Description

CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near transcription start sites, and may be associated with promoter regions. Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. This methylation helps distinguish the newly synthesized DNA strand from the parent strand, which aids in the final stages of DNA proofreading after duplication. However, over evolutionary time methylated Cs tend to turn into Ts because of spontaneous deamination. The result is that CpGs are relatively rare unless there is selective pressure to keep them or a region is not methylated for some reason, perhaps having to do with the regulation of gene expression. CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole.

Methods

CpG islands are predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. Each segment is then evaluated for the following criteria:

• GC content roughly 50% or greater
• length greater than 200
• ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the basis of the GC content of the segment

The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length.

Credits

This track was generated using a modification of a program developed by G. Miklem and L. Hillier.