Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station TX 77845, USA.
Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
G3 (Bethesda). 2022 Nov 4;12(11). doi: 10.1093/g3journal/jkac214.
The DNA transposon Tc1 was the first transposable element to be characterized in Caenorhabditis elegans and to date, remains the best-studied transposable element in Caenorhabditis worms. While Tc1 copy-number is regulated at approximately 30 copies in the laboratory Bristol N2 and the vast majority of C. elegans strains, the Bergerac strain and its derivatives have experienced a marked Tc1 proliferation. Given the historical importance of the Bergerac strain in the development of the C. elegans model, we implemented a modern genomic analysis of three Bergerac strains (CB4851, RW6999, and RW7000) in conjunction with multiple phenotypic assays to better elucidate the (1) genomic distribution of Tc1 and (2) phenotypic consequences of transposable element deregulation for the host organism. The median estimates of Tc1 copy-number in the Bergerac strains ranged from 451 to 748, which is both (1) greater than previously estimated and (2) likely to be an underestimate of the actual copy-numbers since coverage-based estimates and digital droplet polymerase chain reaction results both suggest higher Tc1 numbers. All three Bergerac strains had significantly reduced trait means compared with the N2 control for each of four fitness-related traits, with specific traits displaying significant differences between Bergerac strains. Tc1 proliferation was genome-wide, specific to Tc1, and particularly high on chromosomes V and X. There were fewer Tc1 insertions in highly expressed chromatin environments than expected by chance. Furthermore, Tc1 integration motifs were also less frequent in exon than noncoding sequences. The source of the proliferation of Tc1 in the Bergerac strains is specific to Tc1 and independent of other transposable elements. The Bergerac strains contain none of the alleles that have previously been found to derepress transposable element activity in C. elegans. However, the Bergerac strains had several Tc1 insertions near or within highly germline-transcribed genes which could account for the recent germline proliferation.
转座子 Tc1 是第一个在秀丽隐杆线虫中被鉴定的转座元件，也是迄今为止在秀丽隐杆线虫中研究得最好的转座元件。虽然 Tc1 的拷贝数在实验室 Bristol N2 和绝大多数秀丽隐杆线虫品系中被调控在大约 30 个拷贝，但 Bergerac 品系及其衍生物经历了 Tc1 的显著增殖。鉴于 Bergerac 品系在秀丽隐杆线虫模型发展中的历史重要性，我们对三个 Bergerac 品系（CB4851、RW6999 和 RW7000）进行了现代基因组分析，并结合多种表型分析，以更好地阐明（1）Tc1 的基因组分布，以及（2）转座元件失调控对宿主生物的表型后果。Bergerac 品系的 Tc1 拷贝数中位数估计值在 451 到 748 之间，这既（1）高于以前的估计值，又（2）可能是实际拷贝数的低估，因为基于覆盖度的估计值和数字液滴聚合酶链反应结果都表明 Tc1 数量更高。与 N2 对照相比，所有三个 Bergerac 品系的四个与适应性相关的性状的特征平均值都显著降低，具体性状在 Bergerac 品系之间也有显著差异。Tc1 的增殖是全基因组的，特异性地针对 Tc1，并且在染色体 V 和 X 上特别高。在高度表达的染色质环境中，Tc1 插入的数量比预期的要少。此外，在exon 中 Tc1 整合基序的频率也低于非编码序列。Bergerac 品系中 Tc1 增殖的原因是特定于 Tc1 的，与其他转座元件无关。Bergerac 品系不含以前在秀丽隐杆线虫中发现的能够解除转座元件活性的等位基因。然而，Bergerac 品系在靠近或在高度生殖系转录基因内有几个 Tc1 插入，这可能是最近生殖系增殖的原因。
