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.
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.
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.
Carlson EA. The Gene; A Critical History. 1966. Saunders: Philadelphia.
Everson T. The Gene: A Historical Perspective. 2007. Greenwood Press: Westport.
Fox Keller E. The Century of the Gene. 2000. Harvard University Press: Cambridge.
Gerstein MB, Bruce C, Rozowsky JS, et al. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007; 17, 669–681.
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.
Griffiths PE, Neumann-Held EM. The many faces of the gene. Bioscience. 1999; 49, 656–662.
Akiva P, Toporik A, Edelheit S, et al. Transcription-mediated gene fusion in the human genome. Genome Res. 2006; 16, 30–36.
Spilianakis CG, Lalioti MD, Town T, et al. Interchromosomal associations between alternatively expressed loci. Nature. 2005; 435, 637–645.
Dixon JR, Jung I, Selvaraj S, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015; 518, 331–336.
Bouwman BAM, de Laat W. Getting the genome in shape: the formation of loops, domains and compartments. Genome Biol. 2015; 16, 154.
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.
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.
Bischof M. Introduction to integrative biophysics. In Integrative Biophysics (eds. Popp F-A, Beloussov L), 2010; pp. 1–115. Springer-Science+Business Media: Dordrecht.
O’Sullivan J, Hendy M, Pichugina T, et al. The statistical-mechanics of chromosome conformation capture. Nucleus. 2013; 4, 1–9.
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.
Kauffman SA. The Origins of Order: Self Organization and Selection in Evolution. 1993. Oxford University Press: New York.
Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 2007; 8, 413–423.
Dixon JR, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485, 376–380.
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.
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.
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.
Merkenschlager M, Nora EP. CTCF and cohesin in genome folding and transcriptional gene regulation. Annu Rev Genomics Hum Genet. 2016; 17, 17–43.
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.
Brangwynne CP, Tompa P, Pappu RV. Polymer physics of intracellular phase transitions. Nat Phys. 2015; 11, 899–904.
Kampmann M. Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential. Mol Microbiol. 2005; 57, 889–899.
Bénichou O, Chevalier C, Meyer B, Voituriez R. Facilitated diffusion of proteins on chromatin. Phys Rev Lett. 2011; 106, 38102.
Erdel F, Müller-Ott K, Rippe K. Establishing epigenetic domains via chromatin-bound histone modifiers. Ann N Y Acad Sci. 2013; 1305, 29–43.
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.
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.
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.
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.
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.
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.
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.
Williams A, Spilianakis CG, Flavell RA. Interchromosomal association and gene regulation in trans. Trends Genet. 2010; 26, 188–197.
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.
Vickers MH. Early life nutrition, epigenetics and programming of later life disease. Nutrients. 2014; 6, 2165–2178.
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.
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.
Fall T, Ingelsson E. Genome-wide association studies of obesity and metabolic syndrome. Mol Cell Endocrinol. 2014; 382, 740–757.
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.
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.
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.
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.
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.
Manolio TA, Collins FS, Cox NJ, et al. Finding the missing heritability of complex diseases. Nature. 2009; 461, 747–753.
Vattikuti S, Guo J, Chow CC. Heritability and genetic correlations explained by common SNPs for metabolic syndrome traits. PLoS Genet. 2012; 8, e1002637.
Farh KK, Marson A, Zhu J, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015; 518, 337–343.
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.
Marsman J, Horsfield JA. Long distance relationships: enhancer–promoter communication and dynamic gene transcription. Biochim Biophys Acta Gene Regul Mech. 2012; 1819, 1217–1227.
Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012; 489, 109–113.
Chen J, Tian W. Explaining the disease phenotype of intergenic SNP through predicted long range regulation. Nucleic Acids Res. 2016; 44, 8641–8654.
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.
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.
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.
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.
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.
Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet. 2015; 16, 197–212.
Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using chromosome conformation capture. Methods. 2012; 58, 192–203.
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.
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.
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.
Dean A. In the loop: long range chromatin interactions and gene regulation. Brief Funct Genomics. 2011; 10, 3–10.
Harmston N, Lenhard B. Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res. 2013; 41, 7185–7199.
Doss S. Cis-acting expression quantitative trait loci in mice. Genome Res. 2005; 15, 681–691.
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.
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.
Ong C-T, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet. 2014; 15, 239–246.
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.
Wang H, Maurano MT, Qu H, et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 2012; 22, 1680–1688.
Maurano M, Wang H, John S, et al. Role of DNA methylation in modulating transcription factor occupancy. Cell Rep. 2015; 12, 1184–1195.
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.
Flavahan WA, Drier Y, Liau BB, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2015; 529, 110–114.
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.
Dekker J. The three “C” s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006; 3, 17–21.
de Wit E, de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 2012; 26, 11–24.
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.
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.
Pasaniuc B, Price AL. Dissecting the genetics of complex traits using summary association statistics. Nat Rev Genet. 2016; 18, 117–127.
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.
Yilmaz Z, Davis C, Loxton NJ, et al. Association between MC4R rs17782313 polymorphism and overeating behaviors. Int J Obes. 2015; 39, 114–120.
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.
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.
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.
Lamm E. The genome as a developmental organ. J Physiol. 2014; 592, 2283–2293.
Bard JBL. Waddington’s legacy to developmental and theoretical biology. Biol Theory. 2008; 3, 188–197.