Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity

• Published in: DNA repair 2020-06, Vol.90, p.102848-102848, Article 102848
• Main Authors: Svetec Miklenić, Marina, Gatalica, Nikolina, Matanović, Angela, Žunar, Bojan, Štafa, Anamarija, Lisnić, Berislav, Svetec, Ivan Krešimir
• Format: Article
• Language: English
• Subjects: Base Sequence; DNA, Fungal - metabolism; Flap Endonucleases - metabolism; Inverted Repeat Sequences; Palindromes in DNA; Quasipalindromes with short spacers; Recombination, Genetic; RecQ Helicases - metabolism; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae Proteins - metabolism; Yeast Saccharomyces cerevisiae
• ISSN: 1568-7864; 1568-7856
• DOI: 10.1016/j.dnarep.2020.102848

•Short spacers have negative effect on quasipalindrome recombinogenicity in yeast.•Quasipalindromes up to 150 bp long are stabilized by a spacer as short as 10 bp.•Palindrome stimulated recombination rate is modestly affected in sgs1Δ and rad27Δ. Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.