• 中文核心期刊要目总览
  • 中国科技核心期刊
  • 中国科学引文数据库(CSCD)
  • 中国科技论文与引文数据库(CSTPCD)
  • 中国学术期刊文摘数据库(CSAD)
  • 中国学术期刊(网络版)(CNKI)
  • 中文科技期刊数据库
  • 万方数据知识服务平台
  • 中国超星期刊域出版平台
  • 国家科技学术期刊开放平台
  • 荷兰文摘与引文数据库(SCOPUS)
  • 日本科学技术振兴机构数据库(JST)
王运梅, 叶凌群, 王明山, 张锦锦, SaberKhederzadeh, DavidM Irwin, 任小蝶, 张亚平, 吴东东. 2022: 整合基因组学和转录组学揭示鸡RNA编辑的功能和进化景观. 动物学研究, 43(6): 1011-1022. DOI: 10.24272/j.issn.2095-8137.2022.331
引用本文: 王运梅, 叶凌群, 王明山, 张锦锦, SaberKhederzadeh, DavidM Irwin, 任小蝶, 张亚平, 吴东东. 2022: 整合基因组学和转录组学揭示鸡RNA编辑的功能和进化景观. 动物学研究, 43(6): 1011-1022. DOI: 10.24272/j.issn.2095-8137.2022.331
Yun-Mei Wang, Ling-Qun Ye, Ming-Shan Wang, Jin-Jin Zhang, Saber Khederzadeh, David M Irwin, Xiao-Die Ren, Ya-Ping Zhang, Dong-Dong Wu. 2022: Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics. Zoological Research, 43(6): 1011-1022. DOI: 10.24272/j.issn.2095-8137.2022.331
Citation: Yun-Mei Wang, Ling-Qun Ye, Ming-Shan Wang, Jin-Jin Zhang, Saber Khederzadeh, David M Irwin, Xiao-Die Ren, Ya-Ping Zhang, Dong-Dong Wu. 2022: Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics. Zoological Research, 43(6): 1011-1022. DOI: 10.24272/j.issn.2095-8137.2022.331

整合基因组学和转录组学揭示鸡RNA编辑的功能和进化景观

Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics

  • 摘要: 目前有关RNA编辑在哺乳动物、头足类动物和昆虫等中的进化和功能研究已有了很好的进展,但在鸟类中仍存在很大空白。该研究中,通过整合转录组学和全基因组学分析,我们详细地描绘了鸡中腺嘌呤核苷转为次黄嘌呤核苷(Adenosine-to-inosine, A-to-I)的RNA编辑模式的位点(RNA editing sites, RESs)图谱。此外,我们还研究了RNA编辑在家鸡驯化过程中可能的作用机制。我们发现,鸡肝脏的编辑水平最低,这与已报道的人的肌肉编辑水平最低的结论不同。而鸡大脑的编辑活性和特异性均显著高于非神经组织,这与大脑的功能复杂性一致,因为在一定程度上,组织特异的编辑活性或许可以为其特定的功能作出解释。同时,我们的研究结果还显示,影响RESs二级结构形成的关键序列在鸟类进化过程中是保守的,并在家鸡的驯化过程中受到负选择。大多数RESs可能构成一个选择池,用以筛选出在驯化过程起功能性作用的少数RESs,譬如参与神经系统和免疫系统的进化等。最后,我们的结果也揭示,在鸡里,RNA编辑酶ADARs对RNA编辑的调控可能受到非ADAR(non-ADAR)因子的影响,这些因子的表达水平在ADAR基因被敲除后发生了显著的变化。总而言之,我们提供了鸡RESs和non-ADAR编辑调控因子的综合列表,它们或将促进我们对RNA编辑在动物功能和进化中的可能作用的理解。

     

    Abstract: The evolutionary and functional features of RNA editing are well studied in mammals, cephalopods, and insects, but not in birds. Here, we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine (A-to-I) RNA editing sites (RESs) in the chicken. In addition, we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication. We detected the lowest editing level in the liver of chickens, compared to muscles in humans, and found higher editing activity and specificity in the brain than in non-neural tissues, consistent with the brain’s functional complexity. To a certain extent, specific editing activity may account for the specific functions of tissues. Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution. Furthermore, the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication, including evolution of nervous and immune systems. Regulation of RNA editing in chickens by adenosine deaminase acting on RNA (ADAR) enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown. Collectively, we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken, thus contributing to our current understanding of the functions and evolution of RNA editing in animals.

     

/

返回文章
返回