Hooper LV, Gordon JI, Venter JC, Savage DC, Brocks JJ, Logan GA, Buick R, Summons RE, Nelson KE, Paulsen IT, et al. Commensal host-bacterial relationships in the gut. Science (New York, NY). 2001;292:1115–8.
Article
CAS
Google Scholar
Sommer F, Backhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol. 2013;11:227–38.
Article
CAS
PubMed
Google Scholar
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peterson LW, Artis D. Intestinal epithelial cells: regulators of barrier function and immune homeostasis. Nat Rev Immunol. 2014;14:141–53.
Article
CAS
PubMed
Google Scholar
Rosenstiel P. Stories of love and hate: innate immunity and host-microbe crosstalk in the intestine. Curr Opin Gastroenterol. 2013;29:125–32.
Article
CAS
PubMed
Google Scholar
Sommer F, Nookaew I, Sommer N, Fogelstrand P, Backhed F. Site-specific programming of the host epithelial transcriptome by the gut microbiota. Genome Biol. 2015;16:62.
Article
PubMed
PubMed Central
Google Scholar
El Aidy S, Derrien M, Merrifield CA, Levenez F, Dore J, Boekschoten MV, Dekker J, Holmes E, Zoetendal EG, van Baarlen P, et al. Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME J. 2013;7:743–55.
Article
CAS
PubMed
Google Scholar
El Aidy S, Merrifield CA, Derrien M, van Baarlen P, Hooiveld G, Levenez F, Dore J, Dekker J, Holmes E, Claus SP, et al. The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut. 2013;62:1306–14.
Article
CAS
PubMed
Google Scholar
El Aidy S, van Baarlen P, Derrien M, Lindenbergh-Kortleve DJ, Hooiveld G, Levenez F, Dore J, Dekker J, Samsom JN, Nieuwenhuis EE, Kleerebezem M. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol. 2012;5:567–79.
Article
CAS
PubMed
Google Scholar
Larsson E, Tremaroli V, Lee YS, Koren O, Nookaew I, Fricker A, Nielsen J, Ley RE, Backhed F. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut. 2012;61:1124–31.
Article
CAS
PubMed
Google Scholar
Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, Mulder I, Lan A, Bridonneau C, Rochet V, Pisi A, De Paepe M, Brandi G, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity. 2009;31:677–89.
Article
CAS
PubMed
Google Scholar
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 2014;24:1504–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alenghat T, Osborne LC, Saenz SA, Kobuley D, Ziegler CG, Mullican SE, Choi I, Grunberg S, Sinha R, Wynosky-Dolfi M, et al. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 2013;504(7478):153–7.
Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, Deroos P, Liu H, Cross JR, Pfeffer K, Coffer PJ, Rudensky AY. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 2013;504(7480):451–5.
Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J. 2011;25:1449–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mischke M, Plosch T. More than just a gut instinct-the potential interplay between a baby's nutrition, its gut microbiome, and the epigenome. Am J Physiol Regul Integr Comp Physiol. 2013;304:R1065–9.
Article
CAS
PubMed
Google Scholar
Celluzzi A, Masotti A. How our other genome controls our epi-genome. Trends Microbiol. 2016;24(10):777–87.
Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Mol Cell. 2016;64:982–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vertino PM, Sekowski JA, Coll JM, Applegreen N, Han S, Hickey RJ, Malkas LH. DNMT1 is a Component of a Multiprotein DNA Replication Complex. Cell Cycle. 2002;1:416–23.
Article
CAS
PubMed
Google Scholar
Pradhan S, Esteve P-O. Mammalian DNA (cytosine-5) methyltransferases and their expression. Clin Immunol. 2003;109:6–16.
Article
CAS
PubMed
Google Scholar
Goll MG, Bestor TH. Eukaryotic cytosine methyltransferases. Annu Rev Biochem. 2005;74:481–514.
Article
CAS
PubMed
Google Scholar
Holliday R, Pugh J. DNA modification mechanisms and gene activity during development. Science. 1975;187:226–32.
Article
CAS
PubMed
Google Scholar
Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet. 1975;14:9–25.
Article
CAS
PubMed
Google Scholar
Hasler R, Feng Z, Backdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA, Wilson GA, Feber A, et al. A functional methylome map of ulcerative colitis. Genome Res. 2012;22:2130–7.
