Sharma AA, Jen R, Butler A, Lavoie PM. The developing human preterm neonatal immune system: a case for more research in this area. Clin Immunol. 2012;145:61–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stoll BJ, Hansen NI, Adams-Chapman I, Fanaroff AA, Hintz SR, Vohr B, et al. Neurodevelopmental and growth impairment among extremely low-birth-weight infants with neonatal infection. JAMA. 2004;292:2357–65.
Article
CAS
PubMed
Google Scholar
Levy O. Innate immunity of the newborn: basic mechanisms and clinical correlates. Nat Rev Immunol. 2007;7:379–90.
Article
CAS
PubMed
Google Scholar
Adkins B. Neonatal immunology: responses to pathogenic microorganisms and epigenetics reveal an “immunodiverse” developmental state. Immunol Res. 2013;57:246–57.
Article
CAS
PubMed
Google Scholar
Gordon S. Alternative activation of macrophages. Nat Rev Immunol. 2003;3:23–35.
Article
CAS
PubMed
Google Scholar
Raghupathy R. Pregnancy: success and failure within the Th1/Th2/Th3 paradigm. Semin Immunol. 2001;13:219–27.
Article
CAS
PubMed
Google Scholar
Smart JM, Kemp AS. Ontogeny of T-helper 1 and T-helper 2 cytokine production in childhood. Pediatr Allergy Immunol. 2001;12:181–7.
Article
CAS
PubMed
Google Scholar
Strunk T, Temming P, Gembruch U, Reiss I, Bucsky P, Schultz C. Differential maturation of the innate immune response in human fetuses. Pediatr Res. 2004;56:219–26.
Article
CAS
PubMed
Google Scholar
Tatad AM, Nesin M, Peoples J, Cheung S, Lin H, Sison C, et al. Cytokine expression in response to bacterial antigens in preterm and term infant cord blood monocytes. Neonatology. 2008;94:8–15.
Article
CAS
PubMed
Google Scholar
Philbin VJ, Dowling DJ, Gallington LC, Cortes G, Tan Z, Suter EE, et al. Imidazoquinoline Toll-like receptor 8 agonists activate human newborn monocytes and dendritic cells through adenosine-refractory and caspase-1-dependent pathways. J Allergy Clin Immunol. 2012;130:195–204.e199.
Article
CAS
PubMed
PubMed Central
Google Scholar
Strunk T, Prosser A, Levy O, Philbin V, Simmer K, Doherty D, et al. Responsiveness of human monocytes to the commensal bacterium Staphylococcus epidermidis develops late in gestation. Pediatr Res. 2012;72:10–8.
Article
CAS
PubMed
Google Scholar
Sharma AA, Jen R, Kan B, Sharma A, Marchant E, Tang A, et al. Impaired NLRP3 inflammasome activity during fetal development regulates IL-1beta production in human monocytes. Eur J Immunol. 2015;45:238–49.
Article
CAS
PubMed
Google Scholar
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823–37.
Article
CAS
PubMed
Google Scholar
Saksouk N, Simboeck E, Dejardin J. Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin. 2015;8:3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107:21931–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 2011;21:1273–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wagner EJ, Carpenter PB. Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol. 2012;13:115–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell. 2009;4:80–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martino DJ, Tulic MK, Gordon L, Hodder M, Richman TR, Metcalfe J, et al. Evidence for age-related and individual-specific changes in DNA methylation profile of mononuclear cells during early immune development in humans. Epigenetics. 2011;6:1085–94.
Article
CAS
PubMed
Google Scholar
Lederhuber H, Baer K, Altiok I, Sadeghi K, Herkner KR, Kasper DC. MicroRNA-146: tiny player in neonatal innate immunity? Neonatology. 2011;99:51–6.
Article
CAS
PubMed
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tian Y, Jia Z, Wang J, Huang Z, Tang J, Zheng Y, et al. Global mapping of H3K4me1 and H3K4me3 reveals the chromatin state-based cell type-specific gene regulation in human Treg cells. PLoS One. 2011;6:e27770.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sheedy FJ, Palsson-McDermott E, Hennessy EJ, Martin C, O’Leary JJ, Ruan Q, et al. Negative regulation of TLR4 via targeting of the proinflammatory tumor suppressor PDCD4 by the microRNA miR-21. Nat Immunol. 2010;11:141–7.
Article
CAS
PubMed
Google Scholar
McGettrick AF, O’Neill LA. How metabolism generates signals during innate immunity and inflammation. J Biol Chem. 2013;288:22893–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Everts B, Amiel E, Huang SC, Smith AM, Chang CH, Lam WY, et al. TLR-driven early glycolytic reprogramming via the kinases TBK1-IKKvarepsilon supports the anabolic demands of dendritic cell activation. Nat Immunol. 2014;15:323–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith CL, Dickinson P, Forster T, Craigon M, Ross A, Khondoker MR, et al. Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun. 2014;5:4649.
