Epigenome – A mediator for host-microbiome crosstalk

Guinane, 2013, Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ, Therap Adv Gastroenterol, 6, 295, 10.1177/1756283X13482996 Houghteling, 2015, Why is initial bacterial colonization of the intestine important to infants' and children's health?, J Pediatr Gastroenterol Nutr, 60, 294, 10.1097/MPG.0000000000000597 Calkins, 2011, Fetal origins of adult disease, Curr Probl Pediatr Adolesc Health Care, 41, 158, 10.1016/j.cppeds.2011.01.001 Clevers, 2013, The intestinal crypt, a prototype stem cell compartment, Cell, 154, 274, 10.1016/j.cell.2013.07.004 Rajilic-Stojanovic, 2014, The first 1000 cultured species of the human gastrointestinal microbiota, FEMS Microbiol Rev, 38, 996, 10.1111/1574-6976.12075 Miro-Blanch, 2019, Epigenetic regulation at the interplay between gut microbiota and host metabolism, Front Genet, 10, 638, 10.3389/fgene.2019.00638 Waddington, 2012, The epigenotype. 1942, Int J Epidemiol, 41, 10, 10.1093/ije/dyr184 Turner, 2009, Epigenetic responses to environmental change and their evolutionary implications, Philos Trans R Soc Lond B Biol Sci, 364, 3403, 10.1098/rstb.2009.0125 Marchese, 2014, Long non-coding RNAs and chromatin modifiers: their place in the epigenetic code, Epigenetics, 9, 21, 10.4161/epi.27472 Han, 2019, Epigenetic enzyme mutations: role in tumorigenesis and molecular inhibitors, Front Oncol, 9, 194, 10.3389/fonc.2019.00194 Tompkins, 2012, Epigenetic stability, adaptability, and reversibility in human embryonic stem cells, Proc Natl Acad Sci U S A, 109, 12544, 10.1073/pnas.1209620109 Chan, 2012, Epigenetic biomarkers, Curr Top Microbiol Immunol, 355, 189 Robertson, 2005, DNA methylation and human disease, Nat Rev Genet, 6, 597, 10.1038/nrg1655 Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat Rev Genet, 11, 204, 10.1038/nrg2719 Lister, 2009, Human DNA methylomes at base resolution show widespread epigenomic differences, Nature, 462, 315, 10.1038/nature08514 Li, 2018, DNA methylation reprogramming of functional elements during mammalian embryonic development, Cell Discov, 4, 41, 10.1038/s41421-018-0039-9 Kim, 2017, DNA methylation: an epigenetic mark of cellular memory, Exp Mol Med, 49, e322, 10.1038/emm.2017.10 Greenberg, 2019, The diverse roles of DNA methylation in mammalian development and disease, Nat Rev Mol Cell Biol, 20, 590, 10.1038/s41580-019-0159-6 Moore, 2013, DNA methylation and its basic function, Neuropsychopharmacology, 38, 23, 10.1038/npp.2012.112 Elhamamsy, 2017, Role of DNA methylation in imprinting disorders: an updated review, J Assist Reprod Genet, 34, 549, 10.1007/s10815-017-0895-5 Bardhan, 2013, Epigenetics and colorectal cancer pathogenesis, Cancers (Basel), 5, 676, 10.3390/cancers5020676 Karatzas, 2014, DNA methylation changes in inflammatory bowel disease, Ann Gastroenterol, 27, 125 Shahid, 2020, Genetics, Histone Code Bannister, 2011, Regulation of chromatin by histone modifications, Cell Res, 21, 381, 10.1038/cr.2011.22 Dong, 2013, The correlation between histone modifications and gene expression, Epigenomics, 5, 113, 10.2217/epi.13.13 Ray, 2019, Epigenetics, DNA Organization, and Inflammatory Bowel Disease, Inflamm Bowel Dis, 25, 235, 10.1093/ibd/izy330 Zhao, 2019, Epigenetic modifications of histones in cancer, Genome Biol, 20, 245, 10.1186/s13059-019-1870-5 Hayatsu, 1970, Reaction of sodium bisulfite with uracil, cytosine, and their derivatives, Biochemistry, 9, 2858, 10.1021/bi00816a016 Frommer, 1992, A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands, Proc Natl Acad Sci U S A, 89, 1827, 10.1073/pnas.89.5.1827 Lu, 2017, PrimerSuite: a High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR, Sci Rep, 7, 41328, 10.1038/srep41328 Wojdacz, 2010, Limitations and advantages of MS-HRM and bisulfite sequencing for single locus methylation studies, Expert Rev Mol Diagn, 10, 575, 10.1586/erm.10.46 Pidsley, 2016, Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling, Genome Biol, 17, 208, 10.1186/s13059-016-1066-1 Kuo, 1980, Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA, Nucleic Acids Res, 8, 4763, 10.1093/nar/8.20.4763 Ramsahoye, 2002, Measurement of genome-wide DNA cytosine-5 methylation by reversed-phase high-pressure liquid chromatography, Methods Mol Biol, 200, 17 Roberts, 2018, High Performance Liquid Chromatography Separation of Epigenetic Cytosine Variants, Methods Protoc, 1, 10.3390/mps1020010 