,浙江农林大学,亚热带森林培育国家重点实验室培育基地,杭州 311300Progress in circular RNAs of plants
Jia Luo, Xingli Wang, Zhichao Sun, Di Wu, Wei Zhang, Zhengjia Wang,Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China第一联系人:
编委: 赵方庆
收稿日期:2018-01-8修回日期:2018-03-21网络出版日期:2018-06-20
| 基金资助: |
Received:2018-01-8Revised:2018-03-21Online:2018-06-20
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骆甲,硕士研究生,专业方向：林木遗传育种E-mail:
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骆甲, 王型力, 孙志超, 吴迪, 张玮, 王正加. 植物环状RNA研究进展. 遗传[J], 2018, 40(6): 467-477 doi:10.16288/j.yczz.18-009
Jia Luo, Xingli Wang, Zhichao Sun, Di Wu, Wei Zhang, Zhengjia Wang.
非编码RNA (non-coding RNA)是一类直接发挥催化和调控功能的转录本,包含miRNA (microRNA)、lncRNA (long non-coding RNA)和circRNA (circular RNA)等,占真核细胞总RNA的95%以上[1],在生物体许多生理生化过程中发挥了重要作用[1,2,3]。miRNA是一类长度约为21 nt的非编码RNA,主要通过引导效应蛋白AGO (Argonaute)抑止编码mRNA的表达[4]。研究表明,circRNA能够特异性结合miRNA,使其失去调控mRNA的功能[5]。在哺乳动物中,一个miRNA通常含有1~2个特异性结合位点,当miRNA表达量占主导地位时,circRNA具有的miRNA海绵功能不再有效[6, 7]。
不同于线性RNA,circRNA具有高度保守性以及不易被降解的特性[8],在生物体内行使miRNA海绵、调控可变剪切、长距离传递信号等功能[9]。根据组成来源,circRNA分为外显子circRNA、基因间circRNA和内含子circRNA。circRNA主要形成方式有4种：(1)反向可变剪切(back-splicing)环化[10,11,12];(2)内含子驱动反向互补序列形成环化[13, 14];(3)来自单个基因内不同内含子序列配对环化[13];(4)受到RNA结合蛋白调控的外显子环化[10, 15]。circRNA作为内源性非编码RNA 在真核生物的生长发育过程中发挥着重要作用[12, 16~20],引起人们广泛的关注。
植物circRNA的研究还处于起步阶段,转录组测序以及生物信息学分析证实circRNA在植物中同样具有高保守性,但动植物间circRNA发生机制及功能的差异性尚不明确。随着研究的不断深入,已陆续证明植物circRNA能通过内源性竞争、干扰可变剪切、结合蛋白等方式,在植物生长发育、生物与非生物胁迫等生物过程中发挥了重要作用[18, 19, 21]。本文综述了近年来植物circRNA形成机制、鉴定方法、数据库、表达模式等研究进展,概括了植物circRNA结构特征和调控潜能,为其在植物发育过程中的功能研究提供参考。
1 植物circRNA鉴定
20世纪70年代,Sanger等[22]在植物病毒中发现了闭合的circRNA分子,并在真核细胞中验证了circRNA的存在,当时circRNA被认为是剪切错误的产物[23,24,25]。随着高通量测序和基因组分析技术的发展,Salzman等[17]首次指出circRNA由mRNA前体可变剪切而来,是一类3°与5°共价闭合且广泛大量存在于真核生物体内的RNA,参与转录后调控过程[16, 26]。Jack等[26]在人类成纤维细胞中检测出25 000多个可区分的RNA,其中外显子circRNA约占总量的14.4%。Memczak等[16]通过重新计算多个动物数据库中RNA测序数据,共鉴定出 1950个人类(Homo sapiens) circRNA、1903个小鼠(Mus musculus) circRNA和724个线虫(Caenorhabditis elegans) circRNA。Guo等[27]通过优化算法对去poly(A)的RNA测序数据进行分析,新注释了7112个人类circRNA和635个小鼠circRNA,并关联得到一个具有miRNA海绵功能的circ-ZNF91。Wang等[28]通过鉴定真菌、原生生物和模式植物的circRNA,证实circRNA是一个古老且保守、具有调控功能的细胞转录产物。
自2014年拟南芥(Arabidopsis thaliana)根部首次发现circRNA后[28],7个物种的circRNA被陆续鉴定(表1)。Ye等[21]重新计算已公开的转录组数据,补充报道了水稻(Oryza sativa)和拟南芥中有12037和6012个circRNA。2015年,Lu等[19]在水稻中鉴定出2354个circRNA,其中外显子circRNA为1356个,包含微型反向重复转座元件(miniature inverted repeat transposable elements, MITEs)的circRNA为 92个[21]。Liu等[29]对不同生长阶段的拟南芥叶片进行转录组测序,验证发现circRNA除保守的序列信息外,还具有时空表达特异性。circRNA在番茄(Solanum lycopersicum)冷害逆境响应、小麦(Triticum aestivum)干旱逆境响应、猕猴桃(Pseudomonas syringae)对溃疡病菌响应以及植物类病毒感染荔枝(Litchi chinensis)的过程中均起到重要的调控作用[30,31,32,33]。同时,叶绿体和线粒体基因组的可变剪切也可以得到circRNA[21, 34, 35],说明circRNA参与包括光合作用和呼吸作用在内的多个重要生命过程的调控。
