Population epigenetics

Keller, 1995, Fixation of epigenetic states in a population, J Theor Biol, 176, 211, 10.1006/jtbi.1995.0192 Richards, 2008, Population epigenetics, Curr Opin Genet Dev, 18, 221, 10.1016/j.gde.2008.01.014 Bonasio, 2010, Molecular signals of epigenetic states, Science, 330, 612, 10.1126/science.1191078 Birney, 2016, Epigenome-wide association studies and the interpretation of disease -omics, PLoS Genet, 12, e1006105, 10.1371/journal.pgen.1006105 Richmond, 2016, DNA methylation and BMI: investigating identified methylation sites at HIF3A in a causal framework, Diabetes, 65, 1231, 10.2337/db15-0996 Dekkers, 2016, Blood lipids influence DNA methylation in circulating cells, Genome Biol, 17, 138, 10.1186/s13059-016-1000-6 Gertz, 2011, Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation, PLoS Genet, 7, e1002228, 10.1371/journal.pgen.1002228 Bell, 2011, DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines, Genome Biol, 12, R10, 10.1186/gb-2011-12-1-r10 Bell, 2012, Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population, PLoS Genet, 8, e1002629, 10.1371/journal.pgen.1002629 Drong, 2013, The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue, PLoS One, 8, e55923, 10.1371/journal.pone.0055923 Smith, 2014, Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type, BMC Genomics, 15, 145, 10.1186/1471-2164-15-145 Bonder, 2014, Genetic and epigenetic regulation of gene expression in fetal and adult human livers, BMC Genomics, 15, 860, 10.1186/1471-2164-15-860 Lemire, 2015, Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci, Nat Commun, 6, 6326, 10.1038/ncomms7326 McClay, 2015, High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction, Genome Biol, 16, 291, 10.1186/s13059-015-0842-7 Zhang, 2014, Linking the genetic architecture of cytosine modifications with human complex traits, Hum Mol Genet, 23, 5893, 10.1093/hmg/ddu313 McRae, 2014, Contribution of genetic variation to transgenerational inheritance of DNA methylation, Genome Biol, 15, R73, 10.1186/gb-2014-15-5-r73 Banovich, 2014, Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels, PLoS Genet, 10, e1004663, 10.1371/journal.pgen.1004663 Brem, 2002, Genetic dissection of transcriptional regulation in budding yeast, Science, 296, 752, 10.1126/science.1069516 Degner, 2012, DNase I sensitivity QTLs are a major determinant of human expression variation, Nature, 482, 390, 10.1038/nature10808 Grundberg, 2013, Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements, Am J Hum Genet, 93, 876, 10.1016/j.ajhg.2013.10.004 Houseman, 2012, DNA methylation arrays as surrogate measures of cell mixture distribution, BMC Bioinforma, 13, 86, 10.1186/1471-2105-13-86 Jaffe, 2014, Accounting for cellular heterogeneity is critical in epigenome-wide association studies, Genome Biol, 15, R31, 10.1186/gb-2014-15-2-r31 Houseman, 2014, Reference-free cell mixture adjustments in analysis of DNA methylation data, Bioinformatics, 30, 1431, 10.1093/bioinformatics/btu029 Zou, 2014, Epigenome-wide association studies without the need for cell-type composition, Nat Methods, 11, 309, 10.1038/nmeth.2815 Zilberman, 2007, Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription, Nat Genet, 39, 61, 10.1038/ng1929 Ball, 2009, Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells, Nat Biotechnol, 27, 361, 10.1038/nbt.1533 Richmond, 2015, Prenatal exposure to maternal smoking and offspring DNA methylation across the lifecourse: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC), Hum Mol Genet, 24, 2201, 10.1093/hmg/ddu739 Markunas, 2014, Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy, Environ Health