Stephens, 2013, Epigenetic regulation and measurement of epigenetic changes, Biol Res Nurs, 15, 373, 10.1177/1099800412444785 Liu, 2019, Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution, Nat Biotechnol, 37, 424, 10.1038/s41587-019-0041-2 Hoppers, 2020, Enzymatic Methyl-seq: Next Generation Methylomes, J Biomol Tech, 31, S15 Thornburg, 2010, In utero life and epigenetic predisposition for disease, Adv Genet, 71, 57, 10.1016/B978-0-12-380864-6.00003-1 Smith, 2012, A unique regulatory phase of DNA methylation in the early mammalian embryo, Nature, 484, 339, 10.1038/nature10960 Kobayashi, 2013, High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice, Genome Res, 23, 616, 10.1101/gr.148023.112 O'Neill, 2015, Survival signalling in the preimplantation embryo, Adv Exp Med Biol, 843, 129, 10.1007/978-1-4939-2480-6_5 Li, 2019, Prenatal epigenetics diets play protective roles against environmental pollution, Clin Epigenetics, 11, 82, 10.1186/s13148-019-0659-4 Guo, 2015, The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells, Cell, 161, 1437, 10.1016/j.cell.2015.05.015 Zhu, 2018, Single-cell DNA methylome sequencing of human preimplantation embryos, Nat Genet, 50, 12, 10.1038/s41588-017-0007-6 Elliott, 2015, Epigenetic regulation of the intestinal epithelium, Cell Mol Life Sci, 72, 4139, 10.1007/s00018-015-1997-9 Kraiczy, 2016, Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease, Mucosal Immunol, 9, 647, 10.1038/mi.2015.88 Jorgensen, 2019, Role of DNA Methylation in the Development and Differentiation of Intestinal Epithelial Cells and Smooth Muscle Cells, J Neurogastroenterol Motil, 25, 377, 10.5056/jnm19077 Yu, 2015, Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome, Genome Biol, 16, 211, 10.1186/s13059-015-0763-5 Ganz, 2019, Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development, Dev Biol, 455, 473, 10.1016/j.ydbio.2019.08.002 Howell, 2018, DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome, Gastroenterology, 154, 585, 10.1053/j.gastro.2017.10.007 Rao, 2018, Histone deacetylase activity has an essential role in establishing and maintaining the vertebrate neural crest, Development, 145 Foley, 2009, Prospects for epigenetic epidemiology, Am J Epidemiol, 169, 389, 10.1093/aje/kwn380 Law, 1992, Early growth and abdominal fatness in adult life, J Epidemiol Community Health, 46, 184, 10.1136/jech.46.3.184 St-Pierre, 2016, Effects of prenatal maternal stress on serotonin and fetal development, Placenta, 48, S66, 10.1016/j.placenta.2015.11.013 Bateson, 2004, Developmental plasticity and human health, Nature, 430, 419, 10.1038/nature02725 Heijmans, 2008, Persistent epigenetic differences associated with prenatal exposure to famine in humans, Proc Natl Acad Sci U S A, 105, 17046, 10.1073/pnas.0806560105 Dolinoy, 2006, Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome, Environ Health Perspect, 114, 567, 10.1289/ehp.8700 Weaver, 2005, Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: altering epigenetic marking later in life, J Neurosci, 25, 11045, 10.1523/JNEUROSCI.3652-05.2005 Ursell, 2012, Defining the human microbiome, Nutr Rev, 70, S38, 10.1111/j.1753-4887.2012.00493.x Almeida, 2019, A new genomic blueprint of the human gut microbiota, Nature, 568, 499, 10.1038/s41586-019-0965-1 Martin, 2019, The Influence of the Gut Microbiome on Host Metabolism Through the Regulation of Gut Hormone Release, Front Physiol, 10, 428, 10.3389/fphys.2019.00428 Rinninella, 2019, What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases, Microorganisms, 7, 10.3390/microorganisms7010014 Mueller, 2015, The infant microbiome development: mom matters, Trends Mol Med, 21, 109, 10.1016/j.molmed.2014.12.002 Neu, 2011, Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis, Clin Perinatol, 38, 321, 10.1016/j.clp.2011.03.008 Laursen, 2016, Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity, mSphere, 1, 10.1128/mSphere.00069-15 Rodriguez, 2015, The composition of the gut microbiota throughout life, with an emphasis on early life, Microb Ecol Health Dis, 26, 26050 Yang, 2016, The Infant Microbiome: implications for Infant Health and Neurocognitive Development, Nurs Res, 65, 76, 10.1097/NNR.0000000000000133 Robertson, 2019, The Human Microbiome and Child Growth - First 1000 Days and Beyond, Trends Microbiol, 27, 131, 10.1016/j.tim.2018.09.008 Sharma, 2019, The Epigenetic Connection Between the Gut Microbiome