engleski

Size-dependent palindrome-induced intrachromosomal recombination in yeast

Homologous interactions between DNA repeats found in genomes of all organisms are potential source of various genetic alterations. Closely spaced inverted repeats and palindromes (inverted repeats without spacer DNA) present a special class of repeated sequences since they can engage both in inter- and in intra-strand base-pairing creating secondary structures known as hairpins and cruciforms. Two types of models have been proposed to explain palindrome-induced genomic instability, first that predicts frequent errors during replication of DNA adopting secondary structures and second, requiring an enzymatic activity that transforms cruciforms and hairpins to recombinogenic lesions, like double-strand breaks (DSBs). Both types of models are supported by experimental data and several genetic disorders can be explained by genetic instability of specific palindromic and quasipalindromic sequences. Interestingly, short palindromes, quasipalindromes and inverted repeats are frequently found in different important cis-acting genetic elements like operators, terminators or origins of replication. Stimulation of recombination between inverted repeats was shown to be size-dependent and we postulated that there could be some critical size below which a palindrome would not present a threat to the genomic integrity. In order to test this hypothesis we developed a sensitive recombination assay that measures the loss of the URA3 gene placed between two directly repeated copies of the CYC1 region (1, 7 kb) on the yeast chromosome V. Palindromic sequences of different sizes (up to112 bp) were inserted either within one copy of the CYC1 gene or within the vector sequence separating the repeats. For palindromes longer then 50 bp a size-dependent increase in the pop-out rate was observed regardless to their position in the construct. During pop-out recombination palindromic insertion present in the CYC1 gene was lost in 79/80 uracil auxotrophs examined. These results suggest that the palindromes longer then 40-50 bp can be transformed in vivo to DSBs that are repaired by homologous recombination. By sequence analysis we also found that the palindromes longer then 12 bp are highly over represented, but, in accordance with our data, the size of the longest palindrome present in the yeast genome is 44 bp.

yeast genome; palindrome; intrachromosomal recombination

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