{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:46:04Z","timestamp":1790084764400,"version":"4.0.1"},"reference-count":54,"publisher":"Impact Journals, LLC","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Oncotarget"],"published-print":{"date-parts":[[2017,1,24]]},"DOI":"10.18632\/oncotarget.14042","type":"journal-article","created":{"date-parts":[[2016,12,22]],"date-time":"2016-12-22T16:29:38Z","timestamp":1482424178000},"page":"6085-6101","source":"Crossref","is-referenced-by-count":65,"title":["Genome-wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis"],"prefix":"10.18632","volume":"8","author":[{"given":"Aniruddha","family":"Chatterjee","sequence":"first","affiliation":[{"name":"Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand"},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter A","family":"Stockwell","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Otago, Dunedin, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Ahn","sequence":"additional","affiliation":[{"name":"Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Euan J","family":"Rodger","sequence":"additional","affiliation":[{"name":"Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand"},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna L","family":"Leichter","sequence":"additional","affiliation":[{"name":"Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R","family":"Eccles","sequence":"additional","affiliation":[{"name":"Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand"},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"7892","published-online":{"date-parts":[[2016,12,20]]},"reference":[{"key":"1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1479-5876-8-56","article-title":"Epigenetics of human cutaneous melanoma: setting the stage for new therapeutic strategies","volume":"8","author":"Maio","year":"2010","journal-title":"J Transl Med"},{"key":"2","doi-asserted-by":"crossref","first-page":"87","DOI":"10.3322\/caac.21262","article-title":"Global cancer statistics, 2012","volume":"65","author":"Jemal","year":"2015","journal-title":"CA Cancer J Clin"},{"key":"3","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.4161\/15592294.2014.988062","article-title":"Aberrant CpG methylation of the TFAP2A gene constitutes a mechanism for loss of TFAP2A expression in human metastatic melanoma","volume":"9","author":"Domann","year":"2014","journal-title":"Epigenetics"},{"key":"4","doi-asserted-by":"crossref","first-page":"11","DOI":"10.3322\/caac.21166","article-title":"Cancer statistics, 2013","volume":"63","author":"Jemal","year":"2013","journal-title":"CA Cancer J Clin"},{"key":"5","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1038\/nature00766","article-title":"Mutations of the BRAF gene in human cancer","volume":"417","author":"Ewing","year":"2002","journal-title":"Nature"},{"key":"6","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1126\/science.1235122","article-title":"Cancer genome landscapes","volume":"339","author":"Kinzler","year":"2013","journal-title":"Science"},{"key":"7","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev.pathmechdis.3.121806.151523","article-title":"Metastatic cancer cell","volume":"3","author":"Stamenkovic","year":"2008","journal-title":"Annu Rev Pathol"},{"key":"8","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/301089a0","article-title":"Hypomethylation distinguishes genes of some human cancers from their normal counterparts","volume":"301","author":"Vogelstein","year":"1983","journal-title":"Nature"},{"key":"9","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1038\/nrc3130","article-title":"A decade of exploring the cancer epigenome-biological and translational implications","volume":"11","author":"Jones","year":"2011","journal-title":"Nat Rev Cancer"},{"key":"10","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13059-015-0674-5","article-title":"DNA methylation and epigenomics: new technologies and emerging concepts","volume":"16","author":"Eccles","year":"2015","journal-title":"Genome Biol"},{"key":"11","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1111\/j.1755-148X.2011.00828.x","article-title":"DNA-methylation profiling distinguishes malignant melanomas from benign nevi","volume":"24","author":"Thomas","year":"2011","journal-title":"Pigment Cell Melanoma Res"},{"key":"12","doi-asserted-by":"crossref","first-page":"1462","DOI":"10.1101\/gr.091447.109","article-title":"Genome-wide screen of promoter methylation identifies novel markers in melanoma","volume":"19","author":"Weissman","year":"2009","journal-title":"Genome Res"},{"key":"13","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13059-015-0594-4","article-title":"Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma","volume":"16","author":"Dummer","year":"2015","journal-title":"Genome Biol"},{"key":"14","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1093\/hmg\/ddt420","article-title":"Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis","volume":"23","author":"Murali","year":"2014","journal-title":"Hum Mol Genet"},{"key":"15","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nm.3863","article-title":"Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR","volume":"21","author":"Moran","year":"2015","journal-title":"Nat