Co-Localization of the Oncogenic Transcription Factor MYCN and the DNA Methyl Binding Protein MeCP2 at Genomic Sites in Neuroblastoma

Derek M Murphy,Kenneth Bryan,Patrick G Buckley,Sudipto Das,Raymond L Stallings,Karen M Watters,Joseph Najbauer

doi:10.1371/journal.pone.0021436

Derek M Murphy, Kenneth Bryan + Show 5 more

Open Access

https://doi.org/10.1371/journal.pone.0021436

Copy DOI

Abstract

BackgroundMYCN is a transcription factor that is expressed during the development of the neural crest and its dysregulation plays a major role in the pathogenesis of pediatric cancers such as neuroblastoma, medulloblastoma and rhabdomyosarcoma. MeCP2 is a CpG methyl binding protein which has been associated with a number of cancers and developmental disorders, particularly Rett syndrome.Methods and FindingsUsing an integrative global genomics approach involving chromatin immunoprecipitation applied to microarrays, we have determined that MYCN and MeCP2 co-localize to gene promoter regions, as well as inter/intragenic sites, within the neuroblastoma genome (MYCN amplified Kelly cells) at high frequency (70.2% of MYCN sites were also positive for MeCP2). Intriguingly, the frequency of co-localization was significantly less at promoter regions exhibiting substantial hypermethylation (8.7%), as determined by methylated DNA immunoprecipitation (MeDIP) applied to the same microarrays. Co-immunoprecipitation of MYCN using an anti-MeCP2 antibody indicated that a MYCN/MeCP2 interaction occurs at protein level. mRNA expression profiling revealed that the median expression of genes with promoters bound by MYCN was significantly higher than for genes bound by MeCP2, and that genes bound by both proteins had intermediate expression. Pathway analysis was carried out for genes bound by MYCN, MeCP2 or MYCN/MeCP2, revealing higher order functions.ConclusionsOur results indicate that MYCN and MeCP2 protein interact and co-localize to similar genomic sites at very high frequency, and that the patterns of binding of these proteins can be associated with significant differences in transcriptional activity. Although it is not yet known if this interaction contributes to neuroblastoma disease pathogenesis, it is intriguing that the interaction occurs at the promoter regions of several genes important for the development of neuroblastoma, including ALK, AURKA and BDNF.

Highlights

MYCN is a member of the MYC family of basic helix-loop-helix transcription factors which regulate a diverse range of cellular processes including proliferation, differentiation and apoptosis [1]
Our results indicate that MYCN and MeCP2 protein interact and co-localize to similar genomic sites at very high frequency, and that the patterns of binding of these proteins can be associated with significant differences in transcriptional activity
It is not yet known if this interaction contributes to neuroblastoma disease pathogenesis, it is intriguing that the interaction occurs at the promoter regions of several genes important for the development of neuroblastoma, including ALK, AURKA and BDNF

Summary

Introduction

MYCN is a member of the MYC family of basic helix-loop-helix (bHLH) transcription factors which regulate a diverse range of cellular processes including proliferation, differentiation and apoptosis [1]. High level amplification of MYCN occurs in multiple pediatric cancers, and for neuroblastoma it is the most important genetic prognostic indicator of poor clinical outcome [2]. Further evidence that this transcription factor directly contributes to tumorigenesis is provided by the development of neuroblastoma-like tumors in a transgenic mouse model overexpressing MYCN [3]. We further demonstrated that aberrantly high levels of MYCN promote the occupancy of weaker affinity E-box elements, commandeering the functional role of other transcription factors [9]. MeCP2 is a CpG methyl binding protein which has been associated with a number of cancers and developmental disorders, Rett syndrome

Methods

Results

Discussion

Conclusion