Table 1
表1
表1 7种植物circRNA鉴定信息
Table 1
| 物种 | 测序组织 | 数据来源 | circRNA数量(外显子circRNA数量) |
|---|---|---|---|
| 拟南芥(Arabidopsis thaliana) | 叶片[21] | 数据库编号PRJNA218215 | 6012 (5152) |
| 叶片[29] | 数据库编号GSE43616 | 168 (158) | |
| 水稻(Oryza sativa) | 水稻根部[21] | 数据库编号PRJNA215013 | 12037 (6074) |
| 幼穗和成熟叶片[36] | 栽培稻自测 | 2354 (1356) | |
| 根部[37] | 水培稻自测 | 3011 (1846) | |
| 小麦(Triticum aestivum) | 幼苗叶片[30] | 干旱逆境处理自测 | 88 (6) |
| 大麦(Hordeum vulgare) | 叶片和未成熟的种子[34] | 铁锌溶液喷施叶面处理自测 | 62 (5) |
| 番茄(Solanum lycopersicum) | 果皮[32] | 冷胁迫处理自测 | 854 (615) |
| 猕猴桃(Pseudomonas syringae) | 幼叶[33] | 病菌胁迫处理自测 | 3582 (2293) |
| 大豆(Glycine max) | 根茎叶[38] | 温室种植自测 | 5372 (2494) |
新窗口打开|下载CSV
目前,公开发表的circRNA预测软件有10余种(表2),其中包含植物特异的circRNA预测软件PcircRNA_finder[39]。基于不同算法,可将软件分为两种：一是针对内含子驱动模式下的反向可变剪切接头序列(back-spliced junction)设计的预测软件,如find_circ[40]、CIRCexplorer[13]、CIRI[41, 42]和apSplice[43]等;二是通过基因组注释信息推测得到反向可变剪切接头序列,然后与注释的外显子序列进行匹配,预测得到新circRNA的软件,如KNIFE[44, 45]、NCLscan[46]等。根据预测软件的准确度、敏感度等方面来评估性能[47, 48],在对相同样本数据进行分析时,CIRCexplorer和KNIFE的准确度和敏感度都在较高水平;find_circ具有高准确度,而MapSplice具有较高的检测敏感度;PcircRNA_finder在植物circRNA的鉴定中更具优势[39]。虽然一些程序支持无参组装测序结果并进行独立注释信息,但是完善的基因组注释能够进一步提高剪切接头检测的灵敏度、扩大剪切信号的检测范围以及降低错误率。不同的软件在计算成本上也有不同的要求,因此 综合两种或多种不同软件预测的结果将有效提高circRNA鉴定的效率。
Table 2
表2
表2 7种circRNA预测方法
Table 2
| 软件名称 | 编写语言 | 比对方法 | 比对程序 | 敏感度 | 准确度 | 计算速度 | 备注 |
|---|---|---|---|---|---|---|---|
| CIRCexplorer | Python | 有参 | TopHat/STAR | 高 | 高 | 慢 | 基因注释需求 |
| CIRI | Perl | 无参 | BWA-MEM | 高 | 低 | 慢 | 高RAM需求 |
| find_circ | Python | 无参 | Bowtie2 | 低 | 低 | 快 | 低RAM需求 |
| circRNA_finder | Perl | 无参 | STAR | 低 | 低 | 快 | 双端测序验证 |
| Mapsplice | Python | 有参 | Bowtie1 | 高 | 高 | 慢 | 基因注释要求 |
| KNIFE | Python& Perl | 有参 | Bowtie 1& 2 | 高 | 高 | 慢 | 外显子注释要求 |
| PcircRNA_finder | Perl | 有参 | Tophat-Fusion | 高 | 高 | 慢 | 植物特异 |
新窗口打开|下载CSV
随着研究数据的不断积累和分析流程的重新设计,已建立起一系列不同作用和功能的数据库(表3),这些数据库不仅包含了circRNA的序列、基因组注释、功能预测等信息,同时也提供可变剪切预测、互作分析以及可视化等工具。
Table 3
表3
表3 常见circRNA数据库
Table 3
| 数据库 | circRNA数量 | 样本来源 | 数据来源 | 网址 | 信息说明 | 文献 |
|---|---|---|---|---|---|---|
| circBase | 199 161 | 动物组织样本 | 文献及其他数据库 | http://circbase.org/ | 包含所有的circRNA转录本注释信息,预测其剪接形式,并且提供剪切位点间序列的比对信息。提供Blast比对工具及fasta格式数据下载功能 | [49] |
| Circ2Traits | 1951 | 人类疾病组织样本 | 文献及其他数据库 | http://gyanxet-beta.com/circdb/ | 包含计算circRNA与疾病相关的miRNA互作的可能性,构建miRNA与蛋白质、长链非编码RNA和circRNA之间的互作网络及富集分析,circRNA与疾病相关SNP互作位点分析 | [50] |
| CircNet | 282 948 | 动物组织样本 | 数据库 | http://circnet.mbc.nctu.edu.tw/ | 包含新鉴定的circRNA、整合miRNA靶基因网络,circRNA可变剪切体的表达谱、基因组注释以及序列信息 | [51] |
