The Journal Club provides a brief survey of some existing epigenetics and epigenomics literature, featuring seminal, recent, and review pieces. Here the citations to the literary sources have been loosely broken down into categories. Each category also has three general questions to facilitate discussion.
Epigenetics:
How are epigenetic processes regulating genetic activity? What are some different forms of epigenetic mechanisms?
Boffelli D, Martin DIK. 2012. Epigenetics Inheritance: A Contributor to Species Differentiation? DNA and Cell Biology 31:S11-S16.
Callinan PA, Feinberg AP. 2006. The emerging science of epigenomics. Human Molecular Genetics 15:R95-101.
Chang, Andrew YF, and Ben-Yang Liao. “Recruitment of Histone Modifications to Assist mRNA Dosage Maintenance after Degeneration of Cytosine DNA Methylation during Animal Evolution.” Genome Research, July 18, 2017, gr.221739.117. doi:10.1101/gr.221739.117.
Esteller M. 2008. Epigenetics in evolution and disease. Lancet 372:590-596.
Gama-Sosa MA, Midgett RM, Slagel VA, Githens S, Kuo KC, Gehrke CW, Ehrlich M. 1983. Tissue-Specific Differences in DNA Methylation in Various Mammals. Biochimica et Biophysica Acta 740:212-219.
He, Xin-Jian, Taiping Chen, and Jian-Kang Zhu. “Regulation and Function of DNA Methylation in Plants and Animals.” Cell Research 21, no. 3 (March 2011): 442–65. doi:10.1038/cr.2011.23.
McRae AF, Powell JE, Henders AK, Bowdler L, Hemani G, Shah S, Painter JN, Martin NG, Visscher PM, Montgomery GW. 2014. Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biology 15:R73.
Smith ZD, Meissner A. 2013. DNA methylation: roles in mammalian development. Nature Reviews Genetics 14:204-220.
Waddington CH. 1942. The epigenotype. Endeavour 1:18-20.
Weaver ICG, Cervoni N, Champagne FA, D’Alessio AC, Sharma S, Seckl JR, Dymov S, Szyf M, Meaney MJ. 2004. Epigenetic programming by maternal behavior. Nature Neuroscience 7:847-854.
Anthropological Epigenetics:
How might epigenetics enhance anthropological research? Could anthropological methods or theories improve how we interpret results of human epigenomics research?
Fagny, Maud, Etienne Patin, Julia L. MacIsaac, Maxime Rotival, Timothée Flutre, Meaghan J. Jones, Katherine J. Siddle, et al. “The Epigenomic Landscape of African Rainforest Hunter-Gatherers and Farmers.” Nature Communications 6 (November 30, 2015): 10047. doi:10.1038/ncomms10047.
Gokhman, David, Eran Meshorer, and Liran Carmel. “Epigenetics: It’s Getting Old. Past Meets Future in Paleoepigenetics.” Trends in Ecology & Evolution 31, no. 4 (April 2016): 290–300. doi:10.1016/j.tree.2016.01.010.
Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M. 2013. DNA methylation contributes to natural human variation. Genome Research 23:1363-1372.
Kenney, M., & Müller, R. (2018). Of rats and women: narratives of motherhood in environmental epigenetics. In The Palgrave Handbook of Biology and Society (pp. 799-830). Palgrave Macmillan, London.
Kuzawa, Christopher W, and Zaneta M Thayer. “Timescales of Human Adaptation: The Role of Epigenetic Processes.” Epigenomics 3, no. 2 (April 2011): 221–34. doi:10.2217/epi.11.11.
Lock, M. (2013). The epigenome and nature/nurture reunification: a challenge for anthropology. Medical Anthropology, 32(4), 291-308.
Loi, M., Del Savio, L., & Stupka, E. (2013). Social epigenetics and equality of opportunity. Public health ethics, 6(2), 142-153.
