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遗传  2019, Vol. 41 Issue (6): 469-485    DOI: 10.16288/j.yczz.19-061
生物学   综述 |遗传学 本期目录 | 过刊浏览 |
环状RNA的产生、研究方法及功能
刘旭庆1,高宇帮1,2,赵良真1,蔡宇晨1,王汇源1,苗苗1,顾连峰1(),张航晓1()
1. 福建农林大学林学院,基础林学与蛋白质组学中心,福州 350002
2. 福建农林大学生命科学学院,福州 350002
Biogenesis, research methods, and functions of circular RNAs
Liu Xuqing1,Gao Yubang1,2,Zhao Liangzhen1,Cai Yuchen1,Wang Huiyuan1,Miao Miao1,Gu Lianfeng1(),Zhang Hangxiao1()
1. Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2. College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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摘要: 

随着高通量测序技术的发展,环状RNA (circular RNAs, circRNAs)逐渐成为非编码RNA研究领域的热点。本文系统综述了环状RNA侧翼内含子自身互补配对驱动、RNA结合蛋白驱动以及套索驱动这3种环状RNA形成模型,并从高通量文库构建、生物信息学鉴别和常用的实验验证等3个方面对环状RNA的研究方法进行了介绍。同时,本文详细归纳了环状RNA作为microRNA (miRNA)或蛋白的海绵体、调控宿主基因的选择性剪接和表达、翻译成多肽等多种功能。最后通过系统综述植物环状RNA的特征及最新研究进展,为环状RNA在植物学中的进一步研究提供了新的视野。

关键词 环状RNA反向剪接选择性剪接海绵体    
Abstract

The field of circular non-coding RNAs have been gradually attracted wide attention with the developments of high-throughput sequencing. In this review, we systematically summarize three driving models for circRNAs biogenesis: intron-pairing-driven, RNA binding protein-driven and lariat-driven. In addition, we also briefly introduce the current research methods of circRNAs, which include high-throughput library construction methods, identification through bioinformatics and common experimental verification. Here, we also systematically summarize the functions of circRNAs, including microRNA (miRNA) or protein sponges, regulating the alternative splicing (AS) and expression of host genes, and extensive translation. Finally, we provide a systematic characterization and the latest research progress of circRNAs, which provide a new perspective for further studies of circRNAs in plants.

Key wordscircular RNAs    back-splicing    alternative splicing    sponge
收稿日期: 2019-04-09      出版日期: 2019-05-07
基金资助:国家自然科学基金项目(31800566);福建省自然科学基金项目(2018J01608);国家重点研发计划项目(2016YFD0600106);国家重点研发计划项目(2018YFD0600101);校国际合作(KXGH17016);福建省科技创新团队项目(118/KLA18069A))
第一作者简介: 刘旭庆,硕士研究生,专业方向:林木遗传育种。E-mail:1752501050@qq.com
通讯作者简介: 顾连峰,张航晓     E-mail: lfgu@fafu.edu.cn;hxzhang@fafu.edu.cn
Corresponding author: Gu Lianfeng,Zhang Hangxiao     E-mail: lfgu@fafu.edu.cn;hxzhang@fafu.edu.cn
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引用本文:

刘旭庆,高宇帮,赵良真,蔡宇晨,王汇源,苗苗,顾连峰,张航晓. 环状RNA的产生、研究方法及功能[J]. 遗传, 2019, 41(6): 469-485.
Liu Xuqing,Gao Yubang,Zhao Liangzhen,Cai Yuchen,Wang Huiyuan,Miao Miao,Gu Lianfeng,Zhang Hangxiao. Biogenesis, research methods, and functions of circular RNAs. Hereditas(Beijing), 2019, 41(6): 469-485.

链接本文:

http://www.chinagene.cn/CN/10.16288/j.yczz.19-061      或      http://www.chinagene.cn/CN/Y2019/V41/I6/469

