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Oligonucleotide‐based microarray for DNA methylation analysis: Principles and applications
Author(s) -
Shi Huidong,
Maier Sabine,
Nimmrich Inko,
Yan Pearlly S.,
Caldwell Charles W.,
Olek Alexander,
Huang Tim HuiMing
Publication year - 2002
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.10313
Subject(s) - dna methylation , illumina methylation assay , bisulfite sequencing , biology , epigenetics , oligonucleotide , cpg site , promoter , methylation , computational biology , differentially methylated regions , microarray , gene , microbiology and biotechnology , genetics , gene expression
Gene silencing via promoter CpG island hypermethylation offers tumor cells growth advantages. This epigenetic event is pharmacologically reversible, and uncovering a unique set of methylation‐silenced genes in tumor cells can bring a new avenue to cancer treatment. However, high‐throughput tools capable of surveying the methylation status of multiple gene promoters are needed for this discovery process. Herein we describe an oligonucleotide‐based microarray technique that is both versatile and sensitive in revealing hypermethylation in defined regions of the genome. DNA samples are bisulfite‐treated and PCR‐amplified to distinguish CpG dinucleotides that are methylated from those that are not. Fluorescently labeled PCR products are hybridized to arrayed oligonucleotides that can discriminate between methylated and unmethylated alleles in regions of interest. Using this technique, two clinical subtypes of non‐Hodgkin's lymphomas, mantle cell lymphoma, and grades I/II follicular lymphoma, were further separated based on the differential methylation profiles of several gene promoters. Work is underway in our laboratory to extend the interrogation power of this microarray system in multiple candidate genes. This novel tool, therefore, holds promise to monitor the outcome of various epigenetic therapies on cancer patients. © 2002 Wiley‐Liss, Inc.