in Obesity and Diabetes, Front Genet, 10, 1329, 10.3389/fgene.2019.01329 Wu, 2012, The role of gut microbiota in immune homeostasis and autoimmunity, Gut Microbes, 3, 4, 10.4161/gmic.19320 Bhat, 2017, Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals, Nutr Rev, 75, 374, 10.1093/nutrit/nux001 Rooks, 2016, Gut microbiota, metabolites and host immunity, Nat Rev Immunol, 16, 341, 10.1038/nri.2016.42 Li, 2018, Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens, Front Cell Infect Microbiol, 8, 314, 10.3389/fcimb.2018.00314 Cortese, 2016, Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease, Epigenetics, 11, 205, 10.1080/15592294.2016.1155011 den Besten, 2013, The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism, J Lipid Res, 54, 2325, 10.1194/jlr.R036012 Sun, 2017, Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases, J Gastroenterol, 52, 1, 10.1007/s00535-016-1242-9 Parada Venegas, 2019, Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases, Front Immunol, 10, 277, 10.3389/fimmu.2019.00277 Schilderink, 2013, Dietary inhibitors of histone deacetylases in intestinal immunity and homeostasis, Front Immunol, 4, 226 Hoverstad, 1986, Short-chain fatty acids in germfree mice and rats, J Nutr, 116, 1772, 10.1093/jn/116.9.1772 Dalile, 2019, The role of short-chain fatty acids in microbiota-gut-brain communication, Nat Rev Gastroenterol Hepatol, 16, 461, 10.1038/s41575-019-0157-3 Wu, 2020, Microbiota-derived metabolite promotes HDAC3 activity in the gut, Nature, 10.1038/s41586-020-2604-2 Zheng, 2020, Interaction between microbiota and immunity in health and disease, Cell Res, 30, 492, 10.1038/s41422-020-0332-7 Takahashi, 2011, Epigenetic control of the host gene by commensal bacteria in large intestinal epithelial cells, J Biol Chem, 286, 35755, 10.1074/jbc.M111.271007 Ganal, 2012, Priming of natural killer cells by nonmucosal mononuclear phagocytes requires instructive signals from commensal microbiota, Immunity, 37, 171, 10.1016/j.immuni.2012.05.020 Navabi, 2017, Epithelial Histone Deacetylase 3 Instructs Intestinal Immunity by Coordinating Local Lymphocyte Activation, Cell Rep, 19, 1165, 10.1016/j.celrep.2017.04.046 Woo, 2019, Microbiota Inhibit Epithelial Pathogen Adherence by Epigenetically Regulating C-Type Lectin Expression, Front Immunol, 10, 928, 10.3389/fimmu.2019.00928 DeGruttola, 2016, Current Understanding of Dysbiosis in Disease in Human and Animal Models, Inflamm Bowel Dis, 22, 1137, 10.1097/MIB.0000000000000750 Nishida, 2018, Gut microbiota in the pathogenesis of inflammatory bowel disease, Clin J Gastroenterol, 11, 1, 10.1007/s12328-017-0813-5 Aleksandrova, 2017, Diet, Gut Microbiome and Epigenetics: Emerging Links with Inflammatory Bowel Diseases and Prospects for Management and Prevention, Nutrients, 9, 10.3390/nu9090962 Hur, 2015, Gut Microbiota and Metabolic Disorders, Diabetes Metab J, 39, 198, 10.4093/dmj.2015.39.3.198 Harsch, 2018, The Role of Gut Microbiota in Obesity and Type 2 and Type 1 Diabetes Mellitus: new Insights into "Old" Diseases, Med Sci (Basel), 6 Davis, 2016, The Gut Microbiome and Its Role in Obesity, Nutr Today, 51, 167, 10.1097/NT.0000000000000167 Kulecka, 2016, Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice, Nutr Metab (Lond), 13, 57, 10.1186/s12986-016-0116-8 Caesar, 2010, Effects of gut microbiota on obesity and atherosclerosis via modulation of inflammation and lipid metabolism, J Intern Med, 268, 320, 10.1111/j.1365-2796.2010.02270.x Caricilli, 2013, The role of gut microbiota on insulin resistance, Nutrients, 5, 829, 10.3390/nu5030829 Patel, 2015, Intestinal microbiota and its relationship with necrotizing enterocolitis, Pediatr Res, 78, 232, 10.1038/pr.2015.97 Elgin, 2016, Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis, Clin Ther, 38, 706, 10.1016/j.clinthera.2016.01.005 Till, 2015, Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung's associated enterocolitis, Front Microbiol, 6, 1154, 10.3389/fmicb.2015.01154 Kellermayer, 2011, Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice, FASEB J, 25, 1449, 10.1096/fj.10-172205 Gupta, 2016, Fecal microbiota transplantation: in perspective, Therap Adv Gastroenterol, 9, 229, 10.1177/1756283X15607414 Landry, 2017, Engineering Diagnostic and Therapeutic Gut Bacteria, Microbiol Spectr, 5, 10.1128/microbiolspec.BAD-0020-2017 Morovic, 2020, Epigenetics: a New Frontier in Probiotic Research, Trends Microbiol