| CSCD | 1 121 871 | 肿瘤组织样本 | 228个肿瘤组织细胞系RNA测序数据 | http://gb.whu.edu.cn/CSCD | 包含每一个circRNA的miRNA应答元件位点、RNA蛋白结合位点、开放阅读框(ORF)以及每一个circRNA的线性转录本的剪接事件的预测信息 | [52] |
| circRNADb | 32 914 | 人类组织样本 | 重新整合多个数据库 | http://reprod.njmu.edu.cn/circrnadb | 包含人类外显子circRNA外显子剪接事件、基因组序列、内部核糖体进入位点(IRES)、开放阅读框信息及证据支撑的参考文献 | [53] |
| PlantcircBase | 77 595 | 水稻、拟南芥、玉米、番茄和 大麦 | 生物信息学预测或实验验证 | http://ibi.zju.edu.cn/plantcircbase/ | 包含circRNA的miRNA海绵功能信息,circRNA-miRNA-mRNA互作网络图,基于基因组位置对circRNA结构的可视化以及提供circRNA的序列查询工具 | [54] |
| PlantCircNet | 139 276 | 拟南芥、水稻及其他8种植物 | 数据库 | http://bis.zju.edu.cn/plantcircnet/index.php | 包含互作网络图的可视化工具,过表达miRNA靶基因的GO富集工具,以及circRNA基因组注释、序列、剪切体的信息 | [55] |
| AtCircDB | 84 685 | 拟南芥 | 622个拟南芥RNA测序数据 | http://genome.sdau.edu.cn/circRNA | 包含拟南芥全面的组织特异性circRNA数据,提供检索、可视化以及下载拟南芥circRNA数据 | [56] |
新窗口打开|下载CSV
2 植物circRNA特征
2.1 植物circRNA序列组成和结构
研究发现,circRNA的生物合成通常受到顺式作用元件和反式作用因子的调控,环化外显子的侧翼内含子序列ALU重复片段和反向互补序列能够大大提高其环化的效率[13, 26, 57]。但是,与动物相比,植物中大多数外显子circRNA侧翼序列并不包含大量的重复序列和反向互补序列[19, 21, 35]。这表明在植物中“内含子驱动环化”模式并不是形成circRNA的主要机制。此外,超过33%的植物circRNA在上下游序列中包含两个及多个不同的接头序列,可能弥补了序列缺失从而提高其环化效率[35]。植物circRNA具有大量亚型,许多亚型来源于同一个基因的可变剪切,且偏好于多个外显子形成的环化[19, 21]。目前,已在水稻中鉴定得到约2806个circRNA全长序列,其中只有206个circRNA的侧翼包含经典的GT/AG剪切信号[21],这表明植物中的circRNA可能并不是依赖经典的circRNA剪切信号序列驱动环化。
另外,当外显子相邻内含子序列较长时,一 般不具备线性剪切能力[10, 26]。例如,水稻和拟南 芥的circRNA都比线性亚型具有更长的侧翼内含 子[19, 21, 40],这可能是由于更长的内含子序列可以捕捉到更多短的反向互补序列从而提升环化效率,而侧翼序列中包含较长的内含子序列,可能通过提高相邻外显子之间的空间距离,阻止线性剪切的发生。
2.2 植物circRNA来源和保守性
通常来说,植物circRNA的表达丰度较低,通过细胞类型特异性以及组织特异性表达来发挥其调控功能[19, 21, 32, 35, 58]。除了核基因组序列能够产生植物circRNA,叶绿体和线粒体基因组序列也能够产生植物circRNA[21, 34, 35],说明circRNA也可能参与调控光合作用和呼吸作用过程。同时,circRNA通过与miRNA互作、结合蛋白和干扰剪切过程等方式来调节基因的表达,从而有效地提升了植物转录调控过程的多样性和复杂性[59]。植物circRNA的组成可以分别来源于外显子、内含子或由其两者共同组成[60],且植物外显子和内含子circRNA的功能表达与组织特异性紧密联系[51]。通过不同的剪切模式,同一个基因座可以转录出circRNA或者线性mRNA,circRNA的表达与其亲本基因表达存在显著相关性。例如猕猴桃中AC_ciRNA_04842正调控Achn372061的表达[33]。此外,在水稻中过表达Os08circ16564可以较大程度抑制其亲本基因的表达,显示circRNA能够负调控其来源基因[19],但调控机制还需深入研究。Ye等[21]在拟南芥和水稻中发现700多个直系同源基因,其中300多个circRNA均来自于基因组相同位点,说明在不同的植物中circRNA高度保守。但是,在这些保守的circRNA侧翼内含子中并没有发现相似的序列或者共享相同的基序,说明在植物中circRNA的生物合成可能还存在其他机制[21]。
3 植物circRNA功能
3.1 具有miRNA海绵特征
由于circRNA缺少poly(A)尾巴和5′端,不受核糖核酸酶(RNase)的降解,在脱帽和降解过程中一般会与miRNA结合[61],参与转录后调控[21, 62]。Hansen等[62]认为植物中的circRNA作为miRNA海绵在植物生长发育过程中具有调控功能,成为circRNA早期功能研究的重点。circRNA在发挥海绵功能时,需要多个miRNA结合位点或在细胞质中高水平表达[6, 7]。通过紫外 交联免疫沉淀结合高通量测序技术(crosslinking- immunprecipitation and high-throughput sequencing,HITS-CLIP),研究人员发现人类中circCDR1as能够结合miR-7和miRNA效应蛋白AGO2,并且具有70多个保守的miR-7结合位点[21, 62];circSry包含16个miR-138的结合位点,能够调控靶mRNA来减弱circSry的过表达[63]。与动物不同,植物中只有少数的circRNA拥有miRNA结合位点(拟南芥5%,水稻6.6%)[16, 19, 21, 35]。Lu等[19]发现水稻中过表达的Os08circ16564可能与OsmiR172互作,降低其亲本基因的表达水平,但不影响OsmiR172本身的表达,这说明该circRNA分子在体内并没有作为miR172海绵。另外,circRNA的二级结构可能包含潜在的miRNA结合位点,从而降低预测的准确度。
