The isolation of CpG islands from human chromosomal regions 11q13 and Xp22by segregation of partly melted molecules

We isolated fragments containing parts of CpG islands from human chromosoma l regions chosen for expected differences in gene density by segregation of partly melted molecules. Restriction fragments of P1 bacteriophage clones covering a region of 11q13 and those of cosmid clones derived from Xp22 wer e recovered from bands in denaturing gradient gels that were retained follo wing prolonged exposure to electric field. Forty-five independent fragments derived from 11q13 and five from Xp22 were isolated. Nucleotide sequence a nalysis revealed that 11 of the 45 fragments from 11q13 contained CpG islan ds including four derived from known genes in 11q13. None of the five fragm ents derived from Xp22 resembled CpG islands. The number of CpG island frag ments obtained was consistent with the expectation based on the number of N od restriction endonuclease sites present at these regions. Adjustment of p arameters in our quasi-theoretical approach to the rate of fragment dissoci ation improves the discrimination between retention and non-retention. The results support probable identification of CpG island fragments by their re duced rate of strand dissociation when retarded in a denaturing gradient ge l.