CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome

Lawrence E. Heisler, Dax Torti, Paul C. Boutros, John Watson, Charles Chan, Neil Winegarden, Mark Takahashi, Patrick Yau, Tim H M Huang, Peggy J. Farnham, Igor Jurisica, James R. Woodgett, Rod Bremner, Linda Z. Penn, Sandy D. Der

Research output: Contribution to journalArticle

75 Scopus citations

Abstract

An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20 736 clones from a CGI Library and used these to construct CGI arrays. The utility of this library requires proper annotation and assessment of the clones, including CpG content, genomic origin and proximity to neighboring genes. Alignment of clone sequences to the human genome (UCSC hg17) identified 9595 distinct genomic loci; 64% were defined by a single clone while the remaining 36% were represented by multiple, redundant clones. Approximately 68% of the loci were located near a transcription start site. The distribution of these loci covered all 23 chromosomes, with 63% overlapping a bioinformatically identified CGI. The high representation of genomic CGI in this rich collection of clones supports the utilization of microarrays produced with this library for the study of global epigenetic mechanisms and protein-chromatin interactions. A browsable database is available on-line to facilitate exploration of the CGIs in this library and their association with annotated genes or promoter elements.

Original languageEnglish (US)
Pages (from-to)2952-2961
Number of pages10
JournalNucleic Acids Research
Volume33
Issue number9
DOIs
StatePublished - 2005

ASJC Scopus subject areas

  • Genetics

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    Heisler, L. E., Torti, D., Boutros, P. C., Watson, J., Chan, C., Winegarden, N., Takahashi, M., Yau, P., Huang, T. H. M., Farnham, P. J., Jurisica, I., Woodgett, J. R., Bremner, R., Penn, L. Z., & Der, S. D. (2005). CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Research, 33(9), 2952-2961. https://doi.org/10.1093/nar/gki582