3.2 circRNA表达模式
植物体内circRNA广泛存在,在生长发育过程中具有重要作用。如circRNA通过激素信号转导、卟啉和叶绿素代谢等途径参与叶片衰老、花发育、果实成熟的调控[29, 38, 58, 64]。同时,circRNA在应对不同的环境胁迫时会出现差异表达现象。如在水稻磷饥饿处理时,27个外显子circRNA差异表达[25];小麦在干旱胁迫情况下,发现了62个差异表达的circRNA[30];在番茄响应冷胁迫过程中,检测到163个circRNA差异表达[32];同时,大麦(Hordeum vulgare)用微量元素铁锌处理以及拟南芥在不同的光强度下,也发现了不同程度差异表达的circRNA[21, 34]。在病原体侵入以及植物类病毒感染的生物胁迫过程中,circRNA同样通过特异性表达实现不同的生物响应[31, 33],表明circRNA是植物体应对环境压力过程中重要的功能调控者。由于circRNA的闭环结构没有5°端和3°端,不容易被RNA外切酶降解[63],在应对生物与非生物胁迫时circRNA具有较长的响应周期,可能在植物长距离传递信号中发挥一定功能。已有研究表明,植物类病毒能够利用circRNA基序直接在细胞与细胞间进行长距离运输[65,66,67],这些分子能够结合不同的功能蛋白,通过木质部和韧皮部来传递细胞与细胞间信息的信号。但是,植物内源性circRNA相关机制与功能研究尚未见报道。
3.3 circRNA与蛋白互作
除了具有miRNA海绵功能外,circRNA通过识别、储存、运输不同蛋白,并将其携带到特定的亚细胞位置,通过调控靶mRNA或核糖体生成的方式发挥其功能[68, 69]。如ciR-7/CDR1as能够通过AGO2蛋白实现竞争性结合miR-7[62];circ-PABPN1竞争性结合HuR,抑制后者与PABPN1的mRNA结合,降低PABPN1翻译效率[70];circANRIL与PES1富含赖氨酸结构域的碳端相结合,竞争抑制PES1与核糖体结合,调控核糖体生成过程[71]。同时,circRNA能够通过蛋白互作,参与包括细胞衰老、细胞周期、泛素化等多种生命过程。如circ-FOXO3通过与不同的因子互作参与衰老过程,促进MDM2介导p53蛋白泛素化降解过程[72, 73]。FOXO3蛋白可微弱地结合circ-FOXO3,抑制FOXO3与MDM2的结合,促进FOXO3的富集[74]。circ-Amotl1通过诱导c-Myc进入细胞核内从而促进肿瘤的发生,能够与Myb、NF1、Akt、E2F1、E2F4、EGF等多种蛋白相互作 用[75, 76]。但是,由于circRNA与线性RNA在结构上存在明显差异,通过传统的RNA结合蛋白实验验证难以实现[77]。目前circRNA与蛋白互作分析的验证方法主要基于免疫沉淀分析,包括蛋白质体外结合实验(RNA pull-down)、RNA结合蛋白免疫沉淀(RNA binding protein immunoprecipitation)等技术,荧光原位杂交技术和RNase保护分析的方法能够更为准确获得互作circRNA的序列。合理利用功能数据库(表4)预测分析结果,并结合实验验证,能够填补植物中circRNA与蛋白互作研究的空缺。Table 4
表4
表4 circRNA功能预测的在线工具
Table 4
| 数据库 | 类别 | 网址 | 说明 | 文献 |
|---|---|---|---|---|
| Circinteractome | 核糖核蛋白复合物预测分析 | http://circinteractome.nia.nih.gov | 提供人类circRNA上的RNA结合蛋白和miRNA结合位点信息,检测引物设计工具,设计用于circRNA沉默的siRNA,以及鉴定circRNA上潜在的内部核糖体切入位点 | [78] |
| circlncRNAnet | lncRNAs-circRNAs互作与共表达预测分析 | http://app.cgu.edu.tw/ circlnc/ | 提供灵活的框架及多个分析模块,可接受和处理用户定义的NGS表达数据,得到表达谱、共表达网络和通路以及分子相互作用信息 | [79] |
| deepBase | 非编码RNA与蛋白的互作预测分析 | http://biocenter.sysu. edu.cn/deepBase/ | 提供19个物种不同的非编码RNA进化、表达和功能分化信息,预测蛋白质-lncRNA-circRNA互作网路 | [80] |
| SomamiR 2.0 | miRNA-lncRNA-circRNA互作预测分析 | http://compbio.uthsc.edu/SomamiR | 提供体细胞突变对miRNA和lncRNA及circRNA互作的影响的分析,集成数据库miR2GO工具,及定位miRNA靶位点分析 | [81] |
| CIRCpedia | 可变剪切位点预测 | http://www.picb.ac.cn/rnomics/circpedia/ | 提供人、小鼠、果蝇及蠕虫样本不同细胞系中circRNAs中可变剪切注释信息,提供可变反向剪切circRNA的鉴定工具 | [82] |
新窗口打开|下载CSV
3.4 circRNA翻译
