1. Godfrey, KM, Reynolds, RM, Prescott, SL, et al. Influence of maternal obesity on the long-term health of offspring. Lancet Diabetes Endocrinol. 2017; 5, 53–64.
2. O’Reilly, JR, Reynolds, RM. The risk of maternal obesity to the long-term health of the offspring. Clin Endocrinol (Oxf). 2013; 78, 9–16.
3. Ong, M-L, Lin, X, Holbrook, JD. Measuring epigenetics as the mediator of gene/environment interactions in DOHaD. J Dev Orig Health Dis. 2015; 6, 10–16.
4. Carlson, EA. The Gene; A Critical History. 1966. Saunders: Philadelphia.
5. Everson, T. The Gene: A Historical Perspective. 2007. Greenwood Press: Westport.
6. Fox Keller, E. The Century of the Gene. 2000. Harvard University Press: Cambridge.
7. Gerstein, MB, Bruce, C, Rozowsky, JS, et al. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007; 17, 669–681.
8. Lamm, E. The metastable genome: a Lamarckian organ in a Darwinian world? In Transformations of Lamarckism: From Subtle Fluids to Molecular Biology (eds. Jablonka E, Gissis S), 2011; 480pp. MIT Press: Cambridge, Massachusetts.
9. Griffiths, PE, Neumann-Held, EM. The many faces of the gene. Bioscience. 1999; 49, 656–662.
10. Akiva, P, Toporik, A, Edelheit, S, et al. Transcription-mediated gene fusion in the human genome. Genome Res. 2006; 16, 30–36.
11. Spilianakis, CG, Lalioti, MD, Town, T, et al. Interchromosomal associations between alternatively expressed loci. Nature. 2005; 435, 637–645.
12. Dixon, JR, Jung, I, Selvaraj, S, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015; 518, 331–336.
13. Bouwman, BAM, de Laat, W. Getting the genome in shape: the formation of loops, domains and compartments. Genome Biol. 2015; 16, 154.
14. Fraser, J, Ferrai, C, Chiariello, AM, et al. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol Syst Biol. 2015; 11, 852–852.
15. Rao, SSP, Huntley, MH, Durand, NC, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159, 1665–1680.
16. Bischof, M. Introduction to integrative biophysics. In Integrative Biophysics (eds. Popp F-A, Beloussov L), 2010; pp. 1–115. Springer-Science+Business Media: Dordrecht.
17. O’Sullivan, J, Hendy, M, Pichugina, T, et al. The statistical-mechanics of chromosome conformation capture. Nucleus. 2013; 4, 1–9.
18. Grand, RS, Gehlen, LR, O’Sullivan, JM. Methods for the investigation of chromosome organization. In Advances in Genetics Research (ed. Urbano KV), 2011; 5, 111–129. NOVA: Science publishers; ebook.
19. Kauffman, SA. The Origins of Order: Self Organization and Selection in Evolution. 1993. Oxford University Press: New York.
20. Kapranov, P, Willingham, AT, Gingeras, TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 2007; 8, 413–423.
21. Dixon, JR, Selvaraj, S, Yue, F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485, 376–380.
22. de Wit, E, Bouwman, BAM, Zhu, Y, et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature. 2013; 501, 227–231.
23. Krijger, PHL, Di Stefano, B, de Wit, E, et al. Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming. Cell Stem Cell. 2016; 18, 597–610.
24. Holwerda, SJB, de Laat, W. CTCF: the protein, the binding partners, the binding sites and their chromatin loops. Philos Trans R Soc Lond B Biol Sci. 2013; 368, 20120369.
25. Merkenschlager, M, Nora, EP. CTCF and cohesin in genome folding and transcriptional gene regulation. Annu Rev Genomics Hum Genet. 2016; 17, 17–43.
26. Mizuguchi, T, Fudenberg, G, Mehta, S, et al. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe
. Nature. 2014; 516, 432–435.
27. Brangwynne, CP, Tompa, P, Pappu, RV. Polymer physics of intracellular phase transitions. Nat Phys. 2015; 11, 899–904.
28. Kampmann, M. Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential. Mol Microbiol. 2005; 57, 889–899.
29. Bénichou, O, Chevalier, C, Meyer, B, Voituriez, R. Facilitated diffusion of proteins on chromatin. Phys Rev Lett. 2011; 106, 38102.
30. Erdel, F, Müller-Ott, K, Rippe, K. Establishing epigenetic domains via chromatin-bound histone modifiers. Ann N Y Acad Sci. 2013; 1305, 29–43.
31. Buckley, SM, Aranda-Orgilles, B, Strikoudis, A, et al. Regulation of pluripotency and cellular reprogramming by the ubiquitin-proteasome system. Cell Stem Cell. 2012; 11, 783–798.
32. Kim, DH, Marinov, GK, Pepke, S, et al. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. Cell Stem Cell. 2015; 16, 88–101.
33. Grand, RS, Pichugina, T, Gehlen, LR, et al. Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure. Nucleic Acids Res. 2014; 42, 12585–12599.
34. Pichugina, T, Sugawara, T, Kaykov, A, et al. A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe
. Sci Rep. 2016; 6, 18757.
35. Dryden, NH, Broome, LR, Dudbridge, F, et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by capture Hi-C. Genome Res. 2014; 24, 1854–1868.
36. Jäger, R, Migliorini, G, Henrion, M, et al. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun. 2015; 6, 6178.
37. Mifsud, B, Tavares-Cadete, F, Young, AN, et al. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet. 2015; 47, 598–606.
38. Williams, A, Spilianakis, CG, Flavell, RA. Interchromosomal association and gene regulation in trans. Trends Genet. 2010; 26, 188–197.
39. Felipe Barella, L, ulio Cezar de Oliveira, J, Cezar de Freitas Mathias, P. Pancreatic islets and their roles in metabolic programming. Nutrition. 2014; 30, 373–379.
40. Vickers, MH. Early life nutrition, epigenetics and programming of later life disease. Nutrients. 2014; 6, 2165–2178.
41. Jarick, I, Vogel, CIG, Scherag, S, et al. Novel common copy number variation for early onset extreme obesity on chromosome 11q11 identified by a genome-wide analysis. Hum Mol Genet. 2011; 20, 840–852.
42. Comuzzie, AG, Cole, SA, Laston, SL, et al. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PLoS One. 2012; 7, e51954.
43. Fall, T, Ingelsson, E. Genome-wide association studies of obesity and metabolic syndrome. Mol Cell Endocrinol. 2014; 382, 740–757.
44. Sjögren, M, Lyssenko, V, Jonsson, A, et al. The search for putative unifying genetic factors for components of the metabolic syndrome. Diabetologia. 2008; 51, 2242–2251.
45. Hara, K, Fujita, H, Johnson, TA, et al. Genome-wide association study identifies three novel loci for type 2 diabetes. Hum Mol Genet. 2014; 23, 239–246.
46. Zeggini, E, Scott, LJ, Saxena, R, et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008; 40, 638–645.
47. Morris, AP, Voight, BF, Teslovich, TM, et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet. 2012; 44, 981–990.
48. Sladek, R, Prokopenko, I. Genome-wide association studies of type 2 diabetes. In The Genetics of Type 2 Diabetes and Related Traits: Biology, Physiology and Translation (ed. Florez CJ), 2016; pp. 13–61. Springer International Publishing: Cham.
49. Manolio, TA, Collins, FS, Cox, NJ, et al. Finding the missing heritability of complex diseases. Nature. 2009; 461, 747–753.
50. Vattikuti, S, Guo, J, Chow, CC. Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits. PLoS Genet. 2012; 8, e1002637.
51. Farh, KK, Marson, A, Zhu, J, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015; 518, 337–343.
52. Schierding, W, Cutfield, WS, O’Sullivan, JM. The missing story behind genome wide association studies: single nucleotide polymorphisms in gene deserts have a story to tell. Front Genet. 2014; 5, 39.
53. Marsman, J, Horsfield, JA. Long distance relationships: enhancer–promoter communication and dynamic gene transcription. Biochim Biophys Acta Gene Regul Mech. 2012; 1819, 1217–1227.
54. Sanyal, A, Lajoie, BR, Jain, G, Dekker, J. The long-range interaction landscape of gene promoters. Nature. 2012; 489, 109–113.
55. Chen, J, Tian, W. Explaining the disease phenotype of intergenic SNP through predicted long range regulation. Nucleic Acids Res. 2016; 44, 8641–8654.
56. Schierding, W, Antony, J, Cutfield, WS, et al. Intergenic GWAS SNPs are key components of the spatial and regulatory network for human growth. Hum Mol Genet. 2016; 25, 3372–3382.
