Investigation of the Mechanism of Meiotic DNA Cleavage by VMA1 -Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site

Abstract

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.Homing endonucleases are site-specific DNA endonucleases encoded within mobile intein-coding sequences or introns and are found in each of the biological kingdoms (1-3). They promote the transfer of intein-coding sequences/introns from an allele containing an intein-coding sequence/intron to an allele lacking an intein-coding sequence/intron, in a process known as homing (1-3). Homing is initiated by endonuclease binding and cleavage at its recognition sequence embedded in the allele lacking an intein-coding sequence/intron. The role of the homing endonuclease is limited to the production of a doublestrand break (DSB) at the recognition sequence. The DSB is then repaired, using the allele containing an intein-coding sequence/intron as a template, by the host recombination machinery, leading to the conversion of an allele lacking the intein-coding sequence/intron to an allele containing the intein-coding sequence/intron (16,23,30). Mobile intein-coding sequences and introns thus spread throughout the population by homing.Mobile intein-coding sequences and introns, as genetic parasites, have evolved several strategies to minimize their impact on host fitness to ensure their persistence in the host genome (2). They are removed at the protein or RNA level by a splicing reaction so as not to interrupt the functional products encoded by their intervening sequence. The lengths of the recognition sequences of their coding endonucleases are 14 to 40 bp, preventing extra digestion of the host genome, because the sequences are expected to be present in a single or a few copies (17). They are usually located in the middle of their own recognition seque...

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