THE MAJORITY OF LONG NONSTOP READING FRAMES ON THE ANTISENSE STRAND CAN BE EXPLAINED BY BIASED CODON USAGE

In recent studies it has been suggested that long reading frames on th e antisense strand of open reading frames (ORFs) are more frequent tha n expected. The vertebrate DNA database was searched for long (greater than 900 bp) antisense non-stop reading frames (aNRFs) that overlap k nown coding regions. The sequences obtained were predominantly positio ned in DNA with a high usage of G or C in the third codon position of the sense ORF. The major class of sequences revealed by the search was that of the heat-shock protein 70 kDa (Hsp70) family. A long Hsp70 aN RF was found in many Hsp70 sequences and occurred in species as divers e as fish, flies, fungi and bacteria. The role of codon usage bias was analysed both in the specific case of the Hsp70 genes and in a genera l species-wide context. The data obtained showed that even the very lo ng aNRFs present in the Hsp70 family could be explained by codon usage bias on the sense strand. Codon usage bias is determined by GC conten t at the third codon position of the sense ORF and, in some species, b y a high expression level of the gene in question. Such an explanation for the occurrence of long aNRFs cannot exclude that some aNRFs are t ranscribed and translated. (C) 1997 Elsevier Science B.V.