Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Comparative analysis of nucleosome positioning potential for light gene orthologs from different drosophilidae species
The subject of specific interest is the comparison of the characteristics of gene orthologs belonging to the species that transferred ourselves from euchromatin to heterochromatin localization in the evolutional process. It is well known, that this gene is actively expressed and involved in some biological processes. We used the nucleotide sequences of different orthologs of light (lt) gene presented in data bases to obtain the nucleosome positioning characteristics. For a series of lt gene orthologs (Drosophila melanogaster, virilis, pseudoobscura, erecta, yakuba, ananassae) the nucleosome positioning potential (NPP) was calculated for 17 kbp fragments in each case. The size distribution of peaks or peak clusters, presented in NPP was characterized by using the calculations of Fourier coefficients. Each coefficient corresponds to the certain nucleosome cluster size and as a whole this calculation may give rise to the formation of the specter of cluster sizes.
As it is revealed by the calculations with program, published earlier , for those lt orthologs, which localization corresponds to the heterochromatin region predominantly the size of peak clusters is up to 500 bp long, the majority localizes in the introns and has the high coefficient values. In the case of lt gene each ortholog has intron-exon structure, the longer ones (~17 kbp) have longer introns. Maximum length of introns is of ~11 kbp and these long introns comprise the repeats of different kind, e.g., LINE, LTR, DNA type. For the orthologs which localization corresponds to the euchromatin region the clusterization is purely expressed, the Fourier coefficients are of the discernibly lower values and predominantly correspond to the cluster sizes of ~1 and ~ 2 kbp long. Also we compared these observations with the other genes incorporating introns of the same length as, for example, the long intron of lt gene D.melanogaster. In the latter case the pattern of nucleosome clusters may be presented by different cluster sizes in the interval 0.5 ? 2.5 kbp (at half wide level) in each gene individually, and the long introns are predominantly enriched by these clusters compared with the exon portion.
Institute of Molecular Genetics of Russian Academy of Science