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dc.contributor.authorMurphy, Derek M
dc.contributor.authorBuckley, Patrick G
dc.contributor.authorBryan, Kenneth
dc.contributor.authorDas, Sudipto
dc.contributor.authorAlcock, Leah
dc.contributor.authorFoley, Niamh H
dc.contributor.authorPrenter, Suzanne
dc.contributor.authorBray, Isabella
dc.contributor.authorWatters, Karen M
dc.contributor.authorHiggins, Desmond
dc.contributor.authorStallings, Raymond L
dc.date.accessioned2010-03-26T09:47:22Z
dc.date.available2010-03-26T09:47:22Z
dc.date.issued2009
dc.identifier.citationGlobal MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. 2009, 4 (12):e8154 PLoS ONEen
dc.identifier.issn1932-6203
dc.identifier.pmid19997598
dc.identifier.doi10.1371/journal.pone.0008154
dc.identifier.urihttp://hdl.handle.net/10147/95034
dc.description.abstractBACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the activity of individual genes, and that of a mediator of global chromatin structure.
dc.language.isoenen
dc.subject.meshBinding Sites
dc.subject.meshCell Line, Tumor
dc.subject.meshChromatin Immunoprecipitation
dc.subject.meshDNA Methylation
dc.subject.meshDNA, Intergenic
dc.subject.meshE-Box Elements
dc.subject.meshGenetic Loci
dc.subject.meshHumans
dc.subject.meshMicroRNAs
dc.subject.meshNeuroblastoma
dc.subject.meshNuclear Proteins
dc.subject.meshOncogene Proteins
dc.subject.meshPromoter Regions, Genetic
dc.subject.meshProtein Binding
dc.subject.meshTranscription Factors
dc.titleGlobal MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.en
dc.contributor.departmentDepartment of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland.en
dc.identifier.journalPloS oneen
refterms.dateFOA2018-08-31T05:10:54Z
html.description.abstractBACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the activity of individual genes, and that of a mediator of global chromatin structure.


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