Affiliations: Department of Biochemistry and Molecular Biology,
USC/Norris Comprehensive Cancer Center, Keck School of Medicine of the
University of Southern California, Los Angeles, CA, USA
Note: [] Corresponding author: Daiya Takai, Department of Respiratory
Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyoku, Tokyo, Japan. Tel.: +81 3
3815 5411 ex.33126; Fax: +81 3 3815 5954; E-mail: [email protected].
Abstract: Clusters of CpG dinucleotides in GC rich regions of the genome
called "CpG islands" frequently occur in the 5' ends of genes. Methylation of
CpG islands plays a role in transcriptional silencing in higher organisms in
certain situations. We have established a CpG-island-extraction algorithm,
which we previously developed [Takai and Jones, 2002], on a web site which has
a simple user interface to identify CpG islands from submitted sequences of up
to 50kb. The web site determines the locations of CpG islands using parameters
(lower limit of %GC, ObsCpG/ExpCpG, length) set by the user, to display the
value of parameters on each CpG island, and provides a graphical map of CpG
dinucleotide distribution and borders of CpG islands. A command-line version of
the CpG islands searcher has also been developed for larger sequences. The CpG
Island Searcher was applied to the latest sequence and mapping information of
human chromosomes 20, 21 and 22, and a total of 2345 CpG islands were extracted
and 534 (23%) of them contained first coding exons and 650 (28%) contained
other exons. The CpG Island Searcher is available on the World Wide Web at
http://www.cpgislands.com or http://www.uscnorris.com/cpgislands/cpg.cgi.
Keywords: CpG island, DNA methylation, gene prediction, Internet