Med"},{"key":"16","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.ccr.2014.07.028","article-title":"Gene body methylation can alter gene expression and is a therapeutic target in cancer","volume":"26","author":"Liang","year":"2014","journal-title":"Cancer Cell"},{"key":"17","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","article-title":"Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications","volume":"27","author":"Andrews","year":"2011","journal-title":"Bioinformatics"},{"key":"18","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/nbt.1530","article-title":"Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming","volume":"27","author":"Hochedlinger","year":"2009","journal-title":"Nat Biotechnol"},{"key":"19","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1093\/bioinformatics\/btu126","article-title":"DMAP: differential methylation analysis package for RRBS and WGBS data","volume":"30","author":"Morison","year":"2014","journal-title":"Bioinformatics"},{"key":"20","doi-asserted-by":"crossref","unstructured":"Chatterjee, Macaulay, Rodger, Stockwell, Parry, Roberts, Slatter, Hung, Devenish, Morison. Placental Hypomethylation Is more Pronounced in Genomic Loci Devoid of Retroelements. G3 (Bethesda). 2016.","DOI":"10.1534\/g3.116.030379"},{"key":"21","doi-asserted-by":"crossref","first-page":"160019","DOI":"10.1038\/sdata.2016.19","article-title":"Genome-scale DNA methylome and transcriptome profiling of human neutrophils","volume":"3","author":"Morison","year":"2016","journal-title":"Sci Data"},{"key":"22","doi-asserted-by":"crossref","first-page":"15785","DOI":"10.1073\/pnas.0507816102","article-title":"Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry","volume":"102","author":"van den Boom","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"23","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/489052a","article-title":"Genomics: ENCODE explained","volume":"489","author":"Segal","year":"2012","journal-title":"Nature"},{"key":"24","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1097\/CMR.0000000000000141","article-title":"LINE-1 hypermethylation in peripheral blood of cutaneous melanoma patients is associated with metastasis","volume":"25","author":"Krepischi","year":"2015","journal-title":"Melanoma Res"},{"key":"25","doi-asserted-by":"crossref","first-page":"e8461","DOI":"10.1371\/journal.pone.0008461","article-title":"A gene expression signature of invasive potential in metastatic melanoma cells","volume":"4","author":"Eccles","year":"2009","journal-title":"PloS One"},{"key":"26","doi-asserted-by":"crossref","first-page":"e1002692","DOI":"10.1371\/journal.pgen.1002692","article-title":"Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome","volume":"8","author":"Gambin","year":"2012","journal-title":"PLoS Genet"},{"key":"27","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13148-015-0091-3","article-title":"Targeted next-generation sequencing reveals high frequency of mutations in epigenetic regulators across treatment-naive patient melanomas","volume":"7","author":"Lin","year":"2015","journal-title":"Clin Epigenetics"},{"key":"28","doi-asserted-by":"crossref","first-page":"685","DOI":"10.4161\/epi.28151","article-title":"Constitutional promoter methylation and risk of familial melanoma","volume":"9","author":"Yang","year":"2014","journal-title":"Epigenetics"},{"key":"29","article-title":"PTEN Methylation Dependent Sinonasal Mucosal Melanoma","author":"Rha","year":"2015","journal-title":"Cancer Res Treat"},{"key":"30","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1749-8104-6-19","article-title":"EBF factors drive expression of multiple classes of target genes governing neuronal development","volume":"6","author":"Vetter","year":"2011","journal-title":"Neural Dev"},{"key":"31","doi-asserted-by":"crossref","first-page":"1893","DOI":"10.1158\/1541-7786.MCR-09-0229","article-title":"Emerging roles of the EBF family of transcription factors in tumor suppression","volume":"7","author":"Liao","year":"2009","journal-title":"Mol Cancer Res"},{"key":"32","doi-asserted-by":"crossref","first-page":"4494","DOI":"10.1158\/0008-5472.CAN-07-6509","article-title":"Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma","volume":"68","author":"Plass","year":"2008","journal-title":"Cancer Res"},{"key":"33","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1002\/ijc.26038","article-title":"Aberrant DNA methylation and tumor suppressive activity of the EBF3 gene in gastric carcinoma","volume":"130","author":"Kim","year":"2012","journal-title":"Int J Cancer"},{"key":"34","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13046-014-0118-1","article-title":"Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia","volume":"34","author":"Li","year":"2015","journal-title":"J Exp Clin Cancer Res"},{"key":"35","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1158\/2159-8290.CD-11-0199","article-title":"Gene signatures associated with mouse postnatal hindbrain neural stem cells and medulloblastoma cancer stem cells identify novel molecular mediators and predict human medulloblastoma molecular classification","volume":"2","author":"Piemonti","year":"2012","journal-title":"Cancer Discov"},{"key":"36","first-page":"39","article-title":"Increased Expression of Early B-cell Factor 3 in Human Hepatocellular