scholar 

  • Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302(5643):249–255

    Article  CAS  PubMed  Google Scholar 

  • Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M et al (2010) Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucl Acids Res 38(22):8164–8177

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Teichmann SA, Veitia RA (2004) Genes encoding subunits of stable complexes are clustered on the yeast chromosomes. Genetics 167(4):2121–2125

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Therizols P, Illingworth RS, Courilleau C, Boyle S, Wood AJ, Bickmore WA (2014) Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells. Science 346(6214):1238–1242

    Article  CAS  PubMed  Google Scholar 

  • Thévenin A, Ein-Dor L, Ozery-Flato M, Shamir R (2014) Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome. Nucl Acids Res 42(15):9854–9861

    Article  PubMed  PubMed Central  Google Scholar 

  • Tjong H, Gong K, Chen L, Alber F (2012) Physical tethering and volume exclusion determine higher-order genome organization in budding yeast. Genome Res 22(7):1295–1305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tuller T, Rubinstein U, Bar D, Gurevitch M, Ruppin E, Kupiec M (2009) Higher-order genomic organization of cellular functions in yeast. J Comput Biol 16(2):303–316

    Article  CAS  PubMed  Google Scholar 

  • van der Ploeg M (2000) Cytochemical nucleic acid research during the twentieth century. Euro J Histochem EJH 44(1):7–42

    Google Scholar 

  • Valton A-L, Dekker J (2016) TAD disruption as oncogenic driver. Curr Opin Genet Dev 36:34–40

    Google Scholar 

  • Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A et al (2015) Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep 10(8):1297–1309

    Google Scholar 

  • Weber CC, Hurst LD (2011) Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation. Genome Biol 12(3):1–15

    Article  Google Scholar 

  • Wijchers PJ, Krijger PHL, Geeven G, Zhu Y, Denker A, Verstegen MJAM et al (2016) Cause and consequence of tethering a SubTAD to different nuclear compartments. Mol cell 61(3):461–473

    Google Scholar 

  • Wong S, Wolfe KH (2005) Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet 37(7):777–782

    Article  CAS  PubMed  Google Scholar 

  • Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43(11):1059–1065

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, McCord RP, Ho Y-J, Lajoie BR, Hildebrand DG, Simon AC et al (2012) Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148(5):908–921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

AD is grateful to the Azrieli Foundation for the award of an Azrieli Fellowship. This study was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.

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Correspondence to Tamir Tuller .

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Diament, A., Tuller, T. (2016). Three-dimensional Genomic Organization of Genes’ Function in Eukaryotes. In: Pontarotti, P. (eds) Evolutionary Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-41324-2_14

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