CAS
PubMed
PubMed Central
Google Scholar
Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell. 2007;25:15–30.
Article
CAS
PubMed
Google Scholar
Lauberth SM, Nakayama T, Wu X, Ferris AL, Tang Z, Hughes SH, et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell. 2013;152:1021–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marchini G, Nelson A, Edner J, Lonne-Rahm S, Stavreus-Evers A, Hultenby K. Erythema toxicum neonatorum is an innate immune response to commensal microbes penetrated into the skin of the newborn infant. Pediatr Res. 2005;58:613–6.
Article
PubMed
Google Scholar
Karlsson H, Hessle C, Rudin A. Innate immune responses of human neonatal cells to bacteria from the normal gastrointestinal flora. Infect Immun. 2002;70:6688–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Noval Rivas M, Burton OT, Wise P, Zhang YQ, Hobson SA, Garcia Lloret M, et al. A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis. J Allergy Clin Immunol. 2013;131:201–12.
Article
CAS
PubMed
Google Scholar
Marra F, Marra CA, Richardson K, Lynd LD, Fitzgerald MJ. Antibiotic consumption in children prior to diagnosis of asthma. BMC Pulm Med. 2011;11:32.
Article
PubMed
PubMed Central
Google Scholar
Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, et al. Genome-wide analysis of histone modifications in human pancreatic islets. Genome Res. 2010;20:428–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheng J, Blum R, Bowman C, Hu D, Shilatifard A, Shen S, et al. A role for H3K4 monomethylation in gene repression and partitioning of chromatin readers. Mol Cell. 2014;53:979–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samson M, Jow MM, Wong CC, Fitzpatrick C, Aslanian A, Saucedo I, et al. The specification and global reprogramming of histone epigenetic marks during gamete formation and early embryo development in C. elegans. PLoS Genet. 2014;10:e1004588.
Article
PubMed
PubMed Central
Google Scholar
Kittan NA, Allen RM, Dhaliwal A, Cavassani KA, Schaller M, Gallagher KA, et al. Cytokine induced phenotypic and epigenetic signatures are key to establishing specific macrophage phenotypes. PLoS One. 2013;8:e78045.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wen H, Dou Y, Hogaboam CM, Kunkel SL. Epigenetic regulation of dendritic cell-derived interleukin-12 facilitates immunosuppression after a severe innate immune response. Blood. 2008;111:1797–804.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ishii M, Wen H, Corsa CA, Liu T, Coelho AL, Allen RM, et al. Epigenetic regulation of the alternatively activated macrophage phenotype. Blood. 2009;114:3244–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity. 2009;30:155–67.
Article
PubMed
PubMed Central
Google Scholar
Leung A, Trac C, Du J, Natarajan R, Schones DE. Persistent chromatin modifications induced by high fat diet. J Biol Chem. 2016;291:10446–55.
Article
CAS
PubMed
Google Scholar
Gallagher KA, Joshi A, Carson WF, Schaller M, Allen R, Mukerjee S, et al. Epigenetic changes in bone marrow progenitor cells influence the inflammatory phenotype and alter wound healing in type 2 diabetes. Diabetes. 2015;64:1420–30.
Article
CAS
PubMed
Google Scholar
Wiegman CH, Li F, Clarke CJ, Jazrawi E, Kirkham P, Barnes PJ, et al. A comprehensive analysis of oxidative stress in the ozone-induced lung inflammation mouse model. Clin Sci (Lond). 2014;126:425–40.
Article
CAS
Google Scholar
Raghuraman S, Donkin I, Versteyhe S, Barres R, Simar D. The emerging role of epigenetics in inflammation and immunometabolism. Trends Endocrinol Metab. 2016. doi: 10.1016/j.tem.2016.06.008.
Carroll TS, Liang Z, Salama R, Stark R, de Santiago I. Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Front Genet. 2014;5:75.
Article
PubMed
PubMed Central
Google Scholar
Ourthiague DR, Birnbaum H, Ortenlof N, Vargas JD, Wollman R, Hoffmann A. Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA. J Leukoc Biol. 2015;98:119–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu L, Zinkgraf M, Petzold HE, Beers EP, Filkov V, Groover A. The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function. New Phytol. 2015;205:682–94.
Article
CAS
PubMed
Google Scholar
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012;481:389–93.
CAS
PubMed
PubMed Central
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Article
CAS
PubMed
Google Scholar
Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010;11:237.
Article
PubMed
PubMed Central
Google Scholar