Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus
Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus
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DOI：
10.1016/j.ab.2020.113781
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发表时间：
2020-08-01
影响因子：
2.9
通讯作者：
Ray, David A.
中科院分区：
文献类型：
--
作者：
Ghosh, Arnab;Platt, Roy N., II;Ray, David A.
MicroRNA (miRNA) 是 18-24 个核苷酸的调节 RNA。它们通过转录后基因沉默和/或翻译抑制参与遗传和生物途径的调节。数据表明，与现存鳄鱼近亲鸟类相比，咸水鳄（Crocodylus porosus）在过去几百万年的进化速度缓慢。因此，了解咸水鳄在基因组变化相对缓慢的背景下的基因调控，对于基因组学、进化和适应的研究具有潜力。利用 11 种组织类型和 16 个小 RNA 文库，我们报告了咸水鳄鱼中的 644 个 miRNA，其中超过 78% 的 miRNA 对于鳄鱼来说是新的。我们还确定了 miRNA 的潜在靶标，并分析了 miRNA 库与转座元件 (TE) 的关系。结果表明，与逆转录转座子相比，DNA 转座子与 miRNA 的关联性增强。这项工作首次对多孔鳄鱼的 miRNA 进行了全面分析，并探讨了 miRNA 在调节咸水鳄基因组方面的潜在影响。此外，数据表明 TE 作为 miRNA 来源的支持作用，增加了越来越多的证据表明 TE 在基因调控的进化中发挥着重要作用。
MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.