Naslov
Palindrome content of the yeast Saccharomyces cerevisiae genome

Autori
Lisnić, Berislav ; Svetec, Ivan-Krešimir ; Šarić, Hrvoje ; Nikolić, Ivan ; Zgaga, Zoran

Izvornik
Current genetics (0172-8083) 47 (2005), 5; 289-297

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
palindrome; inverted repeat; dinucleotide; Saccharomyces cerevisiae; sequence analysis

Sažetak
Palindromic sequences are important DNA motifs involved in the regulation of different cellular processes but are also a potential source of genetic instability. In order to initiate a systematic study of palindromes at the whole genome level we developed a computer program that may identify, locate and count palindromes in a given sequence in a strictly defined way. All palindromes can be analyzed and sorted according to their size, frequency, GC content or alphabetically. This program was then used to prepare a catalog of all palindromic sequences present in the Saccharomyces cerevisiae genome, but also in randomly generated equivalents of the yeast genome. For each palindrome size the observed palindrome frequencies were significantly different from those found in the randomly generated genomes. However, while the short palindromes (up to 12 bp) were less frequent, the longer palindromes were more frequent, AT- rich and preferentially located in the intergenic regions. The 44 bp palindrome found between the genes CDC53 and LYS21 on chromosome IV was the longest palindrome identified and contained only two C-G base pairs. Avoidance of coding regions was also observed for 4 - 10 bp palindromes, but was less pronounced. Dinucleotide analysis indicated a strong bias against palindromic dinucleotides that could explain the observed short palindrome avoidance. We discuss the possible mechanisms that may influence the evolutionary dynamics of palindromic sequences in the yeast genome.

Izvorni jezik
Engleski

Znanstvena područja
Biotehnologija

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