Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast. Schizosaccharomyces pombe

In Schizosaccharomyces pombe, DNA replication origins (ORIs) and meiotic recombination hotspots lack consensus sequences and show a bias towards mapping at large intergenic regions (IGRs). To explore whether this preference depended on underlying chromatin features, we have generated genome-wide nucleosome profiles during mitosis and meiosis. We have found that meiotic double-strand break sites (DSB) colocalize strictly with nucleosome-depleted regions (NDRs) and that large IGRs include clusters of NDRs that overlap with almost half of all DSBs. By contrast, ORIs do not colocalize with NDRs and they are regulated independently of DSBs. Physical relocation of NDRs at ectopic loci or modification of their genomic distribution during meiosis was paralleled by the generation of new DSB sites. Over 80% of all meiotic DSBs colocalize with NDRs that are also present during mitosis, indicating that the recombination pattern is largely dependent on constitutive properties of the genome and, to a lesser extent, on the transcriptional profile during meiosis. The organization of ORIs and of DSBs regions in S. pombe reveals similarities and differences relative to Saccharomyces cerevisiae. Overall design: Ten different samples including a total of 14 independent microarray experiments were analyzed. Two samples of immunoprecipitated DNA (including 2 biological replicates of each) for ORC mapping. Four samples of mononucleosomal DNA (including 2 biological replicates of one of them) for nucleosome mapping. Four samples of total RNA for genome-wide transcription mapping (including 2 biological replicates of one of them). Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715) were used for all the experiments.

在粟酒裂殖酵母（Schizosaccharomyces pombe）中，DNA复制起点（DNA replication origins, ORIs）与减数分裂重组热点均缺乏保守共有序列，且倾向于富集于大型基因间区（intergenic regions, IGRs）内。为探究该偏好是否由潜在的染色质特征所介导，我们构建了有丝分裂与减数分裂时期的全基因组核小体图谱。研究发现，减数分裂双链断裂位点（meiotic double-strand break sites, DSBs）与核小体缺失区（nucleosome-depleted regions, NDRs）严格共定位；且大型IGRs中存在多组NDR簇，这些簇覆盖了近半数的DSBs。与之相反，ORIs并不与NDRs共定位，且其调控过程独立于DSBs。对异位位点的NDRs进行物理重定位，或是在减数分裂过程中改变其基因组分布，均会伴随新DSB位点的产生。超过80%的减数分裂DSBs与有丝分裂时期同样存在的NDRs共定位，这表明重组模式在很大程度上依赖于基因组的固有特性，仅在较小程度上受减数分裂时期的转录谱调控。粟酒裂殖酵母中ORIs与DSBs区域的组织模式，与酿酒酵母（Saccharomyces cerevisiae）存在异同之处。整体实验设计：本研究共分析10组不同样本，涵盖14项独立微阵列实验。其中2份用于起源识别复合物（Origin Recognition Complex, ORC）定位检测的免疫沉淀DNA样本（每组各含2次生物学重复）；4份用于核小体定位的单核小体DNA样本（其中1组包含2次生物学重复）；4份用于全基因组转录图谱分析的总RNA样本（其中1组包含2次生物学重复）。所有实验均采用Affymetrix GeneChip 1.0FR平铺式微阵列（GPL7715）完成。