Article
PubMed
PubMed Central
Google Scholar
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92.
Article
CAS
PubMed
Google Scholar
Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, Liang G. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell. 2014;26:577–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lipka DB, Wang Q, Cabezas-Wallscheid N, Klimmeck D, Weichenhan D, Herrmann C, Lier A, Brocks D, Von Paleske L, Renders S, et al. Identification of dna methylation changes at cis-regulatory elements during early steps of hsc differentiation using tagmentation-based whole genome bisulfite sequencing. Cell Cycle. 2014;13:3476–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee HJ, Hore TA, Reik W. Reprogramming the methylome: erasing memory and creating diversity. Cell Stem Cell. 2014;14:710–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu D-H, Gadkari M, Zhou Q, Yu S, Gao N, Guan Y, Schady D, Roshan TN, Chen M-H, Laritsky E, et al. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome. Genome Biol. 2015;16:211.
Article
PubMed
PubMed Central
Google Scholar
Van den Abbeele P, Van de Wiele T, Verstraete W, Possemiers S, Adlercreutz H, Akira S, Uematsu S, Takeuchi O, Alander M, Satokari R, et al. The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiol Rev. 2011;35:681–704.
Article
CAS
PubMed
Google Scholar
Rodriguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, Avershina E, Rudi K, Narbad A, Jenmalm MC, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26:26050.
PubMed
Google Scholar
Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352:539–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cahenzli J, Koller Y, Wyss M, Geuking MB, McCoy KD. Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe. 2013;14:559–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olszak T, An D, Zeissig S, Vera MP, Richter J, Franke A, Glickman JN, Siebert R, Baron RM, Kasper DL, Blumberg RS. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012;336:489–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gollwitzer ES, Saglani S, Trompette A, Yadava K, Sherburn R, McCoy KD, Nicod LP, Lloyd CM, Marsland BJ. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat Med. 2014;20:642–7.
Article
CAS
PubMed
Google Scholar
Heijtz RD, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A, Hibberd ML, Forssberg H, Pettersson S. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A. 2011;108:3047–52.
Article
CAS
PubMed Central
Google Scholar
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J Physiol. 2004;558:263–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sommer F, Adam N, Johansson MEV, Xia L, Hansson GC, Bäckhed F. Altered mucus glycosylation in core 1 O-glycan-deficient mice affects microbiota composition and intestinal architecture. PLoS One. 2014;9:e85254.
Article
PubMed
PubMed Central
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL, Mortazavi A, Williams B, McCue K, Schaeffer L, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
Google Scholar
Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying genes with differential expression in replicated cDNA microarray experiments. Stat Sin. 2002;12:111–39.
Google Scholar
Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, Winsor GL, Hancock RE, Brinkman FS, Lynn DJ. InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res. 2013;41:D1228–33.
Article
CAS
PubMed
Google Scholar
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. 2009;10:48.
Article
PubMed
PubMed Central
Google Scholar
Xue J, Schmidt SV, Sander J, Draffehn A, Krebs W, Quester I, De Nardo D, Gohel TD, Emde M, Schmidleithner L, et al. Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity. 2014;40:274–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, Zhou Q, Xing Y. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014;111:E5593–601.
Article
CAS
PubMed
PubMed Central
Google Scholar
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics (Oxford, England). 2011;27:1571–2.
Article
CAS
Google Scholar
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE, Deaton A, Bird A, Suzuki M, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13:R87.
Article
PubMed
PubMed Central
Google Scholar
Park Y, Wu H. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics. 2016;32:1446–53.
Article
CAS
PubMed
Google Scholar
Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 2015;43:e141.
PubMed
PubMed Central
Google Scholar
Hebestreit K, Dugas M, Klein HU. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics. 2013;29:1647–53.
Article
CAS
PubMed
Google Scholar
Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize Implements and enhances circular visualization in R. Bioinformatics. 2014;30:2811–2.
Article
CAS
PubMed
Google Scholar
Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG. FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. 2015;43:W182–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics. 2002;18:1427–31.
Article
CAS
PubMed
Google Scholar
Tusnady GE, Simon I, Varadi A, Aranyi T. BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Res. 2005;33:e9.
Article
PubMed
PubMed Central
Google Scholar
Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13:R83.
Article
PubMed
PubMed Central
Google Scholar
Hannenhalli S. Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics (Oxford, England). 2008;24:1325–31.
Article
CAS
Google Scholar
Kaser A, Lee AH, Franke A, Glickman JN, Zeissig S, Tilg H, Nieuwenhuis EE, Higgins DE, Schreiber S, Glimcher LH, Blumberg RS. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell. 2008;134:743–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hasegawa D, Calvo V, Avivar-Valderas A, Lade A, Chou H-I, Lee YA, Farias EF, Aguirre-Ghiso JA, Friedman SL. Epithelial Xbp1 is required for cellular proliferation and differentiation during mammary gland development. Mol Cell Biol. 2015;35:1543–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Adolph TE, Tomczak MF, Niederreiter L, Ko HJ, Bock J, Martinez-Naves E, Glickman JN, Tschurtschenthaler M, Hartwig J, Hosomi S, et al. Paneth cells as a site of origin for intestinal inflammation. Nature. 2013;503:272–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glover LE, Colgan SP. Hypoxia and metabolic factors that influence inflammatory bowel disease pathogenesis. Gastroenterology. 2011;140:1748–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benizri E, Ginouves A, Berra E. The magic of the hypoxia-signaling cascade. Cell Mol Life Sci. 2008;65:1133–49.
Article
CAS
PubMed
Google Scholar
Formenti F, Constantin-Teodosiu D, Emmanuel Y, Cheeseman J, Dorrington KL, Edwards LM, Humphreys SM, Lappin TR, McMullin MF, McNamara CJ, et al. Regulation of human metabolism by hypoxia-inducible factor. Proc Natl Acad Sci U S A. 2010;107:12722–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt SV, Krebs W, Ulas T, Xue J, Bassler K, Gunther P, Hardt AL, Schultze H, Sander J, Klee K, et al. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res. 2016;26:151–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004;14:1085–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Legendre P, Legendre L. Numerical ecology. 3rd ed. Cambridge: Elsevier; 2012.
Fatemi M, Hermann A, Gowher H, Jeltsch A. Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA. Eur J Biochem. 2002;269:4981–4.
Article
CAS
PubMed
Google Scholar
Shen L, Inoue A, He J, Liu Y, Lu F, Zhang Y. Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes. Cell Stem Cell. 2014;15:459–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamauchi T. Neuronal Ca2+/calmodulin-dependent protein kinase II—discovery, progress in a quarter of a century, and perspective: implication for learning and memory. Biol Pharm Bull. 2005;28:1342–54.
Article
CAS
PubMed
Google Scholar
Murphree AL, Benedict WF. Retinoblastoma: clues to human oncogenesis. Science. 1984;223:1028–33.
Article
CAS
PubMed
Google Scholar
Muhlbauer M, Chilton PM, Mitchell TC, Jobin C. Impaired Bcl3 up-regulation leads to enhanced lipopolysaccharide-induced interleukin (IL)-23P19 gene expression in IL-10(−/−) mice. J Biol Chem. 2008;283:14182–9.
Article
PubMed
PubMed Central
Google Scholar
Kraiczy J, Nayak K, Ross A, Raine T, Mak TN, Gasparetto M, Cario E, Rakyan V, Heuschkel R, Zilbauer M. Assessing DNA methylation in the developing human intestinal epithelium: potential link to inflammatory bowel disease. Mucosal Immunol. 2016;9:647–58.
Article
CAS
PubMed
Google Scholar
Rakoff-Nahoum S, Kong Y, Kleinstein SH, Subramanian S, Ahern PP, Gordon JI, Medzhitov R. Analysis of gene–environment interactions in postnatal development of the mammalian intestine. Proc Natl Acad Sci U S A. 2015;112:1929–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247–57.
Article
CAS
PubMed
Google Scholar
He Y-F, Li B-Z, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science (New York, NY). 2011;333:1303–\.
Article
CAS
Google Scholar
Kang J, Kalantry S, Rao A. PGC7, H3K9me2 and Tet3: regulators of DNA methylation in zygotes. Cell Res. 2013;23:6–9.
Article
CAS
PubMed
Google Scholar