Perspect, 122, 1147, 10.1289/ehp.1307892 Joubert, 2012, 450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy, Environ Health Perspect, 120, 1425, 10.1289/ehp.1205412 Gonseth, 2016, Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates, Epigenetics, 10.1080/15592294.2016.1209614 Bauer, 2015, A varying T cell subtype explains apparent tobacco smoking induced single CpG hypomethylation in whole blood, Clin Epigenetics, 7, 81, 10.1186/s13148-015-0113-1 Bauer, 2015, Tobacco smoking differently influences cell types of the innate and adaptive immune system-indications from CpG site methylation, Clin Epigenetics, 7, 83 Wang, 2012, Widespread plasticity in CTCF occupancy linked to DNA methylation, Genome Res, 22, 1680, 10.1101/gr.136101.111 Hu, 2013, DNA methylation presents distinct binding sites for human transcription factors, elife, 2, e00726, 10.7554/eLife.00726 Bell, 2000, Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene, Nature, 405, 482, 10.1038/35013100 Henikoff, 2016, Epigenetics, cellular memory and gene regulation, Curr Biol, 26, R644, 10.1016/j.cub.2016.06.011 Fullerton, 2012, Finding a place for genomics in health disparities research, Public Health Genomics, 15, 156, 10.1159/000334717 Pratt, 2015, Traffic, air pollution, minority and socio-economic status: addressing inequities in exposure and risk, Int J Environ Res Public Health, 12, 5355, 10.3390/ijerph120505355 Patel, 2011, Traffic density and stationary sources of air pollution associated with wheeze, asthma, and immunoglobulin E from birth to age 5 years among New York City children, Environ Res, 111, 1222, 10.1016/j.envres.2011.08.004 Spira-Cohen, 2010, Personal exposures to traffic-related particle pollution among children with asthma in the South Bronx, NY, J Expo Sci Environ Epidemiol, 20, 446, 10.1038/jes.2009.34 Kheirbek, 2013, PM2.5 and ozone health impacts and disparities in New York City: sensitivity to spatial and temporal resolution, Air Qual Atmos Health, 6, 473, 10.1007/s11869-012-0185-4 Brunst, 2015, Timing and duration of traffic-related air pollution exposure and the risk for childhood wheeze and asthma, Am J Respir Crit Care Med, 192, 421, 10.1164/rccm.201407-1314OC Brandt, 2015, Exposure to allergen and diesel exhaust particles potentiates secondary allergen-specific memory responses, promoting asthma susceptibility, J Allergy Clin Immunol, 136, 295, 10.1016/j.jaci.2014.11.043 Dhabhar, 2008, Enhancing versus suppressive effects of stress on immune function: implications for immunoprotection versus immunopathology, Allergy Asthma Clin Immunol, 4, 2, 10.1186/1710-1492-4-1-2 Hodes, 2014, Individual differences in the peripheral immune system promote resilience versus susceptibility to social stress, Proc Natl Acad Sci U S A, 111, 16136, 10.1073/pnas.1415191111 Wijetunga, 2014, The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences, Nat Commun, 5, 5195, 10.1038/ncomms6195 Kirchner, 2010, Prenatal exposure to the environmental obesogen tributyltin predisposes multipotent stem cells to become adipocytes, Mol Endocrinol, 24, 526, 10.1210/me.2009-0261 Kopras, 2014, Actions of endocrine-disrupting chemicals on stem/progenitor cells during development and disease, Endocr Relat Cancer, 21, T1, 10.1530/ERC-13-0360 Biemann, 2014, Tributyltin affects adipogenic cell fate commitment in mesenchymal stem cells by a PPARγ independent mechanism, Chem Biol Interact, 214, 1, 10.1016/j.cbi.2014.01.021 Harris, 2006, Vitamin D and African Americans, J Nutr, 136, 1126 Holick, 2008, Vitamin D deficiency: a worldwide problem with health consequences, Am J Clin Nutr, 87, 1080S, 10.1093/ajcn/87.4.1080S