Microarray-based DNA methylation profiling: Technology and applications

Schumacher, A., Kapranov, P., Kaminsky, Z., Flanagan, J., Assadzadeh, A., Yau, P., Virtanen, C., Winegarden, N., Cheng, J., Gingeras, T., Petronis, A. (2006) Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Research, 34 (2). pp. 528-542. ISSN 03051048 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16428248
DOI: 10.1093/nar/gkj461

Abstract

This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA fractions are enriched using a series of treatments with methylation sensitive restriction enzymes, and interrogated on microarrays. We have investigated various aspects of the technology including its replicability, informativeness, sensitivity and optimal PCR conditions using microarrays containing oligonucleotides representing 100 kb of genomic DNA derived from the chromosome 22 COM region in addition to 12 192 element CpG island microarrays. Several new aspects of methylation profiling are provided, including the parallel identification of confounding effects of DNA sequence variation, the description of the principles of microarray design for epigenomic studies and the optimal choice of methylation sensitive restriction enzymes. We also demonstrate the advantages of using the unmethylated DNA fraction versus the methylated one, which substantially improve the chances of detecting DNA methylation differences. We applied this methodology for fine-mapping of methylation patterns of chromosomes 21 and 22 in eight individuals using tiling microarrays consisting of over 340 000 oligonucleotide probe pairs. The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure. © The Author 2006. Published by Oxford Press. all rights reserved.

Item Type: Paper
Uncontrolled Keywords: catechol methyltransferase genomic DNA oligonucleotide restriction endonuclease article chromosome 21 chromosome 22 chromosome map confounding variable controlled study CpG island DNA fingerprinting DNA methylation DNA microarray DNA sequence epigenetics gene mapping gene technology genetic procedures high throughput screening human human genome human tissue intermethod comparison nonhuman nucleotide sequence polymerase chain reaction priority journal process design process development process optimization reproducibility sensitivity analysis Chromosome Mapping Chromosomes Human, Pair 21 Chromosomes Human, Pair 22 CpG Islands DNA Epigenesis Genetic Genome Human Genomics Humans Oligonucleotide Array Sequence Analysis Polymorphism Single Nucleotide Reproducibility of Results
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date Deposited: 08 Mar 2012 17:13
Last Modified: 15 Jul 2013 14:09
PMCID: PMC1345696
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25310

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