NOTI LINKING CLONES AS A TOOL FOR JOINING PHYSICAL AND GENETIC MAPS OF THE HUMAN GENOME

To study the connection among NotI linking clones, CpG islands, and ge nes, the sequence surrounding 143 NotI sites was determined. These Not I linking clones were isolated from human chromosome 3-specific librar ies and contain an average C + G content of 65%. These clones represen t sequence-tagged sites that can be positioned onto chromosome maps an d used for generating a long-range NotI map of the human genome. A maj ority (about 90%) of these clones contain transcribed sequences, as de tected by Northern blot hybridization, providing an efficient link bet ween physical and functional (genetic) maps. The GenBank nucleotide da tabase was searched with sequences from these NotI linking clones. For many clones, homology was found to human and other vertebrate genes. About 20 clones contained various repeats in their sequences and may r epresent microsatellite loci. Most of these NotI linking clones theref ore represent evolutionarily conserved DNA fragments and also can be u sed for comparative genome mapping of other mammalian species. In addi tion, approximately 20% of all sequenced human CpG island-containing g enes and more than 12% of all well-characterized human genes were foun d to possess NotI restriction sites. This is at least 2-5 times more t han has been previously estimated and suggests that NotI sites have a much stronger association with genes. (C) 1994 Academic Press, Inc.