engleski

Physical and genetic parameters affecting palindrome-stimulated intrachromosomal recombination in Saccharomyces cerevisiae

Palindromic sequences, a type of repetitive DNA motifs characterized by internal two-fold axis of symmetry, can be found in the genetic material of all living organisms. Although frequently located in cis-acting genetic elements, where they play an important role in the regulation of various cellular processes, palindromes have also been recognized as highly recombinogenic motifs that pose a threat to genetic stability. For example, natural palindromes present on several different chromosomes in the human genome are known to provoke constitutional chromosomal translocations that can have significant pathological impact and implications for human health. The ability of palindromes to undermine genome stability and instigate DNA rearrangements has been linked to their potential for forming secondary structures in DNA known as hairpins and cruciforms. Once formed, these secondary structures can be processed to recombinogenic double-strand breaks that can lead to harmful genome rearrangements and cancer. However, parameters that govern the extrusion of palindromic sequences to recombinogenic secondary structures still remain poorly characterized. Using yeast Saccharomyces cerevisiae as a model organism, we decided to systematically investigate the effect of physical and genetic parameters, such as length, position, nucleotide composition, temperature, spacer length and the deletion of MUS81, SPO11, and SAE2 gene on palindrome-stimulated recombination. We demonstrate that palindromic sequences become recombinogenic only after they attain a critical size of approximately 70 bp and that a spacer of only 7 bp completely suppresses recombinogenicity of a 126 bp palindrome. Moreover, high recombination rate in palindrome-containing constructs was completely abolished in SAE2 mutants. Our results can be useful for the prediction of rearrangement-prone palindromic fragile sites in various genetic constructs or sequenced genomes, primarily in the human genome.

palindromes; inverted repeats; recobinogenicity; palindrome size; Saccharomyces cerevisiae

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