Carcinoma and the Effect of EBF3 Overexpression on HepG2 Cell Cycling","volume":"40","author":"Jin","year":"2009","journal-title":"Labmedicine"},{"key":"37","doi-asserted-by":"crossref","first-page":"18493","DOI":"10.1073\/pnas.1003956107","article-title":"Pheochromocytoma in rats with multiple endocrine neoplasia (MENX) shares gene expression patterns with human pheochromocytoma","volume":"107","author":"Beckers","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"38","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.ydbio.2009.07.014","article-title":"Arx acts as a regional key selector gene in the ventral telencephalon mainly through its transcriptional repression activity","volume":"334","author":"Broccoli","year":"2009","journal-title":"Dev Biol"},{"key":"39","doi-asserted-by":"crossref","first-page":"3740","DOI":"10.1093\/hmg\/ddn271","article-title":"Identification of Arx transcriptional targets in the developing basal forebrain","volume":"17","author":"Golden","year":"2008","journal-title":"Hum Mol Genet"},{"key":"40","doi-asserted-by":"crossref","first-page":"979","DOI":"10.4161\/epi.25797","article-title":"Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing","volume":"8","author":"Nakagawa","year":"2013","journal-title":"Epigenetics"},{"key":"41","first-page":"741542","article-title":"Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries","volume":"2012","author":"Morison","year":"2012","journal-title":"J Biomed Biotechnol"},{"key":"42","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/j.gdata.2014.10.008","article-title":"Base-resolution DNA methylation landscape of zebrafish brain and liver","volume":"2","author":"Nakagawa","year":"2014","journal-title":"Genom Data"},{"issue":"590","key":"43","first-page":"307","article-title":"Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended \u2018male sex drive\u2019 hypothesis","volume":"30","author":"Nakagawa","year":"2016","journal-title":"Gene"},{"key":"44","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1093\/nar\/gks150","article-title":"Comparison of alignment software for genome-wide bisulphite sequence data","volume":"40","author":"Morison","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"45","doi-asserted-by":"crossref","first-page":"R87","DOI":"10.1186\/gb-2012-13-10-r87","article-title":"methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles","volume":"13","author":"Mason","year":"2012","journal-title":"Genome Biol"},{"key":"46","doi-asserted-by":"crossref","first-page":"R96","DOI":"10.1186\/gb-2012-13-10-r96","article-title":"EpiExplorer: live exploration and global analysis of large epigenomic datasets","volume":"13","author":"Bock","year":"2012","journal-title":"Genome Biol"},{"key":"47","doi-asserted-by":"crossref","first-page":"17328","DOI":"10.1038\/srep17328","article-title":"Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation","volume":"5","author":"Morison","year":"2015","journal-title":"Sci Rep"},{"key":"48","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Lempicki","year":"2009","journal-title":"Nat Protoc"},{"key":"49","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.2217\/epi-2016-0063","article-title":"scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups","volume":"8","author":"Eccles","year":"2016","journal-title":"Epigenomics"},{"key":"50","first-page":"7","article-title":"Inhibition of invasion and metastasis by DMBT, a novel trehalose derivative, through Akt\/GSK-3beta\/beta-catenin pathway in B16BL6 cells","volume":"222C","author":"Han","year":"2014","journal-title":"Chem Biol Interact"},{"key":"51","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method","volume":"25","author":"Schmittgen","year":"2001","journal-title":"Methods"},{"key":"52","doi-asserted-by":"crossref","first-page":"5819","DOI":"10.1074\/jbc.M111.295964","article-title":"Roles of STAT3 and ZEB1 proteins in E-cadherin down-regulation and human colorectal cancer epithelial-mesenchymal transition","volume":"287","author":"Fang","year":"2012","journal-title":"J Biol Chem"},{"key":"53","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1093\/bioinformatics\/18.11.1427","article-title":"MethPrimer: designing primers for methylation PCRs","volume":"18","author":"Dahiya","year":"2002","journal-title":"Bioinformatics"},{"key":"54","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1097\/CMR.0b013e328341c7e0","article-title":"PAX3 knockdown in metastatic melanoma cell lines does not reduce MITF expression","volume":"21","author":"Eccles","year":"2011","journal-title":"Melanoma Res"}],"container-title":["Oncotarget"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.oncotarget.com\/lookup\/doi\/10.18632\/oncotarget.14042","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,6]],"date-time":"2020-08-06T14:09:20Z","timestamp":1596722960000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.oncotarget.com\/lookup\/doi\/10.18632\/oncotarget.14042"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12,20]]},"references-count":54,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,1,24]]}},"alternative-id":["14042","28030832"],"URL":"https:\/\/doi.org\/10.18632\/oncotarget.14042","relation":{},"ISSN":["1949-2553"],"issn-type":[{"value":"1949-2553","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,20]]}}}