Meiotic Recombination Initiation in and around Retrotransposable Elements in Saccharomyces cerevisiae

Meiotic recombination is initiated by large numbers of developmentally programmed DNA double-strand breaks (DSBs), ranging from dozens to hundreds per cell depending on the organism. DSBs formed in single-copy sequences provoke recombination between allelic positions on homologous chromosomes, but DSBs can also form in and near repetitive elements such as retrotransposons. When they do, they create a risk for deleterious genome rearrangements in the germ line via recombination between non-allelic repeats. A prior study in budding yeast demonstrated that insertion of a Ty retrotransposon into a DSB hotspot can suppress meiotic break formation, but properties of Ty elements in their most common physiological contexts have not been addressed. Here we compile a comprehensive, high resolution map of all Ty elements in the rapidly and efficiently sporulating S. cerevisiae strain SK1 and examine DSB formation in and near these endogenous retrotransposable elements. SK1 has 30 Tys, all but one distinct from the 50 Tys in S288C, the source strain for the yeast reference genome. From whole-genome DSB maps and direct molecular assays, we find that DSB levels and chromatin structure within and near Tys vary widely between different elements and that local DSB suppression is not a universal feature of Ty presence. Surprisingly, deletion of two Ty elements weakened adjacent DSB hotspots, revealing that at least some Ty insertions promote rather than suppress nearby DSB formation. Given high strain-to-strain variability in Ty location and the high aggregate burden of Ty-proximal DSBs, we propose that meiotic recombination is an important component of host-Ty interactions and that Tys play critical roles in genome instability and evolution in both inbred and outcrossed sexual cycles.减数分裂重组（meiotic recombination）由大量发育程序化的DNA双链断裂（DNA double-strand breaks, DSBs）启动，不同物种的单个细胞中，这类断裂的数量从数十到数百不等。单拷贝序列中形成的DSB会引发同源染色体上等位位点间的重组，但DSB也可在反转录转座子（retrotransposons）等重复元件内部及其邻近区域形成。此种情况下，这类断裂会通过非等位重复序列间的重组，对生殖系（germ line）造成有害基因组重排（genome rearrangements）的风险。此前一项针对酿酒酵母（budding yeast）的研究显示，将Ty反转录转座子（Ty retrotransposon）插入DSB热点（DSB hotspot）区域，可抑制减数分裂断裂的形成，但Ty元件在其最常见的生理环境中的特性尚未得到系统研究。本研究构建了快速高效产孢的酿酒酵母菌株SK1中所有Ty元件的全面高分辨率图谱，并针对这些内源性反转录转座子内部及其邻近区域的DSB形成情况开展了分析。SK1菌株共携带30个Ty元件，其中仅1个与酵母参考基因组的来源菌株S288C所含的50个Ty元件一致，其余均存在差异。通过全基因组DSB图谱与直接分子实验检测，我们发现不同Ty元件内部及其邻近区域的DSB水平与染色质结构（chromatin structure）差异显著，且局部DSB抑制并非Ty元件存在的普遍特征。令人意外的是，删除两个Ty元件会削弱其相邻的DSB热点，这表明至少部分Ty插入事件反而会促进而非抑制邻近区域的DSB形成。鉴于Ty元件在菌株间的位置存在高度变异，且Ty近端DSB的总负荷较高，我们提出以下观点：减数分裂重组是宿主与Ty相互作用的重要组成部分，且Ty元件在近交和远交有性周期的基因组不稳定性与进化过程中均发挥关键作用。