Non, Amy L., and Zaneta M. Thayer. “Epigenetics for Anthropologists: An Introduction to Methods.” American Journal of Human Biology 27, no. 3 (May 6, 2015): 295–303. doi:10.1002/ajhb.22679.
Thayer, Zaneta M., and Amy L. Non. “Anthropology Meets Epigenetics: Current and Future Directions.” American Anthropologist 117, no. 4 (December 1, 2015): 722–35. doi:10.1111/aman.12351.
Thayer, Zaneta M., and Christopher W. Kuzawa. “Biological Memories of Past Environments: Epigenetic Pathways to Health Disparities.” Epigenetics 6, no. 7 (July 2011): 798–803. doi:10.4161/epi.6.7.16222.
Non-Human Primate Epigenetics:
Why would it be beneficial to have the ability to compare epigenetic variation between humans and other primates? How might the natural ecologies and social structures non-human primates observe influence potential study designs? Can epigenetic studies improve modern primatological and conservation efforts?
Carbone, Lucia, R. Alan Harris, Gery M. Vessere, Alan R. Mootnick, Sean Humphray, Jane Rogers, Sung K. Kim, et al. “Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution.” PLOS Genetics 5, no. 6 (June 26, 2009): e1000538. doi:10.1371/journal.pgen.1000538.
Cox, L. A., A. G. Comuzzie, L. M. Havill, G. M. Karere, K. D. Spradling, M. C. Mahaney, P. W. Nathanielsz, et al. 2013. Baboons as a Model to Study Genetics and Epigenetics of Human Disease. ILAR Journal 54 (2): 106–21. doi:10.1093/ilar/ilt038.
Enard W, Fassbender A, Model F, Adorján P, Pääbo S, Olek A. 2004. Differences in DNA methylation patterns between humans and chimpanzees. Current Biology 14:R148-R149.
Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M, Heyn H, Hvilsom C, Navarro A, Esteller M, Sharp AJ, Marques-Bonet T. 2013. Dynamics of DNA Methylation in Recent Human and Great Ape Evolution. PLoS Genetics 9:e1003763.
Hernando-Herraez, I., Heyn, H., Fernandez-Callejo, M., Vidal, E., Fernandez-Bellon, H., Prado-Martinez, J., ... & Marques-Bonet, T. (2015). The interplay between DNA methylation and sequence divergence in recent human evolution. Nucleic acids research, 43(17), 8204-8214.
Lea, Amanda J., Jeanne Altmann, Susan C. Alberts, and Jenny Tung. “Resource Base Influences Genome-Wide DNA Methylation Levels in Wild Baboons (Papio Cynocephalus).” Molecular Ecology 25, no. 8 (April 1, 2016): 1681–96. doi:10.1111/mec.13436.
Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D. 2011. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Research 21:2049-2057.
Provencal N, Suderman MJ, Guillemin C, Massart R, Ruggiero A, Wang D, Bennett AJ, Pierre PJ, Friedman DP, Cote SM, Hallett M, Tremblay RE, Suomi SJ, Szyf M. 2012. The Signature of Maternal Rearing in the Methylome in Rhesus Macaque Prefrontal Cortex and T Cells. The Journal of Neuroscience 32:15626-15642.
Ancient Epigenetics:
How might epigenetic variation of ancient sequences inform us about past populations and their environments? What are some complications between traditional methylation sequencing techniques and the inherent nature of working with ancient DNA samples?
Dediu, D., & Levinson, S. C. (2018). Neanderthal language revisited: not only us. Current Opinion in Behavioral Sciences, 21, 49-55.
Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L. 2014. Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan. Science 344:523-527.
Gokhman, David, Eran Meshorer, and Liran Carmel. “Epigenetics: It’s Getting Old. Past Meets Future in Paleoepigenetics.” Trends in Ecology & Evolution 31, no. 4 (April 2016): 290–300. doi:10.1016/j.tree.2016.01.010.
