Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China.
Mol Plant. 2013 Mar;6(2):470-82. doi: 10.1093/mp/sss081. Epub 2012 Aug 28.
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.
长末端重复序列（LTR）反转录转座子是转座子的主要类型之一，通过剧烈的增殖爆发不断改变或修饰基因功能并重组基因组。许多 LTR-TE 优先插入其他 LTR-TE 内，但这些嵌套 LTR-TE 的原因和进化意义尚不清楚。在这项研究中，扫描了总共 1.52Gb 的芸薹属序列，其中包含 2020 个细菌人工染色体 (BAC)，并选择了 6 个具有极嵌套 LTR-TE 的细菌人工染色体 (BAC) 克隆进行进一步分析。在六个 BAC 中的四个中，大多数 LTR-TE 是由 BAC 区域内起源的反转录转座子的快速增殖产生的，只有少数 LTR-TE 是由大约 5-23Mya 来自 BAC 区域外部的反转录转座子的增殖和插入产生的。LTR-TE 也优先插入 TA 丰富的重复区域。通过 Genescan 进行基因预测，在 0.84Mb 的总 BAC 序列中鉴定出 207 个基因。只有少数基因（3/207）可以与芸薹属表达序列标签 (EST) 数据库匹配，这表明大多数基因在反转录转座子插入后失活。这六个 BAC 中有五个被推测为着丝粒。因此，着丝粒区域内的嵌套 LTR-TE 迅速复制、反复插入，并作用于抑制基因的活性和重新排列着丝粒序列的结构。我们的结果表明，LTR-TE 会在局部范围内爆发和增殖，形成嵌套的 LTR-TE 区域，而这些嵌套的 LTR-TE 在着丝粒的形成中起作用。
