Convergence in the evolution of promoters in higher eukaryotic genes transcribed by RNA -polymerase II

The degree of similarity between higher eukarotic promoter sequences transcribed by RNA-polymerase II was to be estimated depending on the species or tissue-specific expression of the corresponding genes. Samples of promoter fragments ([-190; +20] region relative to the transcription start was divided into 7 fragments of 30 bp in length each) have been analyzed for homo sapiens, bos taurus, mus musculus, rat norvegicus, gallus gallus, xenopus laevis and drosophila melanogaster. The sequences were extracted using MGL computer system from the EMBL data library, tissue specificity data from the EPD.

The similarity between the sequences of the i-th fragments of two promoters (i=1,..7) was assumed non-random if a higher alignment score was obtained for them using the program FASTA than for random sequences with the same oligonucleotide content in 95% of cases. The measure of similarity for the group as a whole was the ratio of the number of non-randomly similar pairs of sequences to the total number of all possible pairs in the group.

As turned out, the degree of similarity for the promoters of a species just insignificantly exceeded the random threshold, the highest similarity being observed in the TATA-box and its vicinity. As to the tissue-specific promoters, it was typical of them to have on the whole higher degrees of similarity within a species. That the promoters of non-homologous genes contain non-randomly similar fragments uncovers an important role of convergence in the evolution of promoters.