Identification of DNA methylation in 3′ genomic regions that are associated with upregulation of gene expression in colorectal cancer

Joseph F. Smith, Saleh Mahmood, Fei Song, Arlene Morrow, Dominic Smiraglia, Xueli Zhang, Ashwani Rajput, Michael J. Higgins, Anton Krumm, Nicholas J. Petrelli, Joseph F. Costello, Hiroki Nagase, Christoph Plass, William A. Held

Research output: Contribution to journalArticlepeer-review

Abstract

Restriction landmark genomic scanning (RLGS), a method for the two-dimensional display of end-labeled DNA restriction fragments, was utilized to identify genomic regions of CpG island methylation associated with human colon cancer. An average of 1.5% of the RLGS loci/ spots are lost or significantly reduced in sporadic primary colon tumors relative to normal colon mucosa from the same patient. This may represent tumor specific methylation of about 400 CpG islands in sporadic colon cancer. A number of RLGS loci exhibiting frequent loss associated with colon cancer were cloned. DNA sequence analysis indicated that the RLGS loci identified genomic regions characteristic of CpG islands. A number of methods including bisulfite genomic sequencing as well as quantitative MassARRAY methylation analysis (www.sequenom.com) confirmed tumor specific methylation at several of these loci. DNA database searches indicated that candidate genes associated with these loci include transcription factors and genes involved in signal transduction (52%), and genes of unknown function 137%). Expression analysis using quantitative real time RT-PCR indicates that methylation of some CpG islands located in non-promoter regions were associated with upregulation of gene expression in colorectal cancer. These results indicate that alterations in methylation status within CpG islands in colon tumors may have complex consequences on gene expression and tumorigenesis, sometimes resulting in upregulation or ectopic gene expression that may involve novel regulatory mechanisms.

Original languageEnglish (US)
Pages (from-to)161-172
Number of pages12
JournalEpigenetics
Volume2
Issue number3
DOIs
StatePublished - 2007
Externally publishedYes

Keywords

  • Colon cancer
  • CpG island
  • DNA methylation
  • Epigenetics
  • Epigenomics
  • Restriction landmark genomic scanning (RLGS)

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

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