图1  环状RNA研究的关键事件
图2  环状RNA形成的环化模型 A:内含子自身互补配对。RCMs/ICSs/Alu等互补配对元件促进侧翼内含子配对进而环化。B:RNA结合蛋白驱动。大多数RNA结合蛋白通过结合到可环化外显子的侧翼内含子上来促进环化。C:套索驱动。mRNA前体剪接时会发生外显子跳读事件,产生包含内含子-外显子的套索中间体,随后该中间体发生反向剪接形成环状RNA。
图3  环状RNA的文库构建和生物信息学研究方法 A:RNase R处理的高通量测序文库构建。B:基于反向剪接位点测序片段的环状RNA识别方法。
表1 环状RNA的识别软件 Table 1 The softwares for circRNA identification
工具名称 网址 特点 文献
MapSplice http://www.netlab.uky.edu/p/bioinfo/MapSplice 标记比对(tag alignment)和剪接推理(splice inference)两步法 [1,66]
find_circ https://github.com/marvin-jens/find_circ 只需基因组的fasta序列,独立于基因注释信息运行 [68]
CIRCfinder https://github.com/YangLab/CIRCfinder 识别内含子环状RNA [18]
circRNA_
finder
https://github.com/orzechoj/circRNA_finder.git 准确性高,独立于基因注释信息运行 [70]
segemehl www.bioinf.uni-leipzig.de/Software/segemehl/ 能识别环状RNA,检测剪接、反式剪接及基因融合事件 [71]
KNIFE https://github.com/lindaszabo/KNIFE 依赖Bowtie2进行多阶段校正,结合读段映射质量和校正质量进行环状RNA的静态建模检测 [73]
DCC https://github.com/dieterich-lab/DCC 依赖于过滤器和跨重复集合的整合数据,可以评估环状RNA和宿主基因之间的表达量 [75]
Acfs https://code.google.com/p/acfs/ 允许从头测序,从单端和双端RNA数据中准确鉴定环状RNA及进行丰度定量 [77]
UROBORUS RNA http://uroborus.openbioinformatics.org/ 基于总RNA测序数据,能精确预测到低表达的环状RNA,不能预测内含子环状RNA及基因间隔区形成的环状RNA [79]
PcircRNA_
finder
http://ibi.zju.edu.cn/bioinplant/tools/manual.htm 双末端交叉映射,精确预测植物中的外显子环状RNA [67]
Circseq_cup http://ibi.zju.edu.cn/bioinplant/ 基于反向剪接RNA-seq和双末端RNA-seq数据,组装环状RNA全长序列 [45]
FUCHS https://github.com/dieterich-lab/FUCHS 基于长读段测序数据,分析环状RNA内选择性剪接事件,分析单、双断点事件,分析环状RNA的读取覆盖率 [69]
CIRI-full https://sourceforge.net/projects/ciri-full/ 识别环状RNA,全长组装,定量环状RNA的选择性剪接产物 [63]
CircExplorer2 https://github.com/YangLab/CIRCexplorer2 整合了多种比对算法,侦测环状RNA的选择性剪接,能de nove组装环状RNA全长转录本 [72]
CIRI2 https://sourceforge.net/projects/ciri/files/CIRI2 基于多种子匹配策略、最大似然估计模型,识别反向剪接读段,能过滤来自重复序列和映射误差的误报 [74]
CircView http://gb.whu.edu.cn/CircView/或
https://github.com/GeneFeng/CircView
根据物种注释信息展现环状RNA的结构,允许用户查看环状RNA的调控元件及预测其潜在功能 [76]
PRAPI http://www.bioinfor.org/bioinfor/tool/PRAPI/ 进行环状RNA的矢量绘图 [78]
CircSplice http://gb.whu.edu.cn/CircSplice或
https://github.com/GeneFeng/CircSplice
特异性识别环状RNA内部选择性剪接事件,可实现环状RNA选择性剪接事件的组间差异比较 [64]
表1  环状RNA的识别软件
表2 环状RNA存放数据库 Table 2 Databases for circRNA deposition
名称 网址 描述 文献
circAtlas http://circatlas.biols.ac.cn 包括人、猕猴、小鼠、大鼠(Rattus norvegicus)、野猪(Sus scrofa)、红色原鸡(Gallus gallus)中的环状RNA序列信息,查看保守环状RNA,查询环状RNA与miRNA或RBPs的结合情况等功能 [30]
circBase http://www.circbase.org/ 包含人、小鼠及秀丽隐杆线虫等所有已鉴定的环状RNA数据 [82]
CIRCpedia http://www.picb.ac.cn/rnomics/circpedia 人类环状RNA选择性反向剪接和选择性剪接事件 [72]
TSCD http://gb.whu.edu.cn/TSCD 储存人、小鼠中组织特异性的环状RNA [84]
Circ2Traits http://gyanxet-beta.com/circdb/ 环状RNA与人类疾病的潜在关联,miRNA-circRNA-mRNA- lncRNA (long non-coding RNA)互作网络 [86]
CircInteractome http://circinteractome.nia.nih.gov 在人类环状RNA上查询互作蛋白、相关miRNA的结合位点 [88]
CircNet http://circnet.mbc.nctu.edu.tw/ 储存人类组织特异性的环状RNA,circRNA-miRNA-mRNA互作调控网络 [90]
circRNADb http://reprod.njmu.edu.cn/circrnadb 储存32 914种人类外显子环状RNA,描述了46种具有编码潜力的环状RNA [92]
CSCD http://gb.whu.edu.cn/CSCD 收集了87种人类癌症细胞株,描述了癌症特异性环状RNA [81]
CircR2Disease http://bioinfo.snnu.edu.cn/CircR2Disease/ 100种人类环状RNA与661种疾病之间的相关性 [83]
MiOncoCirc https://nguyenjoshvo.github.io/ 人类癌症细胞株及肿瘤的环状RNA,描述了可作为癌症诊断或治疗的靶点 [21]
AtCircDB http://genome.sdau.edu.cn/circRNA 储存拟南芥中组织特异性的环状RNA,分析circRNA-miRNA互作网络 [85]
PlantCircNet http://bis.zju.edu.cn/plantcircnet/index.php 可视化拟南芥、水稻、大麦(Hordeum vulgare L.)等八种模式植物的circRNA-miRNA-mRNA互作网络 [87]
PlantcircBase http://ibi.zju.edu.cn/plantcircbase/ 水稻、拟南芥、玉米、番茄及大麦中的环状RNA,预测
circRNA-miRNA-mRNA互作网络,环状RNA结构可视化
[89]
CircFunBase http://bis.zju.edu.cn/CircFunBase 收集了超过7000种人、小鼠及植物中的功能性环状RNA,可视化circRNA-miRNA互作网络 [91]
ASmiR http://forestry.fafu.edu.cn/bioinfor/db/ASmiR 毛竹(Phyllostachys edulis)、水稻、拟南芥等多种植物中miRNA靶位点和线性RNA之间以及miRNA和环状RNA的选择性剪接之间的相互调控 [80]
表2  环状RNA存放数据库
图4  环状RNA的功能 A:充当miRNA或蛋白的海绵体。B:通过R-loop介导调控宿主基因的选择性剪接事件。C:调控宿主基因的表达。左图为环状RNA通过与U1 snRNA及Pol Ⅱ转录复合物互作,进而调控宿主基因的表达;右图为m6A修饰的环状RNA会影响宿主基因的稳定性。D:翻译功能。环状RNA能翻译多肽。E:衍生假基因。环状RNA经反转录衍生假基因,并整合进基因组。
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