circRNA并非是一类真正的非编码RNA,其中一部分具有可编码性[83, 84]。在真核生物中,经典的mRNA翻译依赖于40s核糖体亚基与5′端帽子结合发生翻译过程[85]。由于circRNA分子的闭合结构无法与核糖体亚基结合[63],因此circRNA可能依赖于其他翻译蛋白的途径。如Mounir等[86]在水稻中发现了一种具有内部核糖体结合位点(IRES)的circRNA结构类病毒,当IRES元件插入到起始密码子AUG的上游时,能够启动翻译过程[87];Yang等[88]在人类细胞中证实circRNA能够通过N6-甲基腺苷(m6A)途径翻译蛋白;Zhou等[89]发现eIF4G2参与m6A修饰调控的circRNA翻译过程,证明m6A修饰对circRNA的翻译具有直接影响。m6A是真核生物体内RNA腺嘌呤碱基非常重要的甲基化修饰,参与RNA剪接、翻译等多个过程,在体内主要通过YTH结构域家族蛋白识别来调节RNA二级结构的稳定性以及调控RNA与蛋白的互作[90]。目前,对拟南芥中m6A修饰已有了初步认识,其修饰位点通常位于mRNA的起始和终止密码子附近[91, 92],但是尚未见其他植物circRNA中m6A修饰的相关研究报道。4 结语与展望
近年来,circRNA的生物合成、分子调控等功能陆续被报道,多个蛋白分别参与调控RNA的剪接作用。例如,FUS蛋白介导circRNA的形成[93];作为CRISPR家族Cas-9的同源蛋白Csy4,共表达后促进环化效率[94];Fei等[95]使用CRISPR技术筛选前列腺癌相关基因,聚类分析得到HNRNPL拼接因 子,并通过RIP-seq实验验证了该因子参与调控RNA可变剪切和circRNA形成过程。这些研究不仅说明circRNA在各个生命周期过程中具有极大的调控潜能,同时又受到其他分子的相互制约,提示circRNA的发生以及调控机制的复杂性,值得进一步研究。目前,仍存在着大量未知领域,如circRNA如何实现miRNA海绵作用,如何更有效地使用生物信息学工具预测circRNA,circRNA在特殊组织和病变中如何表达调控等。高通量测序与生物信息学分析显示circRNA广泛表达于不同的植物中,且表达具有时空组织特异性。对circRNA特异性表达进行深入分析,不仅能够丰富已有植物生长发育关键途径的调控网络,而且能够作为植物病害提前发现的重要线索。同时,植物circRNA表达与来源基因的相关性分析也为科研人员提供了新的研究思路。合理利用综合数据库及生物信息学工具,将进一步推进circRNA的功能研究,通过开发植物特异circRNA分析软件及植 物综合数据库能够提高预测分析的准确度。综上 所述,circRNA的研究虽然已取得了一定的研究进展,但是对于植物circRNA的认识仍是一个漫长的过程。
参考文献 原文顺序
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In biology as in real estate, location is a cardinal organizational principle that dictates the accessibility and flow of informational traffic. An essential question in nuclear organization is the nature of the address code--how objects are placed and later searched for and retrieved. Long noncoding RNAs (lncRNAs) have emerged as key components of the address code, allowing protein complexes, genes, and chromosomes to be trafficked to appropriate locations and subject to proper activation and deactivation. lncRNA-based mechanisms control cell fates during development, and their dysregulation underlies some human disorders caused by chromosomal deletions and translocations.
URLPMID:22337053 [本文引用: 1]
It is clear that RNA has a diverse set of functions and is more than just a messenger between gene and protein. The mammalian genome is extensively transcribed, giving rise to thousands of non-coding transcripts. Whether all of these transcripts are functional is debated, but it is evident that there are many functional large non-coding RNAs (ncRNAs). Recent studies have begun to explore the functional diversity and mechanistic role of these large ncRNAs. Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions.
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Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review outlines the emerging understanding of lincRNAs in vertebrate animals, with emphases on how they are being identified and current conclusions and questions regarding their genomics, evolution and mechanisms of action.
