Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues
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DOI：
10.1093/gbe/evaa068
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发表时间：
2020-04
影响因子：
3.3
通讯作者：
G. M. Pasquesi;B. W. Perry;Michael W. Vandewege;Robert Ruggiero;Drew R. Schield;T. Castoe
中科院分区：
文献类型：
--
作者：
G. M. Pasquesi;B. W. Perry;Michael W. Vandewege;Robert Ruggiero;Drew R. Schield;T. Castoe
摘要转座因子（TEs）是脊椎动物基因组中的重要组成部分，但人们对其在不同组织中的表达和调控以及在不同脊椎动物谱系中的变化知之甚少。我们提出了第一个比较分析整合TE的表达和TE调节途径的活性在体细胞和配子组织的一组不同的12种脊椎动物。我们同时进行基因和TE表达分析，以表征整个脊椎动物的TE表达和TE调节模式，并研究这些功能之间的关系。我们发现在组织和物种间TE负调控相关基因的表达存在显著差异，但在生殖系组织中，特别是睾丸中的表达一直很高。除了哺乳动物外，大多数脊椎动物在性腺组织中显示出极高水平的TE调节途径活性，其中卵巢组织中TE调节途径活性降低可能是相对生殖细胞密度较低的结果。我们还发现，所有的脊椎动物谱系检查表现出显着高水平的TE衍生的转录体细胞和配子组织，最近活跃的TE家族显示出较高的表达在配子组织。尽管大多数TE衍生的转录物来源于失活的古老TE家族（并且可能不能转座），但细胞质中如此高水平的TE衍生的RNA可能具有次要的、未被认识到的生物学相关性。
Abstract Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance.