An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites.

IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Jiyao Liu,Tianyou Zhao,Caiqing Zheng,Ling Ma,Fan Song,Li Tian,Wanzhi Cai,Hu Li,Yuange Duan
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引用次数: 0

Abstract

Adar-mediated adenosine-to-inosine (A-to-I) mRNA editing is a conserved mechanism that exerts diverse regulatory functions during the development, evolution, and adaptation of metazoans. The accurate detection of RNA editing sites helps us understand their biological significance. In this work, with an improved genome assembly of honeybee (Apis mellifera), we used a new orthology-based methodology to complement the traditional pipeline of (de novo) RNA editing detection. Compared to the outcome of traditional pipeline, we retrieved many novel editing sites in CDS that are deeply conserved between honeybee and other distantly related insects. The newly retrieved sites were missed by the traditional de novo identification due to the stringent criteria for controlling false-positive rate. Caste-specific editing sites are identified, including an Ile>Met auto-recoding site in Adar. This recoding was even conserved between honeybee and bumblebee, suggesting its putative regulatory role in shaping the phenotypic plasticity of eusocial Hymenoptera. In summary, we proposed a complementary approach to the traditional pipeline and retrieved several previously unnoticed CDS editing sites. From both technical and biological aspects, our works facilitate future researches on finding the functional editing sites and advance our understanding on the connection between RNA editing and the great phenotypic diversity of organisms.
基于同源物的方法是检索进化保守的 A 到 I RNA 编辑位点的补充方法。
Adar 介导的腺苷酸转肌苷酸(A-to-I)mRNA 编辑是一种保守的机制,在元古宙的发育、进化和适应过程中发挥着多种调控功能。准确检测 RNA 编辑位点有助于我们了解其生物学意义。在这项工作中,我们利用改进的蜜蜂(Apis mellifera)基因组组装,使用了一种新的基于选集的方法来补充传统的(从头)RNA编辑检测管道。与传统方法的结果相比,我们在蜜蜂和其他远缘昆虫之间深度保守的CDS中检索到了许多新的编辑位点。由于控制假阳性率的标准非常严格,这些新发现的位点被传统的从头鉴定所遗漏。发现了种姓特异性编辑位点,包括 Adar 中的 Ile>Met 自动重编码位点。这种重编码在蜜蜂和大黄蜂之间甚至是保守的,这表明它在塑造雌雄同体膜翅目昆虫的表型可塑性方面可能起着调控作用。总之,我们提出了一种对传统管道的补充方法,并检索到了几个以前未被注意到的 CDS 编辑位点。从技术和生物学两方面来看,我们的工作有助于未来寻找功能编辑位点的研究,并推进我们对 RNA 编辑与生物巨大表型多样性之间联系的理解。
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
RNA Biology
RNA Biology 生物-生化与分子生物学
CiteScore
8.60
自引率
0.00%
发文量
82
审稿时长
1 months
期刊介绍: RNA has played a central role in all cellular processes since the beginning of life: decoding the genome, regulating gene expression, mediating molecular interactions, catalyzing chemical reactions. RNA Biology, as a leading journal in the field, provides a platform for presenting and discussing cutting-edge RNA research. RNA Biology brings together a multidisciplinary community of scientists working in the areas of: Transcription and splicing Post-transcriptional regulation of gene expression Non-coding RNAs RNA localization Translation and catalysis by RNA Structural biology Bioinformatics RNA in disease and therapy
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