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Comprehensive analysis of CpG islands in human chromosomes 21 and 22 Daiya Takai and Peter A. Jones, 2002 A Quick Summary: CpG islands are important for gene expression; studies show that methylation of CpG islands plays a significant role in gene silencing. In 1987, Gardiner-Garden and Frommer set the standard definition of what a CpG island is: a 200 base pair stretch of DNA with 50% G + C content and an observed CpG/expected CpG ratio of at least 0.6. In “Comprehensive analysis of CpG islands in human chromosomes 21 and 22,” Takai and Jones suggest that the standard definition may not be strict enough, and set out to prove it. Takai and Jones code a computer program, using a nifty sliding-window algorithm. They use it to analyze human chromosomes 21 and 22, which contain roughly 750 genes between them. Using Gardiner-Garden and Frommer’s criteria on the sequence, their program comes up with 14,062 CpG islands, more than half of which are Alu repeats (not true CpG islands). Using stricter criteria—minimum length of 500 bp, G + C content of at least 55%, and obs/exp of at least .65—Takai and Jones run their program again and come up with 1,101 CpG islands. Their results include 122 Alus, clearly many fewer than the less strict criteria’s results. Their results are preferentially located on the 5’ region of genes, which is desirable, except for the fact that in eliminating the Alu repeats they also may be throwing out results that matter for gene expression. While they’re at it, in order to be truly comprehensive and live up to the title of their article, Takai and Jones do a comparison between the human genome and several others, looking at the frequency of each dinucleotide in randomly chosen segments of DNA. They find that CpG is suppressed in every genome they look at except for E. Coli’s. CpG is most suppressed in the human genome.