{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T12:24:18Z","timestamp":1791289458794,"version":"4.3.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2013,9,1]],"date-time":"2013-09-01T00:00:00Z","timestamp":1377993600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The differentiation of CD8 T cells in response to acute infection results in the acquisition of hallmark phenotypic effector functions; however, the epigenetic mechanisms that program this differentiation process on a genome-wide scale are largely unknown. In this article, we report the DNA methylomes of Ag-specific naive and day-8 effector CD8 T cells following acute lymphocytic choriomeningitis virus infection. During effector CD8 T cell differentiation, DNA methylation was remodeled such that changes in DNA methylation at gene promoter regions correlated negatively with gene expression. Importantly, differentially methylated regions were enriched at cis-elements, including enhancers active in naive T cells. Differentially methylated regions were associated with cell type\u2013specific transcription factor binding sites, and these transcription factors clustered into modules that define networks targeted by epigenetic regulation and control of effector CD8 T cell function. Changes in the DNA methylation profile following CD8 T cell activation revealed numerous cellular processes, cis-elements, and transcription factor networks targeted by DNA methylation. Together, the results demonstrated that DNA methylation remodeling accompanies the acquisition of the CD8 T cell effector phenotype and repression of the naive cell state. Therefore, these data provide the framework for an epigenetic mechanism that is required for effector CD8 T cell differentiation and adaptive immune responses.<\/jats:p>","DOI":"10.4049\/jimmunol.1301395","type":"journal-article","created":{"date-parts":[[2013,8,17]],"date-time":"2013-08-17T05:10:15Z","timestamp":1376716215000},"page":"3419-3429","source":"Crossref","is-referenced-by-count":190,"title":["Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function"],"prefix":"10.1093","volume":"191","author":[{"given":"Christopher D","family":"Scharer","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University , Atlanta, GA 30322"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin G","family":"Barwick","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University , Atlanta, GA 30322"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin A","family":"Youngblood","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University , Atlanta, GA 30322"},{"name":"Emory Vaccine Center, Emory University , Atlanta, GA 30322"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafi","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University , Atlanta, GA 30322"},{"name":"Emory Vaccine Center, Emory University , Atlanta, GA 30322"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy M","family":"Boss","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Emory University , Atlanta, GA 30322"},{"name":"Emory Vaccine Center, Emory University , Atlanta, GA 30322"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,9,15]]},"reference":[{"key":"2025032405343204600_r1","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1084\/jem.20001021","article-title":"Estimating the precursor frequency of naive antigen-specific CD8 T cells","volume":"195","author":"Blattman","year":"2002","journal-title":"J. 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Immunol."},{"key":"2025032405343204600_r19","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nature09367","article-title":"Comprehensive methylome map of lineage commitment from haematopoietic progenitors","volume":"467","author":"Ji","year":"2010","journal-title":"Nature"},{"key":"2025032405343204600_r20","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1207306","article-title":"Global DNA demethylation during mouse erythropoiesis in vivo","volume":"334","author":"Shearstone","year":"2011","journal-title":"Science"},{"key":"2025032405343204600_r21","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1101\/gr.091470.109","article-title":"Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity","volume":"19","author":"Schmidl","year":"2009","journal-title":"Genome Res."},{"key":"2025032405343204600_r22","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1016\/j.immuni.2012.09.010","article-title":"T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development","volume":"37","author":"Ohkura","year":"2012","journal-title":"Immunity"},{"key":"2025032405343204600_r23","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.immuni.2011.06.015","article-title":"Chronic virus infection enforces demethylation of the locus that encodes PD-1 in antigen-specific CD8(+) T cells","volume":"35","author":"Youngblood","year":"2011","journal-title":"Immunity"},{"key":"2025032405343204600_r24","doi-asserted-by":"crossref","first-page":"4083","DOI":"10.4049\/jimmunol.176.7.4083","article-title":"Rapid demethylation of the IFN-gamma gene occurs in memory but not naive CD8 T cells","volume":"176","author":"Kersh","year":"2006","journal-title":"J. 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Virol."