Gokhman, David, Lily Agranat-Tamir, Genevieve Housman, Malka Nissim-Rafinia, Maria Nieves-Colón, Hongcang Gu, Manuel Ferrando-Bernal, et al. “Recent Regulatory Changes Shaped Human Facial and Vocal Anatomy.” bioRxiv, March 1, 2017, 106955. doi:10.1101/106955.
Pedersen JS, Valen E, Velazquez AMV, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MTP, Krogh A, Willerslev E, Orlando L. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Research 24:454-466.
Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., ... & Nielsen, R. (2017). Archaic adaptive introgression in TBX15/WARS2. Molecular biology and evolution, 34(3), 509-524.
Smith RWA, Monroe C, Bolnick DA. 2015. Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing. PLoS ONE 10:e0125344.
Epigenetics and Biosocial Inheritance:
How are aspects of the social environment potentially transmitted to future generations? Does epigenetics research have the ability to enlighten researchers to the reasons for racial disparities in health outcomes? Does epigenetic variation play a role in gender identity?
Guthman, Julie, and Becky Mansfield. 2013 The Implication of Epigenetics: A new direction for Geographic inquiry on health, space and nature-Society relations. Progress in Human Geography 37(4):486-504.
Hoke MK, McDade T. 2015. Biosocial Inheritance: A frameworks for the study of intergenerational transmission of health disparities. Ann Anthropol Pract 38:187–213.
Mansfield, Becky. 2012 Race and the new epigenetic biopolitics of environmental health. BioSocieties 7(4):352–372.
Miska, Eric A., and Anne C. Ferguson-Smith. "Transgenerational inheritance: Models and mechanisms of non–DNA sequence–based inheritance." Science 354 (2016): 59-63.
Niewohner, Jorg. 2011 Epigenetics: Embedded bodies and the molecularisation of biography and milieu. BioSocieties 6:279-298.
Richardson, S. 2015. “Maternal Bodies in the Postgenomic Order: Gender and the Explanatory Landscape of Epigenetics.” in Postgenomics Durham: Duke University Press.
Stringhini, S., & Vineis, P. (2018). Epigenetic Signatures of Socioeconomic Status Across the Lifecourse. In The Palgrave Handbook of Biology and Society (pp. 541-559). Palgrave Macmillan, London.
Epigenetics and Ethics:
What are some critical, reflective considerations made toward epigenetic research, its praxis, and the potential to carry unique ethical liabilities? How has epigenetic and epigenomic research become positioned in human biomedical research? Are there ways in which epigenetics research presents novel ethical dilemmas and should these limit how researchers engage in epigenetic studies?
Dupras, C., Ravitsky, V., & Williams‐Jones, B. (2014). Epigenetics and the environment in bioethics. Bioethics, 28(7), 327-334.
Hendrickx, K., & Van Hoyweghen, I. (2018). An Epigenetic Prism to Norms and Values. Frontiers in genetics, 9, 63.
Landecker, H., & Panofsky, A. (2013). From social structure to gene regulation, and back: A critical introduction to environmental epigenetics for sociology. Annual Review of Sociology, 39, 333-357.
Lappé, M., & Landecker, H. (2015). How the genome got a life span. New genetics and society, 34(2), 152-176.
Mansfield, B., & Guthman, J. (2015). Epigenetic life: biological plasticity, abnormality, and new configurations of race and reproduction. cultural geographies, 22(1), 3-20.
Meloni, M. (2015). Epigenetics for the social sciences: justice, embodiment, and inheritance in the postgenomic age. New Genetics and Society, 34(2), 125-151.
Niewöhner, J. (2011). Epigenetics: Embedded bodies and the molecularisation of biography and milieu. BioSocieties, 6(3), 279-298.
Niewöhner, J. (2015). Epigenetics: localizing biology through co-laboration. New Genetics and Society, 34(2), 219-242.
Pickersgill, M., Niewöhner, J., Müller, R., Martin, P., & Cunningham-Burley, S. (2013). Mapping the new molecular landscape: social dimensions of epigenetics. New genetics and society, 32(4), 429-447.
