title: Aberrant silencing of cancer-related genes by CpG hypermethylation occurs independently of their spatial organization in the nucleus.
abstract: Aberrant promoter DNA-hypermethylation and repressive chromatin constitutes a frequent mechanism of gene inactivation in cancer. There is great interest in dissecting the mechanisms underlying this abnormal silencing. Studies have shown changes in the nuclear organization of chromatin in tumor cells as well as the association of aberrant methylation with long-range silencing of neighboring genes. Furthermore, certain tumors show a high incidence of promoter methylation termed as the CpG island methylator phenotype. Here, we have analyzed the role of nuclear chromatin architecture for genes in hypermethylated inactive versus nonmethylated active states and its relation with long-range silencing and CpG island methylator phenotype. Using combined immunostaining for active/repressive chromatin marks and fluorescence in situ hybridization in colorectal cancer cell lines, we show that aberrant silencing of these genes occurs without requirement for their being positioned at heterochromatic domains. Importantly, hypermethylation, even when associated with long-range epigenetic silencing of neighboring genes, occurs independent of their euchromatic or heterochromatic location. Together, these results indicate that, in cancer, extensive changes around promoter chromatin of individual genes or gene clusters could potentially occur locally without preference for nuclear position and/or causing repositioning. These findings have important implications for understanding relationships between nuclear organization and gene expression patterns in cancer.
authors.affiliation: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA.
authors.forename: Hariharan P
authors.initials: HP
authors.lastname: Easwaran
authors.forename: Leander
authors.initials: L
authors.lastname: Van Neste
authors.forename: Leslie
authors.initials: L
authors.lastname: Cope
authors.forename: Subhojit
authors.initials: S
authors.lastname: Sen
authors.forename: Helai P
authors.initials: HP
authors.lastname: Mohammad
authors.forename: Gayle J
authors.initials: GJ
authors.lastname: Pageau
authors.forename: Jeanne B
authors.initials: JB
authors.lastname: Lawrence
authors.forename: James G
authors.initials: JG
authors.lastname: Herman
authors.forename: Kornel E
authors.initials: KE
authors.lastname: Schuebel
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Baylin
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D055106:Genome-Wide Association Study; D006801:Humans; D017403:In Situ Hybridization; D017404:In Situ Hybridization, Fluorescence; D018799:Intercellular Adhesion Molecule-1 / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D000070957:MutL Protein Homolog 1; D009369:Neoplasms / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D000094742:Secreted Frizzled-Related Proteins
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D018799:Intercellular Adhesion Molecule-1; D000070957:MutL Protein Homolog 1; D009687:Nuclear Proteins; D011518:Proto-Oncogene Proteins; C501486:MLH1 protein, human; C118723:SFRP4 protein, human; D000094742:Secreted Frizzled-Related Proteins