The impact of differential transposition activities of autonomous and non-autonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata.

IF 3.3 3区 生物学 Genetics Pub Date : 2024-04-05 DOI:10.1093/genetics/iyae052
Ryuhei Hatanaka, Katsunori Tamagawa, Nami Haruta, Asako Sugimoto
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Abstract

Transposable elements (TEs) are DNA sequences capable of moving within genomes and significantly influence genomic evolution. The nematode Caenorhabditis inopinata exhibits a much higher TE copy number than its sister species, C. elegans. In this study, we identified a novel autonomous TE belonging to the hAT superfamily from a spontaneous TE-insertion mutant in C. inopinata and named this transposon Ci-hAT1. Further bioinformatic analyses uncovered three additional autonomous hAT elements-Ci-hAT2, Ci-hAT3, and Ci-hAT4-along with over 1,000 copies of two non-autonomous miniature inverted-repeat transposable elements (MITEs), mCi-hAT1 and mCi-hAT4, likely derived from Ci-hAT1 and Ci-hAT4 through internal deletion. We tracked at least three sequential transpositions of Ci-hAT1 over several years. However, the transposition rates of the other three autonomous hAT elements were lower, suggesting varying activity levels. Notably, the distribution patterns of the two MITE families differed significantly: mCi-hAT1 was primarily located in the chromosome arms, a pattern observed in the TEs of other Caenorhabditis species, whereas mCi-hAT4 was more evenly distributed across chromosomes. Additionally, interspecific transcriptome analysis indicated that C. inopinata genes with upstream or intronic these MITE insertions tend to be more highly expressed than their orthologous genes in C. elegans. These findings highlight the significant role of de-silenced TEs in driving the evolution of genomes and transcriptomes, leading to species-specific genetic diversity.
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自主和非自主 hAT 转座元件的不同转座活动对 Caenorhabditis inopinata 基因组结构和基因表达的影响。
可转座元件(Transposable elements,TE)是能够在基因组内移动的 DNA 序列,对基因组进化有重大影响。线虫 Caenorhabditis inopinata 的可转座元件拷贝数远远高于其姊妹物种 C. elegans。在这项研究中,我们从C. inopinata的一个自发TE插入突变体中发现了一个属于hAT超家族的新型自主TE,并将其命名为Ci-hAT1转座子。进一步的生物信息学分析发现了另外三个自主的 hAT 元件--Ci-hAT2、Ci-hAT3 和 Ci-hAT4,以及超过 1,000 个拷贝的两个非自主的微型倒转重复转座元件(MITE)--mCi-hAT1 和 mCi-hAT4,它们很可能是通过内部缺失从 Ci-hAT1 和 Ci-hAT4 衍生而来的。几年来,我们跟踪了至少三次 Ci-hAT1 的连续转座。然而,其他三个自主 hAT 元件的转座率较低,这表明它们的活动水平各不相同。值得注意的是,这两个 MITE 家族的分布模式存在显著差异:mCi-hAT1 主要位于染色体臂,这也是在其他 Caenorhabditis 物种的 TEs 中观察到的模式,而 mCi-hAT4 则更均匀地分布在染色体上。此外,种间转录组分析表明,具有上游或内含这些 MITE 插入物的 C. inopinata 基因往往比其在 elegans 中的同源基因表达得更高。这些发现凸显了去沉默的 TE 在推动基因组和转录组进化中的重要作用,从而导致物种特有的遗传多样性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genetics
Genetics 生物-遗传学
CiteScore
6.20
自引率
6.10%
发文量
177
期刊介绍: GENETICS is published by the Genetics Society of America, a scholarly society that seeks to deepen our understanding of the living world by advancing our understanding of genetics. Since 1916, GENETICS has published high-quality, original research presenting novel findings bearing on genetics and genomics. The journal publishes empirical studies of organisms ranging from microbes to humans, as well as theoretical work. While it has an illustrious history, GENETICS has changed along with the communities it serves: it is not your mentor''s journal. The editors make decisions quickly – in around 30 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is a peer reviewed, peer-edited journal, with an international reach and increasing visibility and impact. All editorial decisions are made through collaboration of at least two editors who are practicing scientists. GENETICS is constantly innovating: expanded types of content include Reviews, Commentary (current issues of interest to geneticists), Perspectives (historical), Primers (to introduce primary literature into the classroom), Toolbox Reviews, plus YeastBook, FlyBook, and WormBook (coming spring 2016). For particularly time-sensitive results, we publish Communications. As part of our mission to serve our communities, we''ve published thematic collections, including Genomic Selection, Multiparental Populations, Mouse Collaborative Cross, and the Genetics of Sex.
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