Rothstein, M. A. (2013). Epigenetic Exceptionalism: Currents in Contemporary Bioethics. The Journal of Law, Medicine & Ethics, 41(3), 733-736.
Rothstein, M. A., Cai, Y., & Marchant, G. E. (2009). Ethical implications of epigenetics research. Nature Reviews Genetics, 10(4), 224-224.
Epigenetics and Environment:
What are some common environmental exposures known to influence epigenetic variation that might regularly be found in the average household or work environment? How might epigenetic approaches be used to investigate associations between environmental science and health? What are the roles of hormone disruptors in maintaining epigenetic profiles?
Cortessis, V. K., Thomas, D. C., Levine, A. J., Breton, C. V., Mack, T. M., Siegmund, K. D., ... & Laird, P. W. (2012). Environmental epigenetics: prospects for studying epigenetic mediation of exposure–response relationships. Human genetics, 131(10), 1565-1589.
Guthman, J., & Mansfield, B. (2013). The implications of environmental epigenetics: A new direction for geographic inquiry on health, space, and nature-society relations. Progress in Human Geography, 37(4), 486-504.
Ho, S. M., Johnson, A., Tarapore, P., Janakiram, V., Zhang, X., & Leung, Y. K. (2012). Environmental epigenetics and its implication on disease risk and health outcomes. ILAR journal, 53(3-4), 289-305.
Martin, E. M., & Fry, R. C. (2018). Environmental Influences on the Epigenome: Exposure-Associated DNA Methylation in Human Populations. Annual review of public health, (0).
Meehan, R. R., Thomson, J. P., Lentini, A., Nestor, C. E., & Pennings, S. (2018). DNA methylation as a genomic marker of exposure to chemical and environmental agents. Current Opinion in Chemical Biology, 45, 48-56.
Sage, C., & Burgio, E. (2018). Electromagnetic fields, pulsed radiofrequency radiation, and epigenetics: How wireless technologies may affect childhood development. Child development, 89(1), 129-136.
Skinner, M. K. (2011). Environmental epigenetic transgenerational inheritance and somatic epigenetic mitotic stability. Epigenetics, 6(7), 838.
Epigenetics and Diet:
What does it mean to describe a compound as a “methyl donor”? Which methyl-donning compound is ubiquitous in the one-carbon metabolic pathway? How might people’s cultural beliefs regarding specific foods, food systems, or diet affect the nutritional influences on the epigenome?
Anderson, O. S., Sant, K. E., & Dolinoy, D. C. (2012). Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation. The Journal of nutritional biochemistry, 23(8), 853-859.
Bouchard, C., & Ordovas, J. M. (2012). Fundamentals of nutrigenetics and nutrigenomics. In Progress in molecular biology and translational science (Vol. 108, pp. 1-15). Academic Press.
Burdge, G. C., & Lillycrop, K. A. (2010). Nutrition, epigenetics, and developmental plasticity: implications for understanding human disease. Annual review of nutrition, 30, 315-339.
Fetahu, I. S., Höbaus, J., & Kállay, E. (2014). Vitamin D and the epigenome. Frontiers in physiology, 5, 164.
García-Segura, L., Pérez-Andrade, M., & Miranda-Ríos, J. (2013). The emerging role of MicroRNAs in the regulation of gene expression by nutrients. Journal of nutrigenetics and nutrigenomics, 6(1), 16-31.
Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. 2008. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A 105:17046–9.
Ruemmele, F. M., & Garnier-Lengliné, H. (2012). Why are genetics important for nutrition? Lessons from epigenetic research. Annals of Nutrition and Metabolism, 60(Suppl. 3), 38-43.
Williams, Aaron. “Variation in Dietary Intake and DNA Methylation: The Possibility of a Remnant Thrifty Epigenotype in Populations Remaining at Risk for Seasonal Food Shortages.” Scholars Week, May 18, 2017. http://cedar.wwu.edu/scholwk/2017/Day_two/38.
