title: Identification of DNA methylation in 3' genomic regions that are associated with upregulation of gene expression in colorectal cancer.
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 (37%). 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 up regulation or ectopic gene expression that may involve novel regulatory mechanisms.
authors.affiliation: Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, USA.
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Smith
authors.forename: Saleh
authors.initials: S
authors.lastname: Mahmood
authors.forename: Fei
authors.initials: F
authors.lastname: Song
authors.forename: Arlene
authors.initials: A
authors.lastname: Morrow
authors.forename: Dominic
authors.initials: D
authors.lastname: Smiraglia
authors.forename: Xueli
authors.initials: X
authors.lastname: Zhang
authors.forename: Ashwani
authors.initials: A
authors.lastname: Rajput
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Higgins
authors.forename: Anton
authors.initials: A
authors.lastname: Krumm
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Petrelli
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Costello
authors.forename: Hiroki
authors.initials: H
authors.lastname: Nagase
authors.forename: Christoph
authors.initials: C
authors.lastname: Plass
authors.forename: William A
authors.initials: WA
authors.lastname: Held
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D052138:Genes, Neoplasm / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism; D040641:Quantitative Trait Loci / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions