A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
复制标题
DOI：
10.1101/gr.129585.111
复制
发表时间：
2012-04-01
期刊：
影响因子：
7
通讯作者：
Voytas, Daniel F.
中科院分区：
文献类型：
--
作者：
Baller, Joshua A.;Gao, Jiquan;Voytas, Daniel F.
Ty1 是酿酒酵母中最丰富的逆转录转座子，优先整合到 RNA 聚合酶 III (Pol III) 转录的基因上游。靶向可能是由于Ty1整合复合物和Pal III转录位点的染色质特征之间的相互作用。为了更好地了解 Ty1 靶向决定簇，>150,000 个 Ty1 插入被映射到酿酒酵母基因组序列上。 Logistic 回归用于评估 Ty1 整合模式与各种基因组特征之间的关系，包括组蛋白修饰和转录因子结合位点的全基因组数据集。核小体与 Ty1 插入呈正相关，对 Pol III 转录的基因上游插入进行精细绘图表明，Ty1 优先整合到 H2A/H2B 界面附近的核小体结合 DNA 中。在 Pol III 转录的基因之外，Ty1 避免了编码序列，这种模式不是由于选择，而是反映了对基因侧翼富含核小体的位点的偏好。 Ty1 插入位点也被映射到影响 Ty1 转座频率或整合特异性的四个突变系中（rrm3 Delta、hos2 Delta、rtt109 Delta 和 rad6 Delta）。尽管在 rad6 Delta 菌株中观察到编码序列中的插入明显更多，但突变体中的整合模式在很大程度上得以保留，这表明该突变体缺乏参与泛素化 H2A 的酶，因此靶标特异性有所松动。总体而言，我们的数据表明核小体对于 Ty1 整合是必需的，而次要因素（可能是在 Pol III 转录位点富集的组蛋白修饰或核小体结合因子）决定了首选靶位点。
Ty1, the most abundant retrotransposon in Saccharomyces cerevisiae, integrates preferentially upstream of genes transcribed by RNA polymerase III (Pol III). Targeting is likely due to interactions between the Ty1 integration complex and a feature of chromatin characteristic of sites of Pal Ill transcription. To better understand Ty1 targeting determinants, >150,000 Ty1 insertions were mapped onto the S. cerevisiaegenome sequence. Logistic regression was used to assess relationships between patterns of Ty1 integration and various genomic features, including genome-wide data sets of histone modifications and transcription-factor binding sites. Nucleosomes were positively associated with Ty1 insertions, and fine-scale mapping of insertions upstream of genes transcribed by Pol III indicated that Ty1 preferentially integrates into nucleosome-bound DNA near the H2A/H2B interface. Outside of genes transcribed by Pol III, Ty1 avoids coding sequences, a pattern that is not due to selection, but rather reflects a preference for nucleosome-rich sites flanking genes. Ty1 insertion sites were also mapped in four mutant lines that affect Ty1 transposition frequency or integration specificity (rrm3 Delta, hos2 Delta, rtt109 Delta, and rad6 Delta). Patterns of integration were largely preserved in the mutants, although significantly more insertions into coding sequences were observed in the rad6 Delta strain, suggesting a loosening of target specificity in this mutant that lacks an enzyme involved in ubiquitinating H2A. Overall, our data suggest that nucleosomes are necessary for Ty1 integration, and that a secondary factor, likely a histone modification or nucleosome-bound factor enriched at sites of Pol III transcription, determines preferred target sites.