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Abstract Recently, a non-coding RNA expressed from a human pseudogene was reported to regulate the corresponding protein-coding mRNA by acting as a decoy for microRNAs (miRNAs) that bind to common sites in the 3' untranslated regions (UTRs). It was proposed that competing for miRNAs might be a general activity of pseudogenes. This study raises questions about the potential ability of thousands of non-coding transcripts to interact with miRNAs and influence the expression of miRNA target genes. Three years ago, artificial miRNA decoys termed 'miRNA sponges' were introduced as a means to create loss-of-function phenotypes for miRNA families in cell culture and in virally infected tissue and transgenic animals. Given the efficacy of miRNA sponges expressed from stable chromosomal insertions, it seemed plausible that natural non-coding RNAs might have evolved to sequence-specifically sequester miRNAs. The first such endogenous sponge RNA was discovered in plants and found to attenuate a miRNA-mediated response to an environmental stress. More recently, a viral non-coding RNA was observed to sequester and promote the degradation of a cellular miRNA in infected primate cells. In this review we discuss the potential and proven roles for endogenous miRNA sponges and consider some criteria for screening candidate sponge RNAs. Copyright 2010 Elsevier Ltd. All rights reserved.
URLPMID:22000014 [本文引用: 2]
Abstract Recently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 "sponges" miR-133 and miR-133 [corrected] to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation. Copyright 2011 Elsevier Inc. All rights reserved.
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URLPMID:25404635 [本文引用: 1]
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
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Ashwal-Fluss et02al. provide evidence that circRNA production competes with linear mRNA splicing. They demonstrate that intronic sequences largely determine the production rate of circRNAs and identify a splice factor (muscleblind) that can promote circularization.
URLPMID:25543144 [本文引用: 1]
Abstract Circular RNAs (circRNAs), an abundant class of noncoding RNAs in higher eukaryotes, are generated from pre-mRNAs by circularization of adjacent exons. Using a set of 15 circRNAs, we demonstrated their cell-type-specific expression and circular versus linear processing in mammalian cells. Northern blot analysis combined with RNase H cleavage conclusively proved a circular configuration for two examples, LPAR1 and HIPK3. To address the circularization mechanism, we analyzed the sequence requirements using minigenes derived from natural circRNAs. Both canonical splice sites are required for circularization, although they vary in flexibility and potential use of cryptic sites. Surprisingly, we found that no specific circRNA exon sequence is necessary and that potential flanking intron structures can modulate circularization efficiency. In combination with splice inhibitor assays, our results argue that the canonical spliceosomal machinery functions in circRNA biogenesis, constituting an alternative splicing mode. Copyright 2015 The Authors. Published by Elsevier Inc. All rights reserved.
URLPMID:25449546 [本文引用: 2]
Abstract While the human transcriptome contains a large number of circular RNAs (circRNAs), the functions of most circRNAs remain unclear. Sequence annotation suggests that most circRNAs are generated from splicing in reversed orders across exons. However, the mechanisms of this backsplicing are largely unknown. Here we constructed a single exon minigene containing split GFP, and found that the pre-mRNA indeed produces circRNA through efficient backsplicing in human and Drosophila cells. The backsplicing is enhanced by complementary introns that form double-stranded RNA structure to bring splice sites in proximity, but such structure is not required. Moreover, backsplicing is regulated by general splicing factors and cis-elements, but with regulatory rules distinct from canonical splicing. The resulting circRNA can be translated to generate functional proteins. Unlike linear mRNA, poly-adenosine or poly-thymidine in 3' UTR can inhibit circular mRNA translation. This study revealed that backsplicing can occur efficiently in diverse eukaryotes to generate circular mRNAs.
URLPMID:25242744 [本文引用: 4]
正Exon circularization has been identified from many loci in mammals,but the detailed mechanism of its biogenesis has remained elusive.By using genomewide approaches and circular RNA recapitulation,we demonstrate that exon circularization is dependent on flanking intronic complementary sequences.Such sequences and their distribution exhibit rapid evolutionary changes,
URLPMID:25281217 [本文引用: 1]
Abstract Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the precursor messenger RNA (pre-mRNA) splicing machinery "backsplices" and covalently joins, for example, the two ends of a single exon. However, the mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Using extensive mutagenesis of expression plasmids, we show that miniature introns containing the splice sites along with short (090804 30- to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening exons to circularize in cells. The intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other. More than simple thermodynamics is clearly at play, however, as not all repeats support circularization, and increasing the stability of the hairpin between the repeats can sometimes inhibit circular RNA biogenesis. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3' end processing signal is required, suggesting that circularization may occur post-transcriptionally. These results suggest detailed and generalizable models that explain how the splicing machinery determines whether to produce a circular noncoding RNA or a linear mRNA. 0008 2014 Liang and Wilusz; Published by Cold Spring Harbor Laboratory Press.