57. Smemo, S, Tena, JJ, Kim, K-H, et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014; 507, 371–375.
58. Claussnitzer, M, Dankel, SN, Kim, K-H, et al. FTO obesity variant circuitry and adipocyte browning in humans. N Engl J Med. 2015; 373, 895–907.
59. Tolhuis, B, Palstra, RJ, Splinter, E, et al. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol Cell. 2002; 10, 1453–1465.
60. Drissen, R, Palstra, R-J, Gillemans, N, et al. The active spatial organization of the beta-globin locus requires the transcription factor EKLF. Genes Dev. 2004; 18, 2485–2490.
61. Albert, FW, Kruglyak, L. The role of regulatory variation in complex traits and disease. Nat Rev Genet. 2015; 16, 197–212.
62. Naumova, N, Smith, EM, Zhan, Y, Dekker, J. Analysis of long-range chromatin interactions using chromosome conformation capture. Methods. 2012; 58, 192–203.
63. Zhao, Z, Tavoosidana, G, Sjölinder, M, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006; 38, 1341–1347.
64. Rodley, CDM, Bertels, F, Jones, B, O’Sullivan, JM. Global identification of yeast chromosome interactions using genome conformation capture. Fungal Genet Biol. 2009; 46, 879–886.
65. Schierding, W, O’Sullivan, JM. Connecting SNPs in diabetes: a spatial analysis of meta-GWAS loci. Front Endocrinol (Lausanne). 2015; 6, doi: 10.3389/fendo.2015.00102.
66. Dean, A. In the loop: long range chromatin interactions and gene regulation. Brief Funct Genomics. 2011; 10, 3–10.
67. Harmston, N, Lenhard, B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res. 2013; 41, 7185–7199.
68. Doss, S. Cis-acting expression quantitative trait loci in mice. Genome Res. 2005; 15, 681–691.
69. Davis, JR, Fresard, L, Knowles, DA, et al. An efficient multiple-testing adjustment for eQTL studies that accounts for linkage disequilibrium between variants. Am J Hum Genet. 2016; 98, 216–224.
70. Corradin, O, Cohen, AJ, Luppino, JM, et al. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet. 2016; 48, 1313–1320.
71. Ong, C-T, Corces, VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet. 2014; 15, 239–246.
72. Nora, EP, Goloborodko, A, Valton, A-L, et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell. 2017; 169, 930–944.e22.
73. Wang, H, Maurano, MT, Qu, H, et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 2012; 22, 1680–1688.
74. Maurano, M, Wang, H, John, S, et al. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 2015; 12, 1184–1195.
75. Banovich, NE, Lan, X, McVicker, G, et al. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet. 2014; 10, e1004663.
76. Flavahan, WA, Drier, Y, Liau, BB, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2015; 529, 110–114.
77. Martin, P, McGovern, A, Orozco, G, et al. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci. Nat Commun. 2015; 6, 10069.
78. Dekker, J. The three “C” s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006; 3, 17–21.
79. de Wit, E, de Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 2012; 26, 11–24.
80. Tak, YG, Farnham, PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenet Chromat. 2015; 8, 57.
81. Kichaev, G, Yang, W-Y, Lindstrom, S, et al. Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet. 2014; 10, e1004722.
82. Pasaniuc, B, Price, AL. Dissecting the genetics of complex traits using summary association statistics. Nat Rev Genet. 2016; 18, 117–127.
83. Huang, Y, Cate, SP, Battistuzzi, C, et al. An association between a functional polymorphism in the monoamine oxidase a gene promoter, impulsive traits and early abuse experiences. Neuropsychopharmacology. 2004; 29, 1498–1505.
84. Yilmaz, Z, Davis, C, Loxton, NJ, et al. Association between MC4R rs17782313 polymorphism and overeating behaviors. Int J Obes. 2015; 39, 114–120.
85. Rodley, CDM, Grand, RS, Gehlen, LR, et al. Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system. PLoS One. 2012; 7, e30943.
86. Doynova, MD, Berretta, A, Jones, MB, et al. Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random. Mitochondrion. 2016; 30, 187–196.
87. Jacobson, E, Perry, JK, Long, DS, et al. A potential role for genome structure in the translation of mechanical force during immune cell development. Nucleus. 2016; 7, 462–475.
88. Lamm, E. The genome as a developmental organ. J Physiol. 2014; 592, 2283–2293.
89. Bard, JBL. Waddington’s legacy to developmental and theoretical biology. Biol Theory. 2008; 3, 188–197.