中国科学院昆明动物研究所机构知识库

A-to-I RNA编辑是由ADAR酶家族所介导，能够识别RNA双链，并将双链上部分腺嘌呤碱基脱氨形成次黄嘌呤碱基的一类反应，是一类转录后修饰调控，其在很多疾病和生理过程中发挥着重要作用。二代测序以来，编辑位点的检测获得巨大进步，人们不断地发现了很多A-to-I编辑的规律（第一章）。A-to-I编辑在神经系统起源的时候就出现了。在人类的脑部非常普遍，有可能在人类的智力形成中起着重要作用。另外其在行为复杂的头足类鞘亚纲动物中的分布也极为广泛，并能影响大量的蛋白质编码。目前已经发现，A-to-I编辑在神经系统的功能中，如神经系统的信号传导过程，起着及其重要的作用（第二章）。同时, A-to-I编辑也在其他一些组织中发挥着作用，如ADAR1介导的RNA编辑能够防止天然免疫对自身双链RNA自身免疫；癌症组织中也发现了A-to-I编辑的变化（第三章）。第二代RNA测序已经成功地用于发现不同的转录本，衡量基因的表达水平，检测转录后修饰。尽管已经有了这些大规模的研究，为了更全面地解析人脑转录组的进化模式，对人脑各个子区域的更多和更全面的RNA测序测序是很有必要的。在这里，我们提供了从人脑的不同区域中的总共65亿个RNA测序片段。从中发现了在可变剪接和RNA编辑之间的显著联系，这些可能由剪接及RNA编辑之间的竞争机制所导致。蛋白编码的新基因在新皮质和非新皮质中都显示出了进化到人类世系这个进化过程中的表达变化。我们也发现了在壳核这个组织有这很高水平RNA编辑，并且其也有一个显著增长的新基因的表达。壳核这个组织过去受到的关注并不多，其在认知能力上扮演着一个重要角色，我们的数据表明，其可能在人类进化中起着一个潜在的作用。（第四章）非人灵长类由于和人类的亲缘关系很近，其被作为模式动物用于研究人相关的一些表型特征。A-to-I RNA编辑在灵长类中最为普遍，可以通过研究灵长类来更好地了解它。但是，并没有一个非常完善的非人灵长类的RNA编辑组(RNA editom)。在这里我们对猕猴(Macaca mulatta)进行了大量的基因组和转录组测序。利用这些资源，我们发现猕猴类的RNA编辑水平在出生后经历了一个巨大的增长；并且我们也发现了4个基因中的可以改变蛋白质氨基酸编码的RNA编辑位点，GRIK1 (Q638/R)，GRIA2 (R717/G)，KCNA1 (I400/V)， 和 MFN1 (I234V)，其编辑水平和年龄显著相关。新发现的位于线粒体调控基因的位点MFN1(I234V)可以使基因的功能变弱。我们也进一步发现了很多编辑位点发生在核编码的和线粒体相关的蛋白，表明ADAR1和ADAR2酶具备线粒体必不可少的功能（第五章）。A-to-I RNA编辑在动物中极为普遍。对脑的功能起着重要的作用，同时它也参与了其他很多重要的生物过程。通过研究在不同生物学过程中RNA编辑的变化情况，我们能够推理并验证这些编辑位点在生物学中的作用。但是，如何在各个不同的物种中检测RNA编辑位点，分析其RNA编辑水平，以及找到各生物学功能相关的RNA编辑位点，依然是一个巨大的挑战。为了更好地利用第二代测序的优势来解析A-to-I RNA编辑，在这里我们开发了用于多物种的RNA编辑检测和注释工具，比如说REIA(RNA Editing sites Identification and Annotation)，用于RNA位点检测和计算各个位点的RNA水平。另外，我们也开发了一个注释RNA编辑位点的数据库DREA(Database of RNA Editing Annotation) (http://drea.kiz.ac.cn)，这个数据库可以被用来查找不同区域的RNA编辑位点，以及其在不同生物学过程中RNA编辑水平的变化情况，从而推断他们的功能。我们也还描述了数据库中猕猴的RNA编辑在SIV感染和注释干扰素时的变化情况和其可能的功能。（第六章）

A-to-I RNA editing is mediated by ADAR enzyme family, converts adenosines to inosines in double-stranded RNA substrates. The next-generation of RNA sequencing has largely facilitated the stduy of A-to-I RNA editing, millions of editing sites has been discovered, and more functional consequences of RNA editing has been deciphered(Chapter 1). A-to-I RNA editing could be foud in animals with the primitive nerver system. It is very abundant in human brain, it may be important for the formation of human intelligence. It is also abundant in behaviorally sophisticated coleoid cephalopods , with large number of editing sites could recode proteins (Chapter 2).A-to-I editing could also take part in other biological processes, for example, it could prevent innate immune system be actived by self dsRNA; the changed A-to-I editing could also be observed in cancer tissues (Chapter 3).Next-generation RNA-sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA-editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.(Chapter 4)Nonhuman primates are used as model animals to study human-specific phenotypes, as the species are closely related. A-to-I RNA editing, most prevalent in primates, could be understood by studying these model animals; however, there is no comprehensive RNA editome of nonhuman primates. Here, we sequenced massive transcriptomes and genomes of Macaca mulatta and retrieved 707,246 A-to-I RNA editing sites. Using the resource, we found that the editing level showed a dramatic increase during early postnatal development of the primate brain; the editing level of four amino-acid-changing RNA editing sites located in four genes, GRIK1 (Q638/R), GRIA2 (R717/G), KCNA1 (I400/V), and MFN1 (I234V), significantly correlated with age. The newly discovered edited site in the mitochondrially regulated gene MFN1 (I234/V) could induce weakened gene function. We further found editing occurring frequently in nuclear genes associated with mitochondria and showed that ADAR1 and ADAR2 have an essential mitochondrial function.(Chapter 5)A-to-I editing is a widespread post-transcriptional modification in mammals. It is important for the brain, and may take part in many other important biological processes. RNA editing pattern not only editing sites distribution but also editing level of each sites can be differentiate in disease or organ development, but editing sites detection in diverse species, and calculation of editing level remain a big challenge. In order to fully take the advantage of next-generation sequencing to understand A-to-I editing, we developed REIA(RNA Editing sites Identification and Annotation), to discover new editing sites of a variety of species, and caculate the editing level of each sites across different tissues or cells. We also developed DREA, a database of RNA editing sites annotation(http://drea.kiz.ac.cn), it could be used to search for editing sites in different region, and the editing level variation in different biological processes, in order to infer their function. we also described dynamic changes in editing level and provided potential functional RNA editing sites in the processes of siv infection and interferon injection in our database for further functional studies.(Chapter 6)