Comparative Analysis of Mouse Notl Linking Clones with Mouse and Human Genomic Sequences and Transcripts

Notl cleavage sites are frequently associated with CpG islands that identify the 5 ' regulatory sites of functional genes in the genome. Therefore we analyzed a sample of 22 Notl linking clones prepared from mouse brain DNA, to determine whether these mouse Notl site associated clones could be used for comparative analysis of mouse and human genomes by cross-reaction with both mouse and human genomic DNA and RNA in Southern and Northern hybridization. We further examined whether we could establish the identity of these clones with known genes by comparing the nucleotide sequences surrounding the Notl site with the GenBank database. We observed that 70 % of the clones cross-hybridized with human DNA and that 4 of 11 tested clones (36%) detected a transcript in human HeLa cells RNA whereas 73 % clones (8/11) detected transcripts in mouse RNAs from one or more organs. Single pass sequence analysis was successful on 16 of 19 clones. The GC content in these sequences was very high (48.8 % to 73.8%) suggesting that 12 of 16 sequenced clones contained a CpG island. Three out of 19 clones showed significant similarity with previously analyzed mouse gene sequences in GenBank, including the mouse rRNA gene family, cathepsin and the scip POU-domain genes. In addition, two sequences showed significant similarity to the human and rabbit protein phosphatase 2A-/3 subunit and the human transforming growth factor-0. Thus, 5 of 1