Conserved and Widespread Expression of piRNA-Like Molecules and PIWI-Like Genes Reveal Dual Functions of Transposon Silencing and Gene Regulation in Pinctada fucata (Mollusca)
Conserved and Widespread Expression of piRNA-Like Molecules and PIWI-Like Genes Reveal Dual Functions of Transposon Silencing and Gene Regulation in Pinctada fucata (Mollusca)
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DOI：
10.3389/fmars.2021.730556
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发表时间：
2021-09
期刊：
影响因子：
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通讯作者：
Songqian Huang;Yuki Ichikawa;K. Yoshitake;S. Kinoshita;M. Asaduzzaman;Fumito Omori;Kaoru Maeyama
中科院分区：
文献类型：
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作者：
Songqian Huang;Yuki Ichikawa;K. Yoshitake;S. Kinoshita;M. Asaduzzaman;Fumito Omori;Kaoru Maeyama
PIWI 蛋白和 PIWI 相互作用 RNA (piRNA) 抑制动物体内的转座子活性，从而保护基因组免受有害的插入突变。最近的研究揭示了 piRNA 在各种动物中的其他靶点和功能。 piRNA 在珍珠贝 Pinctada fucata 的体细胞组织中普遍表达，然而，体细胞 piRNA 的作用尚未得到很好的表征。本研究报道了 P. fucata 中的 PIWI/piRNA 通路，包括 piRNA 生物发生和 piRNA 介导的转座子沉默以及基因调控。 PIWI、Zucchini 和 HEN1 的生物发生因子在体细胞和性腺组织中普遍存在，首次通过转录组分析在 P. fucata 中得到鉴定。生物信息学分析表明，不同群体的 piRNA 以组织特异性方式参与乒乓放大环路。此外，根据piRNA的表达情况，在P. fucata基因组中共鉴定出69个piRNA簇，其中包含26%的转座子，并针对DNA/Crypton、LINE/CR1、SINE/Deu和DNA/Academ进行了增强。体细胞组织中piRNA和piRNA簇的表达模式没有显着差异，但体细胞和性腺组织之间差异显着。此外，锁核酸修饰寡核苷酸（LNA 拮抗剂）用于沉默 P. fucata 中的单个 piRNA (piRNA0001) 表达。 piRNA 沉默后，P. fucata 中数百个内源基因出现差异表达。靶标预测显示，piRNA0001靶向了一些内源基因，其中piRNA0001沉默后有12个上调基因和9个下调基因。结果表明，来自体细胞组织的piRNA可能与基因调控有关，而来自性腺组织的piRNA与转座子沉默的关系更为密切。这项研究将增强我们对 piRNA 在软体动物中的作用、转座子沉默以及 PIWI/piRNA 通路对 P. fucata 生殖系细胞外蛋白质编码基因的调节功能的理解。
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus safeguarding the genome from detrimental insertion mutagenesis. Recent studies revealed additional targets and functions of piRNAs in various animals. piRNAs are ubiquitously expressed in somatic tissues of the pearl oyster Pinctada fucata, however, the role of somatic piRNAs has not well characterized. This study reports the PIWI/piRNA pathway, including piRNA biogenesis and piRNA-mediated transposon silencing, and gene regulation in P. fucata. The biogenesis factors of PIWI, Zucchini, and HEN1, which are ubiquitous in somatic and gonadal tissues, were first identified in P. fucata using transcriptome analysis. Bioinformatics analyses suggested that different populations of piRNAs participate in the ping-pong amplification loop in a tissue-specific manner. In addition, a total of 69 piRNA clusters were identified in the genome of P. fucata based on the expression of piRNAs, which contained 26% transposons and enhanced for DNA/Crypton, LINE/CR1, SINE/Deu, and DNA/Academ. The expression patterns of the piRNAs and piRNA clusters in somatic tissues were not substantially different, but varied significantly between the somatic and gonadal tissues. Furthermore, locked-nucleic-acid modified oligonucleotide (LNA-antagonist) was used to silence single piRNA (piRNA0001) expression in P. fucata. Hundreds of endogenous genes were differentially expressed after piRNA silencing in P. fucata. Target prediction showed that some endogenous genes were targeted by piRNA0001, including twelve upregulated and nine downregulated genes after piRNA0001 silencing. The results indicated that piRNAs from somatic tissues may be related to gene regulation, whereas piRNAs from gonadal tissues are more closely associated to transposon silencing. This study will enhance our understanding of the role of piRNAs in mollusks, transposon silencing, and the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germ line cells in P. fucata.