Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
复制标题
转座元件的双重插入为卫星DNA的进化提供了基础
DOI：
10.1101/158386
复制
发表时间：
2017
期刊：
影响因子：
7
通讯作者：
D. Barbash
中科院分区：
文献类型：
--
作者：
Michael P. McGurk;D. Barbash
真核生物基因组充满了重复序列，其形式是分散在整个基因组中的转座元件(TES)，或者是卫星阵列，即大范围的重复序列。许多卫星显然起源于TES，但尚不清楚移动的遗传寄生虫如何转化为兆基大小的串联阵列。需要进行全面的种群基因组采样，以确定串联TE的频率和发生机制，从最初形成到随后作为卫星进行扩展和维持的所有阶段。由于将单个重复序列映射到独特的基因组位置的挑战，最好的可用种群资源，短读DNA序列，通常被认为在分析重复DNA方面的效用有限。在这里，我们开发了一种名为Context的新管道，它证明了配对末端Illumina数据可以成功地用于识别重复序列中的广泛结构变异，包括串联元件。分析了果蝇五个种群的85个基因组，我们发现TES通常形成串联二聚体。我们的结果进一步表明，插入位点偏好是二聚体产生的主要机制，因此，在活跃的转座期间，二聚体迅速形成。这种丰富的TE二聚体有可能为未来扩展到卫星阵列提供来源材料，我们发现DNA转座子HOBO在单行中的拷贝数扩展到~16个串联拷贝。因此，定义TES的过程--转座--会定期产生新卫星产生的序列。
Eukaryotic genomes are replete with repeated sequences, in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequence. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites. The best available population resources, short-read DNA sequences, are often considered to be of limited utility for analyzing repetitive DNA due to the challenge of mapping individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt which demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. Analyzing 85 genomes from five populations of Drosophila melanogaster we discover that TEs commonly form tandem dimers. Our results further suggest that insertion site preference is the major mechanism by which dimers arise and that, consequently, dimers form rapidly during periods of active transposition. This abundance of TE dimers has the potential to provide source material for future expansion into satellite arrays, and we discover one such copy number expansion of the DNA transposon Hobo to ~16 tandem copies in a single line. The very process that defines TEs —transposition— thus regularly generates sequences from which new satellites can arise.
DOI：
10.1073/pnas.97.7.3347
发表时间：
2000-03
影响因子：
11.1
作者：
Liao Gc;E. J. Rehm;Gerald M. Rubin
通讯作者：
Liao Gc;E. J. Rehm;Gerald M. Rubin
影响因子：
7
作者：
Riddle, Nicole C.;Minoda, Aki;Karpen, Gary H.
通讯作者：
Karpen, Gary H.
果蝇 P 元件优先转座到附近的染色体位点。
影响因子：
3.3
作者：
Tower,J;Karpen,GH;Craig,N;Spradling,AC
通讯作者：
Spradling,AC