Rodrigues Nureyev F, Christoff Ana P, da Fonseca Guilherme C, Kulcheski Franceli R, Margis Rogerio
Programa de Posgraduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
Programa de Posgraduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
Front Plant Sci. 2017 Sep 29;8:1686. doi: 10.3389/fpls.2017.01686. eCollection 2017.
Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. We mapped the sRNAs against the nuclear, mitochondrial and plastid genomes to confirm predicted cytosine to uracil (C-to-U) editing events and identify new editing sites in plastids. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The present method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites.
细胞器RNA编辑涉及核苷酸序列的修饰以维持保守的蛋白质功能，主要是通过逆转非中性密码子突变来实现。由于RNA编辑因子的突变或应激干扰导致的质体编辑事件的丧失，会导致发育、生理和光合方面的改变。最近，下一代测序技术极大地发现了小RNA序列并增加了小RNA数据的数量。在此，我们提出一种利用来自拟南芥、大豆和水稻的公共小RNA文库筛选叶绿体RNA编辑的方法。我们将小RNA与核基因组、线粒体基因组和质体基因组进行比对，以确认预测的胞嘧啶到尿嘧啶（C-to-U）编辑事件，并鉴定质体中的新编辑位点。在预测的编辑位点中，分别使用来自拟南芥、大豆和水稻的小RNA确认了40.57%、34.78%和25.31%。单核苷酸多态性分析在各物种中分别揭示了58.2%、43.9%和37.5%的新C-to-U变化，并在tRNA中鉴定出已知和新的推定腺苷到次黄嘌呤（A-to-I）RNA编辑。本方法和数据揭示了小RNA作为鉴定新的和确认已知编辑位点的可靠来源的潜力。