Epigenetics and Development:
What are the epigenetic events observed during fetal development? What role does the intrauterine environment play in determining health status of offspring later in life? How do maternal and paternal epigenomes …
Bianco-Miotto, T., J. M. Craig, Y. P. Gasser, S. J. van Dijk, and S. E. Ozanne. “Epigenetics and DOHaD: From Basics to Birth and beyond.” Journal of Developmental Origins of Health and Disease, September 2017, 1–7. doi:10.1017/S2040174417000733.
Feinberg, A. P., & Irizarry, R. A. (2010). Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences, 107(suppl 1), 1757-1764.
Hallgrímsson, B., Lieberman, D. E., Liu, W., Ford‐Hutchinson, A. F., & Jirik, F. R. (2007). Epigenetic interactions and the structure of phenotypic variation in the cranium. Evolution & development, 9(1), 76-91.
Reynolds, C. M., O’Sullivan, J. M., Segovia, S. A., & Vickers, M. H. (2018). Early-Life Nutrition, Epigenetics, and Altered Energy Balance Later in Life. In Epigenetics of Aging and Longevity (pp. 213-227).
Richardson, S. S. (2014). Don't blame the mothers: careless discussion of epigenetic research on how early life affects health across generations could harm women, warn Sarah S. Richardson and colleagues. Nature, 512(7513), 131-133.
St-pierre J, Hivert M, Perron P, Poirier P, Guay S, Brisson D, Bouchard L. 2012. IGF2 DNA methylation is a modulator of newborn’s fetal growth and development. Epigenetics 7:1125–1132.
Tobi EW, Heijmans BT, Kremer D, Putter H, Delemarre-van de Waal H a., Finken MJJ, Wit JM, Slagboom PE. 2011. DNA methylation of IGF2, GNASAS, INSIGF and LEP and being born small for gestational age. Epigenetics 6:171–176.
Wehkalampi K, Muurinen M, Wirta SB, Hannula-Jouppi K, Hovi P, Järvenpää A-L, Eriksson JG, Andersson S, Kere J, Kajantie E. 2013. Altered Methylation of IGF2 Locus 20 Years after Preterm Birth at Very Low Birth Weight. PLoS One 8:e67379.
Epigenetics and Aging:
How do epigenetic phenomena naturally lend themselves to serving as metrics of chronological age? What is the relationship between epigenetic variation (like DNA methylation) and individual age? How have twin studies helped in understanding epigenetic determinants of age related phenotypes?
Bell, Jordana T., Pei-Chien Tsai, Tsun-Po Yang, Ruth Pidsley, James Nisbet, Daniel Glass, Massimo Mangino, et al. 2012. Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population. PLoS Genetics 8 (4). doi:10.1371/journal.pgen.1002629.
Calvanese V, Lara E, Kahn A, Fraga MF. 2009. The role of epigenetics in aging and age-related diseases. Ageing Research Reviews 8:268-276.
Chen, Brian H., Riccardo E. Marioni, Elena Colicino, Marjolein J. Peters, Cavin K. Ward-Caviness, Pei-Chien Tsai, Nicholas S. Roetker, et al. 2016. DNA Methylation-Based Measures of Biological Age: Meta-Analysis Predicting Time to Death. Aging, September. doi:10.18632/aging.101020.
Christiansen, L., Lenart, A., Tan, Q., Vaupel, J. W., Aviv, A., McGue, M., & Christensen, K. (2016). DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell, 15(1), 149-154.
Declerck, K., & Berghe, W. V. (2018). Back to the future: epigenetic clock plasticity towards healthy aging. Mechanisms of ageing and development.
Hannum, Gregory, Justin Guinney, Ling Zhao, Li Zhang, Guy Hughes, SriniVas Sadda, Brandy Klotzle, et al. 2013. Genome-Wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Molecular Cell 49 (2): 359–67. doi:10.1016/j.molcel.2012.10.016.
Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL. 2016. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol 17:171.
Lin, Qiong, Carola I. Weidner, Ivan G. Costa, Riccardo E. Marioni, Marcelo R. P. Ferreira, Ian J. Deary, and Wolfgang Wagner. 2016. DNA Methylation Levels at Individual Age-Associated CpG Sites Can Be Indicative for Life Expectancy. Aging (Albany NY) 8 (2): 394–401.
Lowe, Donna, Steve Horvath, and Kenneth Raj. 2016. Epigenetic Clock Analyses of Cellular Senescence and Ageing. Oncotarget 7 (8): 8524–31. doi:10.18632/oncotarget.7383.
Marioni, Riccardo E., Sonia Shah, Allan F. McRae, Brian H. Chen, Elena Colicino, Sarah E. Harris, Jude Gibson, et al. 2015. DNA Methylation Age of Blood Predicts All-Cause Mortality in Later Life. Genome Biology 16: 25. doi:10.1186/s13059-015-0584-6.
Epigenetics and Epidemiology:
How might epigenetic epidemiology aid (or obstruct) contemporary public health efforts? Are epidemiological methods equipped to infer relationships between heath and epigenetic variation accurately and reliably?
Egger, G., Liang, G., Aparicio, A., & Jones, P. A. (2004). Epigenetics in human disease and prospects for epigenetic therapy. Nature, 429(6990), 457.
Esteller, M. (2018). The Human Epigenome—Implications for the Understanding of Human Disease. In Molecular Pathology (Second Edition) (pp. 165-182).
Feinberg, A. P., Koldobskiy, M. A., & Göndör, A. (2016). Epigenetic modulators, modifiers and mediators in cancer aetiology and progression. Nature Reviews Genetics, 17(5), 284.
Heijmans, B. T., & Mill, J. (2012). Commentary: The seven plagues of epigenetic epidemiology. International journal of epidemiology, 41(1), 74-78.
Mill, J., & Heijmans, B. T. (2013). From promises to practical strategies in epigenetic epidemiology. Nature Reviews Genetics, 14(8), 585.
Relton, C. L., & Davey Smith, G. (2012). Is epidemiology ready for epigenetics?. International journal of epidemiology, 41(1), 5-9.
Soubry, A. (2018). Epigenetics as a Driver of Developmental Origins of Health and Disease: Did We Forget the Fathers?. BioEssays, 40(1).
Talens RP, Boomsma DI, Tobi EW, et al. Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology. FASEB J 2010; 24: 3135-3144
Epigenetics and Study design:
What are several confounders that need to be addressed when thinking of an epigenetic or epigenomic question? Why might twin modeled studies be effective in studying epigenetic questions?
Bjornsson HT, Sigurdsson MI, Fallin MD, et al. Intra-individual change over time in DNA methylation with familial clustering. JAMA 2008; 299: 2877-2883
Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J. 2005. Epigenetic differences arise during the lifetime of monozygotic twins. PNAS 102:10604-10609.
Fraser et al. Population-specificity of human DNA methylation. Genome Biology. 2012. 13:R8.
Jaffe, Andrew E, and Rafael A Irizarry. 2014. Accounting for Cellular Heterogeneity Is Critical in Epigenome-Wide Association Studies. Genome Biology 15 (2): R31. doi:10.1186/gb-2014-15-2-r31.
Lam LL et al. Factors underlying variable DNA methylation in a human community cohort. Proc. Natl. Acad. Sci. USA. 2012. 109 Suppl 2:17253-60.
Lowe R, Gemma C, Beyan H, et al. Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics 2013
Michels et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat. Methods. 2013. 10: 949-55
Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. 2013. Recommendations for the design and analysis of epigenome-wide association studies. Nature Methods 10:950-955.
