tailieunhanh - Strand symmetry and nonrandom dna trimer arrangement in yeast saccharomyces cerevisiae chromosomes

In this study, we present the biased distribution of trimers and their respective reverse complements in the yeast local chromosomal sequences. We show that the chromosomal strand symmetry is the consequence of the equal distribution of trimers and their respective reverse complements in all intergenic sequences as well as in all sense and antisense sequences of chromosome, and that the arrangement of trimers in the sense and antisense sequences of chromosome shapes the codon usage in yeast. | TẠP CHÍ SINH HỌC, 2013, 35(2): 212-218 STRAND SYMMETRY AND NONRANDOM DNA TRIMER ARRANGEMENT IN YEAST SACCHAROMYCES CEREVISIAE CHROMOSOMES Phan Thi Huyen*, Nguyen Duc Luong Ho Chi Minh city University of Technology, VNU-HCM, *huyencnshbk@ ABSTRACT: According to the Chargaff’s second parity rule, the eukaryotic chromosomes have been reported to be strand symmetric. However, how the nucleotides are arranged in the chromosome and why the chromosomes possess this strand symmetric property have not been known. We found in Saccharomyces cerevisiae that although the frequencies of trimers and those of their respective reverse complements in the whole single stranded sequence of chromosome were almost equal, they were remarkably different in the local regions of chromosome. Results of investigation on trimer arrangement in the intergenic sequences as well as in the sense and antisense sequences of chromosome showed that the frequencies of trimers and those of their respective reverse complements in the intergenic sequences of chromosome were approximately the same, and that the trimer arrangement in the sense and antisense sequences of chromosome shaped the codon usage. The chromosomal strand symmetry is the consequence of the equal distribution of trimers and their respective reverse complements. Keywords: Saccharomyces cerevisiae, intergenic sequences, sense and antisense sequences, trimer, trimer reverse complement, codon usage. INTRODUCTION Among the eukaryotic organisms, Saccharomyces cerevisiae was chosen for its genome to be first sequenced completely in 1996 [7]. Since then, its chromosomal sequences have became a valuable resource for studying the DNA structure and DNA related biological processes in the eukaryotic cell. Structurally, the double-stranded DNA chromosomal sequence primarily interacts with histone proteins to form nucleosomes, creating the chromatin fiber. The nucleosome positioning along the yeast chromosomal sequences has been stated .