Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing
Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing
复制标题
DOI：
10.3389/fgene.2019.00877
复制
发表时间：
2019-08
影响因子：
3.7
通讯作者：
Qi-Lin Zhang;Hong Wang;Qian-Hua Zhu;Xiao-Xue Wang;Yi-min Li;Jun‐yuan Chen;H. Morikawa;Linfeng Yang;Yujun Wang
中科院分区：
文献类型：
--
作者：
Qi-Lin Zhang;Hong Wang;Qian-Hua Zhu;Xiao-Xue Wang;Yi-min Li;Jun‐yuan Chen;H. Morikawa;Linfeng Yang;Yujun Wang
文昌鱼是与脊椎动物祖先最接近的现存无脊椎动物代理人。因此，系统的文昌鱼器官基因鉴定和表达谱分析对于阐明脊椎动物器官功能形成的分子机制和进一步了解脊椎动物器官和基因的进化起源具有重要意义。对microRNAs(MiRNAs)的精确调控对于器官的功能规范和分化至关重要。特别是，那些在器官(OSM)中特异表达的miRNAs在器官的识别、分化和功能中发挥着关键作用。本研究对文昌鱼成体的8个器官的miRNA转录组进行了深度测序分析。总共发现了167个已知的miRNAs和23个新的miRNAs(命名为new_mir)，其中139个是保守的miRNAs，其中79个被鉴定为OSM。此外，对随机选择的8个已知miRNAs的表达模式的分析证明了本研究中使用的miRNA深度测序的准确性。此外，还预测了每种器官类型可能受OSM调控的基因。对这些预测目标进行了功能浓缩，并对已知的OSM进行了进一步的功能分析。我们发现，OSMS可能参与器官的特定功能，如表皮发育、性腺发育、肌肉细胞发育、蛋白分解、脂肪代谢和神经元的生成。此外，还检测到具有非器官特异性功能的OSM，主要包括与先天性免疫和对刺激的反应有关的OSM。这些发现为OSMS在文昌鱼各种器官中的调节作用提供了洞察力。
Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs is thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism and generation of neurons. Moreover, OSMs with non-organ specific functions were detected, and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.