title: CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome.
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.
authors.affiliation: Department of Laboratory Medicine and Pathobiology, Program in Proteomics and Bioinformatics, University of Toronto Toronto, ON M5S 1A8, Canada.
authors.forename: Lawrence E
authors.initials: LE
authors.lastname: Heisler
authors.forename: Dax
authors.initials: D
authors.lastname: Torti
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
authors.forename: John
authors.initials: J
authors.lastname: Watson
authors.forename: Charles
authors.initials: C
authors.lastname: Chan
authors.forename: Neil
authors.initials: N
authors.lastname: Winegarden
authors.forename: Mark
authors.initials: M
authors.lastname: Takahashi
authors.forename: Patrick
authors.initials: P
authors.lastname: Yau
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Peggy J
authors.initials: PJ
authors.lastname: Farnham
authors.forename: Igor
authors.initials: I
authors.lastname: Jurisica
authors.forename: James R
authors.initials: JR
authors.lastname: Woodgett
authors.forename: Rod
authors.initials: R
authors.lastname: Bremner
authors.forename: Linda Z
authors.initials: LZ
authors.lastname: Penn
authors.forename: Sandy D
authors.initials: SD
authors.lastname: Der
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D018899:CpG Islands; D015342:DNA Probes; D030561:Databases, Nucleic Acid; D015894:Genome, Human; D015698:Genomic Library; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016415:Sequence Alignment
chemical_list: D015342:DNA Probes