URLPMID:25768908 [本文引用: 1]
Circular RNAs (circRNAs), formed by non-sequential back-splicing of pre-mRNA transcripts, are a widespread form of non-coding RNA in animal cells. However, it is unclear whether the majority of circRNAs represent splicing by-products without function or are produced in a regulated manner to carry out specific cellular functions. We show that hundreds of circRNAs are regulated during human epithelial-mesenchymal transition (EMT) and find that the production of over one-third of abundant circRNAs is dynamically regulated by the alternative splicing factor, Quaking (QKI), which itself is regulated during EMT. Furthermore, by modulating QKI levels, we show the effect on circRNA abundance is dependent on intronic QKI binding motifs. Critically, the addition of QKI motifs is sufficient to induce de novo circRNA formation from transcripts that are normally linearly spliced. These findings demonstrate circRNAs are both purposefully synthesized and regulated by cell-type specific mechanisms, suggesting they play specific biological roles in EMT.
URLPMID:23446348 [本文引用: 4]
Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse, and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
URLPMID:3270023 [本文引用: 1]
Most human pre-mRNAs are spliced into linear molecules that retain the exon order defined by the genomic sequence. By deep sequencing of RNA from a variety of normal and malignant human cells, we found RNA transcripts from many human genes in which the exons were arranged in a non-canonical order. Statistical estimates and biochemical assays provided strong evidence that a substantial fraction of the spliced transcripts from hundreds of genes are circular RNAs. Our results suggest that a non-canonical mode of RNA splicing, resulting in a circular RNA isoform, is a general feature of the gene expression program in human cells.
URLPMID:28366543 [本文引用: 1]
Circular RNAs (circ-RNAs), a novel class of noncoding RNAs, are a popular topic in animal research because they have potential as post-transcriptional regulators and diagnostic markers. Research in plants is only now emerging, but indicates that circ-RNAs could also be a crucial class of noncoding regulators.
URLPMID:26464523 [本文引用: 9]
Abstract Various stable circular RNAs (circRNAs) are newly identified to be the abundance of noncoding RNAs in Archaea, Caenorhabditis elegans, mice, and humans through high-throughput deep sequencing coupled with analysis of massive transcriptional data. CircRNAs play important roles in miRNA function and transcriptional controlling by acting as competing endogenous RNAs or positive regulators on their parent coding genes. However, little is known regarding circRNAs in plants. Here, we report 2354 rice circRNAs that were identified through deep sequencing and computational analysis of ssRNA-seq data. Among them, 1356 are exonic circRNAs. Some circRNAs exhibit tissue-specific expression. Rice circRNAs have a considerable number of isoforms, including alternative backsplicing and alternative splicing circularization patterns. Parental genes with multiple exons are preferentially circularized. Only 484 circRNAs have backsplices derived from known splice sites. In addition, only 92 circRNAs were found to be enriched for miniature inverted-repeat transposable elements (MITEs) in flanking sequences or to be complementary to at least 18-bp flanking intronic sequences, indicating that there are some other production mechanisms in addition to direct backsplicing in rice. Rice circRNAs have no significant enrichment for miRNA target sites. A transgenic study showed that overexpression of a circRNA construct could reduce the expression level of its parental gene in transgenic plants compared with empty-vector control plants. This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs. 2015 Lu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
URLPMID:3946582 [本文引用: 1]
Abstract An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (芒聢录 100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or 'piggyback' on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.
URLPMID:26204923 [本文引用: 18]
A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.
URLPMID:1069269 [本文引用: 1]
Abstract Viroids are uncoated infectious RNA molecules pathogenic to certain higher plants. Four different highly purified viroids were studied. By ultracentrifugation, thermal denaturation, electron microscopy, and end group analysis the following features were established: (i) the molecular weight of cucumber pale fruit viroid from tomato is 110,000, of citrus exocortis viroid from Gynura 119,000, of citrus exocortis viroid from tomato 119,000 and of potato spindle tuber viroid from tomato 127,000. (ii) Viroids are single-stranded molecules. (iii) Virods exhibit high thermal stability, cooperativity, and self-complementarity resulting in a rod-like native structure. (iv) Viroids are covalently closed circular RNA molecules.
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URLPMID:2429192 [本文引用: 1]
Hepatitis delta (δ) virus (HDV), a satellite virus of the hepatitis B virus (HBV), causes a severe form of viral hepatitis in humans 1 . Here we present evidence based on electron microscopy and electrophoretic behaviour that HDV contains a single stranded circular RNA molecule. This is the first animal virus identified with a circular RNA genome. Circular RNAs have only been found in plant viruses. We have obtained a partial complementary DNA clone representing 6525% of the total genome of HDV. Analysis of this cDNA revealed similarity to two plant viruses that may explain the origin of the virus.
URL [本文引用: 1]
URL [本文引用: 2]
URL [本文引用: 4]
URLPMID:25070500 [本文引用: 1]
Background The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression....
URLPMID:3946582 [本文引用: 2]
Abstract An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (芒聢录 100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or 'piggyback' on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.
