Palindromic sequences are important DNA motifs involved in the

PALINDROMIC SEQUENCES IN THE Saccharomyces cerevisae
Berislav Lisnić, Anamarija Štafa, Ivan-Krešimir Svetec and Zoran Zgaga
Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6,
10000 Zagreb, Croatia; [email protected]
Palindromic sequences can be found in the genomes of all organisms. These important
DNA motifs are frequently involved in the regulation of different cellular processes, but
are also a potential source of genetic instability. Considering this dual nature of
palindromic sequences, a systematic study of the incidence of palindromes at the
genomic level seems particularly interesting. In order to make such a study possible, we
have developed a computer program that can identify, locate and count palindromes in a
given sequence in a strictly defined way. We then used this program to prepare a catalog
of all palindromes present in the chromosomal DNA of the yeast Saccharomyces
cerevisae. For each palindrome size, the observed palindrome counts were significantly
different from those in the randomly generated DNA sequences. However, while the
short palindromes (2–12 bp) were under-represented, the palindromes longer than 12 bp
were over-represented, AT-rich and preferentially located in the intergenic regions. The
longest palindrome identified, located between the genes CDC53 and LYS21 on
chromosome IV, is 44-bp long and contains only two G-C base pairs. Avoidance of
coding regions was also observed for palindromes of 4–12 bp, but was less pronounced.
Moreover, analysis of dinucleotide content indicated a strong bias against palindromic
dinucleotides which could explain the observed short palindrome avoidance. We discuss
some possible mechanisms that may influence the evolutionary dynamics of palindromic
sequences in the yeast genome.