A model of segmental duplication formation in Drosophila melanogaster
A model of segmental duplication formation in Drosophila melanogaster
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DOI：
10.1101/gr.6208307
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发表时间：
2007-10-01
期刊：
影响因子：
7
通讯作者：
Quesneville, Hadi
中科院分区：
文献类型：
--
作者：
Fiston-Lavier, Anna-Sophie;Anxolabehere, Dominique;Quesneville, Hadi
片段重复 (SD) 是 DNA 片段的低拷贝重复，长期以来一直被认为参与基因组组织和进化。但迄今为止，它们的形成机制仍不清楚。我们提出了一个 SD 形成模型，我们将其命名为“重复依赖链退火”（DDSA）。该模型是合成依赖性链退火（SDSA）模型的变体——双链断裂（DSB）同源修复模型。果蝇基因组中的 DSB 修复通常主要通过同源修复发生，更优先通过 SDSA 模型发生。 DDSA 模型预测，在 DSB 之后，对异位同源区域（此处为重复区域）的搜索将启动修复。正如模型所预期的那样，通过对黑腹果蝇基因组的计算分析检测到的 SD 分析表明 SD 末端的转座元件高度富集。此外，它还显示了 SD 在异色区域中的优先位置。该模型的优点是还可以预测合成过程中留下的特定痕迹。观察到的痕迹支持 DDSA 模型作为黑腹果蝇基因组中 SD 形成的一种模型。这些 DDSA 特征的分析还表明修复复合物中解离链的隔离。
Segmental duplications ( SDs) are low- copy repeats of DNA segments that have long been recognized to be involved in genome organization and evolution. But, to date, the mechanism of their formation remains obscure. We propose a model for SD formation that we name " duplication- dependent strand annealing" ( DDSA). This model is a variant of the synthesis- dependent strand annealing ( SDSA) model - a double- strand break ( DSB) homologous repair model. DSB repair in Drosophila melanogaster genome usually occurs primarily through homologous repair, more preferentially through the SDSA model. The DDSA model predicts that after a DSB, the search for an ectopic homologous region - here a repeat - initiates the repair. As expected by the model, the analysis of SDs detected by a computational analysis of the D. melanogaster genome indicates a high enrichment in transposable elements at SD ends. It shows moreover a preferential location of SDs in heterochromatic regions. The model has the advantage of also predicting specific traces left during synthesis. The observed traces support the DDSA model as one model of formation of SDs in D. melanogaster genome. The analysis of these DDSA signatures suggests moreover a sequestration of the dissociated strand in the repair complex.