Rakyan VK, Down TA, Balding DJ, et al. Epigenome-wide association studies for common human diseases. Nat Rev Genet 2011; 12: 529-541
Epigenetics and Computation:
How are data handled in epigenetic research? What are some different forms of data that might need to be considered during analyses? How has standardization of methods been a particular challenge?
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. 2014. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinformatics 30:1363-1369.
Du, Pan, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe, Lifang Hou, and Simon M. Lin. 2010. Comparison of Beta-Value and M-Value Methods for Quantifying Methylation Levels by Microarray Analysis. BMC Bioinformatics 11: 587. doi:10.1186/1471-2105-11-587.
Fortin, Jean-Philippe, Timothy Triche, and Kasper Hansen. 2016. Preprocessing, Normalization and Integration of the Illumina HumanMethylationEPIC Array. bioRxiv, July, 065490. doi:10.1101/065490.
Geeleher, Paul, Lori Hartnett, Laurance J. Egan, Aaron Golden, Raja Affendi Raja Ali, and Cathal Seoighe. 2013. Gene-Set Analysis Is Severely Biased When Applied to Genome-Wide Methylation Data. Bioinformatics (Oxford, England) 29 (15): 1851–57. doi:10.1093/bioinformatics/btt311.
Leek, Jeffrey T., W. Evan Johnson, Hilary S. Parker, Andrew E. Jaffe, and John D. Storey. 2012. The Sva Package for Removing Batch Effects and Other Unwanted Variation in High-Throughput Experiments. Bioinformatics 28 (6): 882–83. doi:10.1093/bioinformatics/bts034.
Maksimovic, Jovana, Belinda Phipson, and Alicia Oshlack. 2016. A Cross-Package Bioconductor Workflow for Analysing Methylation Array Data. F1000Research 5 (June): 1281. doi:10.12688/f1000research.8839.1.
Morris TJ, Beck S. 2015. Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods 72:3-8.
Therneau, Terry M. 2015. Coxme: Mixed Effects Cox Models (version 2.2-5). https://cran.r-project.org/web/packages/coxme/index.html.
Epigenetics and Theory:
Why are some scientists wary of modifying current theories of evolution in order to accommodate recent epigenetic findings? Is the modern synthesis deficient in light of epigenetics and its transgenerational effects? What are the implications for the “nature vs. nurture” debate?
Jorgensen, R. A. (2011). Epigenetics: biology's quantum mechanics. Frontiers in plant science, 2, 10.
Jurkowski, Tomasz P, Mirunalini Ravichandran, and Peter Stepper. “Synthetic Epigenetics—towards Intelligent Control of Epigenetic States and Cell Identity.” Clinical Epigenetics 7, no. 1 (2015): 18. doi:10.1186/s13148-015-0044-x.
Laubach, Z. M., Perng, W., Dolinoy, D. C., Faulk, C. D., Holekamp, K. E., & Getty, T. (2018). Epigenetics and the maintenance of developmental plasticity: extending the signalling theory framework. Biological Reviews.
Lauc, G., Vojta, A., & Zoldoš, V. (2014). Epigenetic regulation of glycosylation is the quantum mechanics of biology. Biochimica et Biophysica Acta (BBA)-General Subjects, 1840(1), 65-70.
Meloni, Maurizio, and Giuseppe Testa. “Scrutinizing the Epigenetics Revolution.” BioSocieties 9, no. 4 (2014): 431–456.
Müller, G. B. (2007). Evo–devo: extending the evolutionary synthesis. Nature reviews genetics, 8(12), 943.
Skinner, M. K. (2015). Environmental epigenetics and a unified theory of the molecular aspects of evolution: a neo-Lamarckian concept that facilitates neo-Darwinian evolution. Genome biology and evolution, 7(5), 1296-1302.
Waddington, C. H. (1957). The Strategy of the Genes, 1957. George Unwin & Unwin, London Google Scholar.
Weinhold, A. (2018). Transgenerational stress-adaption: an opportunity for ecological epigenetics. Plant cell reports, 37(1), 3-9.