Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.

Hdl Handle:
http://hdl.handle.net/10147/95034
Title:
Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.
Authors:
Murphy, Derek M; Buckley, Patrick G; Bryan, Kenneth; Das, Sudipto; Alcock, Leah; Foley, Niamh H; Prenter, Suzanne; Bray, Isabella; Watters, Karen M; Higgins, Desmond; Stallings, Raymond L
Affiliation:
Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland.
Citation:
Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. 2009, 4 (12):e8154 PLoS ONE
Journal:
PloS one
Issue Date:
2009
URI:
http://hdl.handle.net/10147/95034
DOI:
10.1371/journal.pone.0008154
PubMed ID:
19997598
Abstract:
BACKGROUND: 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.
Language:
en
MeSH:
Binding Sites; Cell Line, Tumor; Chromatin Immunoprecipitation; DNA Methylation; DNA, Intergenic; E-Box Elements; Genetic Loci; Humans; MicroRNAs; Neuroblastoma; Nuclear Proteins; Oncogene Proteins; Promoter Regions, Genetic; Protein Binding; Transcription Factors
ISSN:
1932-6203

Full metadata record

DC FieldValue Language
dc.contributor.authorMurphy, Derek Men
dc.contributor.authorBuckley, Patrick Gen
dc.contributor.authorBryan, Kennethen
dc.contributor.authorDas, Sudiptoen
dc.contributor.authorAlcock, Leahen
dc.contributor.authorFoley, Niamh Hen
dc.contributor.authorPrenter, Suzanneen
dc.contributor.authorBray, Isabellaen
dc.contributor.authorWatters, Karen Men
dc.contributor.authorHiggins, Desmonden
dc.contributor.authorStallings, Raymond Len
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

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