},{"key":"2025032405343204600_r38","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/nbt1414","article-title":"A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis","volume":"26","author":"Down","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2025032405343204600_r39","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/ng1990","article-title":"Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome","volume":"39","author":"Weber","year":"2007","journal-title":"Nat. Genet."},{"key":"2025032405343204600_r40","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/gene.2010.24","article-title":"DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks","volume":"11","author":"Hughes","year":"2010","journal-title":"Genes Immun."},{"key":"2025032405343204600_r41","doi-asserted-by":"crossref","first-page":"e1001134","DOI":"10.1371\/journal.pgen.1001134","article-title":"Orphan CpG islands identify numerous conserved promoters in the mammalian genome","volume":"6","author":"Illingworth","year":"2010","journal-title":"PLoS Genet."},{"key":"2025032405343204600_r42","doi-asserted-by":"crossref","first-page":"665","DOI":"10.4049\/jimmunol.120.2.665","article-title":"A cytotoxic proteinase isolated from human lymphocytes","volume":"120","author":"Hatcher","year":"1978","journal-title":"J. Immunol."},{"key":"2025032405343204600_r43","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/S1074-7613(00)80185-5","article-title":"ROG, repressor of GATA, regulates the expression of cytokine genes","volume":"12","author":"Miaw","year":"2000","journal-title":"Immunity"},{"key":"2025032405343204600_r44","doi-asserted-by":"crossref","first-page":"2393","DOI":"10.4049\/jimmunol.1103371","article-title":"ZBTB32 is an early repressor of the CIITA and MHC class II gene expression during B cell differentiation to plasma cells","volume":"189","author":"Yoon","year":"2012","journal-title":"J. Immunol."},{"key":"2025032405343204600_r45","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1016\/j.cell.2008.03.038","article-title":"Chemokine signaling via the CXCR2 receptor reinforces senescence","volume":"133","author":"Acosta","year":"2008","journal-title":"Cell"},{"key":"2025032405343204600_r46","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/374070a0","article-title":"An HMG-box-containing T-cell factor required for thymocyte differentiation","volume":"374","author":"Verbeek","year":"1995","journal-title":"Nature"},{"key":"2025032405343204600_r47","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.4049\/jimmunol.176.3.1439","article-title":"Human naive CD8 T cells down-regulate expression of the WNT pathway transcription factors lymphoid enhancer binding factor 1 and transcription factor 7 (T cell factor-1) following antigen encounter in vitro and in vivo","volume":"176","author":"Willinger","year":"2006","journal-title":"J. Immunol."},{"key":"2025032405343204600_r48","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.immuni.2012.08.009","article-title":"The TCF-1 and LEF-1 transcription factors have cooperative and opposing roles in T cell development and malignancy","volume":"37","author":"Yu","year":"2012","journal-title":"Immunity"},{"key":"2025032405343204600_r49","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1038\/nm.2232","article-title":"Transcriptional analysis of HIV-specific CD8+ T cells shows that PD-1 inhibits T cell function by upregulating BATF","volume":"16","author":"Quigley","year":"2010","journal-title":"Nat. Med."},{"key":"2025032405343204600_r50","doi-asserted-by":"crossref","first-page":"14885","DOI":"10.1073\/pnas.1105133108","article-title":"Basic leucine zipper transcription factor, ATF-like (BATF) regulates epigenetically and energetically effector CD8 T-cell differentiation via Sirt1 expression","volume":"108","author":"Kuroda","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025032405343204600_r51","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1128\/MCB.00690-09","article-title":"A new role for sterol regulatory element binding protein 1 transcription factors in the regulation of muscle mass and muscle cell differentiation","volume":"30","author":"Lecomte","year":"2010","journal-title":"Mol. Cell. Biol."},{"key":"2025032405343204600_r52","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1038\/nature01123","article-title":"Dec1 and Dec2 are regulators of the mammalian molecular clock","volume":"419","author":"Honma","year":"2002","journal-title":"Nature"},{"key":"2025032405343204600_r53","doi-asserted-by":"crossref","first-page":"50112","DOI":"10.1074\/jbc.M206771200","article-title":"Basic helix-loop-helix protein DEC1 promotes chondrocyte differentiation at the early and terminal stages","volume":"277","author":"Shen","year":"2002","journal-title":"J. Biol. Chem."},{"key":"2025032405343204600_r54","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Dunham","year":"2012","journal-title":"Nature"},{"key":"2025032405343204600_r55","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2025032405343204600_r56","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1038\/nature05987","article-title":"DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA","volume":"448","author":"Ooi","year":"2007","journal-title":"Nature"},{"key":"2025032405343204600_r57","doi-asserted-by":"crossref","first-page":"766","DOI":"10.1038\/nature07107","article-title":"Genome-scale DNA methylation maps of pluripotent and differentiated cells","volume":"454","author":"Meissner","year":"2008","journal-title":"Nature"},{"key":"2025032405343204600_r58","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/nature04431","article-title":"The Polycomb group protein EZH2 directly controls DNA methylation","volume":"439","author":"Vir\u00e9","year":"2006","journal-title":"Nature"},{"key":"2025032405343204600_r59","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"2025032405343204600_r60","doi-asserted-by":"crossref","first-page":"21931","DOI":"10.1073\/pnas.1016071107","article-title":"Histone H3K27ac separates active from poised enhancers and predicts developmental state","volume":"107","author":"Creyghton","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025032405343204600_r61","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1101\/gr.136101.111","article-title":"Widespread plasticity in CTCF occupancy linked to DNA methylation","volume":"22","author":"Wang","year":"2012","journal-title":"Genome Res."},{"key":"2025032405343204600_r62","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1084\/jem.20070109","article-title":"CREB\/ATF-dependent T cell receptor-induced FoxP3 gene expression: a role for DNA methylation","volume":"204","author":"Kim","year":"2007","journal-title":"J. Exp. Med."},{"key":"2025032405343204600_r63","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1007\/s00109-010-0642-1","article-title":"Methylation matters: binding of Ets-1 to the demethylated Foxp3 gene contributes to the stabilization of Foxp3 expression in regulatory T cells","volume":"88","author":"Polansky","year":"2010","journal-title":"J. Mol. Med. (Berl.)"},{"key":"2025032405343204600_r64","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1126\/science.1987636","article-title":"Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region","volume":"251","author":"Prendergast","year":"1991","journal-title":"Science"},{"key":"2025032405343204600_r65","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1016\/j.cell.2013.02.004","article-title":"Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives","volume":"152","author":"Spruijt","year":"2013","journal-title":"Cell"},{"key":"2025032405343204600_r66","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/0092-8674(95)90136-1","article-title":"Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome","volume":"83","author":"Thanos","year":"1995","journal-title":"Cell"},{"key":"2025032405343204600_r67","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2025032405343204600_r68","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/1074-7613(95)90113-2","article-title":"A role for the orphan steroid receptor Nur77 in apoptosis accompanying antigen-induced negative selection","volume":"3","author":"Calnan","year":"1995","journal-title":"Immunity"},{"key":"2025032405343204600_r69","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1111\/j.1600-0749.2005.00262.x","article-title":"Upstream stimulating factors: highly versatile stress-responsive transcription factors","volume":"18","author":"Corre","year":"2005","journal-title":"Pigment Cell Res."},{"key":"2025032405343204600_r70","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1007\/s00109-009-0520-x","article-title":"ATF3 transcription factor and its emerging roles in immunity and cancer","volume":"87","author":"Thompson","year":"2009","journal-title":"J. Mol. Med. (Berl.)"},{"key":"2025032405343204600_r71","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.cell.2012.03.003","article-title":"MYC on the path to cancer","volume":"149","author":"Dang","year":"2012","journal-title":"Cell"},{"key":"2025032405343204600_r72","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/86308","article-title":"Defining the specific physiological requirements for c-Myc in T cell development","volume":"2","author":"Douglas","year":"2001","journal-title":"Nat. Immunol."},{"key":"2025032405343204600_r73","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/356801a0","article-title":"Nuclear factor of activated T cells contains Fos and Jun","volume":"356","author":"Jain","year":"1992","journal-title":"Nature"},{"key":"2025032405343204600_r74","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/nsmb.1476","article-title":"De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes","volume":"15","author":"Epsztejn-Litman","year":"2008","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2025032405343204600_r75","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/nature10805","article-title":"Enhancer decommissioning by LSD1 during embryonic stem cell differentiation","volume":"482","author":"Whyte","year":"2012","journal-title":"Nature"},{"key":"2025032405343204600_r76","doi-asserted-by":"crossref","first-page":"9281","DOI":"10.1073\/pnas.1000473107","article-title":"Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues","volume":"107","author":"Velasco","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025032405343204600_r77","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1038\/ni1004","article-title":"Active recruitment of DNA methyltransferases regulates interleukin 4 in thymocytes and T cells","volume":"4","author":"Makar","year":"2003","journal-title":"Nat. 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