URLPMID:28785273 [本文引用: 3]
Leaf growth and senescence are controlled by tight genetic factors involved regulation at multiple levels. Circular RNAs (circRNAs) have recently been reported as the microRNA sponge to accomplish corresponding regulatory roles. This study aims to explore the expression profile and functional role of circRNAs in Arabidopsis leaf growth and senescence. We used publically available RNA-seq data of Arabidopsis leaves to identify the circular RNA expression profile and used quantitative real-time PCR to validate our identified circRNAs. The functions of circRNAs were explored using distinct bioinformatics methods including analysis of network, gene ontology and KEGG pathway. We identified 168 circRNAs, including 40 novel circRNAs, inArabidopsis thalianaleaves, with 158 (94.1%) circRNAs arising from the exons of genes. Real-time PCRs were used to verify 4 highly expressed circRNAs and they all showed consistent expression patterns with the RNA-seq results. Interestingly, 6 and 35 circRNAs were differentially expressed at G- to -M stage and M- to -S stage, respectively. The circRNAs display an upregulation trend during the lifespan of Arabidopsis leaves. Moreover, the expression of circRNAs during senescence is independent of host gene expression to a certain degree. The gene ontology (GO) and KEGG pathway analysis of the targeted mRNA of circRNA鈥搈iRNA鈥搈RNA network showed that the circRNAs may be involved in plant hormone signal transduction, Porphyrin and chlorophyll metabolism during leaves senescence. Our comprehensive analysis of the expression profile of circRNAs and their potential functions during leaf growth and senescence suggest that circRNAs may function as new post-transcriptional regulators in the senescence of Arabidopsis leaves.
URLPMID:5215283 [本文引用: 3]
Circular RNAs (circRNAs) are a type of newly identified non-coding RNAs through high-throughput deep sequencing, which play important roles in miRNA function and transcriptional controlling in human, animals, and plants. To date, there is no report in wheat seedlings regarding the circRNAs identification and roles in the dehydration stress response. In present study, the total RNA was extracted from leaves of wheat seedlings under dehydration-stressed and well-watered conditions, respectively. Then, the circRNAs enriched library based deep sequencing was performed and the circRNAs were identified using bioinformatics tools. Around 88 circRNAs candidates were isolated in wheat seedlings leaves while 62 were differentially expressed in dehydration-stressed seedlings compared to well-watered control. Among the dehydration responsive circRNAs, six were found to act as 26 corresponding miRNAs sponges in wheat. Sixteen circRNAs including the 6 miRNAs sponges and other 10 randomly selected ones were further validated to be circular by real-time PCR assay, and 14 displayed consistent regulation patterns with the transcriptome sequencing results. After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the targeted mRNAs functions, the circRNAs were predicted to be involved in dehydration responsive process, such as photosynthesis, porphyrin, and chlorophyll metabolism, oxidative phosphorylation, amino acid biosynthesis, and metabolism, as well as plant hormone signal transduction, involving auxin, brassinosteroid, and salicylic acid. Herein, we revealed a possible connection between the regulations of circRNAs with the expressions of functional genes in wheat leaves associated with dehydration resistance.
URLPMID:28723412 [本文引用: 2]
In the course of a systematic screen of plant transcriptomic data, the sequence of a novel viroid-like RNA was identified in four contigs in a recent Transcriptome Shotgun Assembly (TSA) from lychee in China. Portions of this sequence are closely related to the central conserved region (CCR) and terminal conserved region (TCR) present in members of the genus Apscaviroid , sequences that are important criteria for viroid classification. RT-PCR with two divergent adjacent primers amplified the full 304 nucleotide sequence of this viroid-like RNA which can be folded into the rod-like secondary structure that is a typical feature of viroids in the family Pospiviroidae . Northern-blot hybridization following denaturing PAGE and sequential polyacrylamide gel electrophoresis (sPAGE) revealed the presence of both circular and linear forms of the viroid-like RNA in lychee leaf tissue. Phylogenetic analysis indicates that this RNA groups with known members of the genus Apscaviroid with a maximum pairwise sequence identity of <62%. Field surveys revealed the presence of this viroid-like RNA in most lychee samples collected in China; however, it was not found in the accessions in a germplasm collection of lychees that originated from a wide range of other countries. None of the four herbaceous hosts and one woody host tested were susceptible to infection with the lychee viroid-like RNA via agroinoculation and RNA inoculation. The provisional name lychee viroid-like RNA (LVd-like RNA) is proposed for this tentative new species in the genus Apscaviroid .
URLPMID:27402275 [本文引用: 4]
Various circular RNAs (circRNAs) are newly identified in animals and plants through high-throughput deep sequencing which play important roles in miRNA function and transcriptional controlling. However, little is known regarding circRNAs in tomato fruit. In this study, we systematically parse the circRNAs in the whole genome using the combination methods of deep sequencing and bioinformatics. In all, 854 circRNAs were identified in our results, among them, 163 circRNAs exhibit chilling responsive expression. Intriguingly, several circRNAs were predicted to involved in chilling responsive process, such as redox reaction, cell wall degradation, Arginine and polyamine metabolism, heat and cold shock protein, energy metabolism, Jasmonic acid and abscisic acid metabolism, low temperature and salt responsive protein and low temperature-induced transcription factors(CBF and WRKY). Furthermore, 102 circRNAs were found to act as the corresponding 24 miRNAs sponges in tomato. These discoveries deciphered the unexpected complexity of the regulatory circRNAs and may open a window for understanding the functions of circRNAs in plants.
URLPMID:5366334 [本文引用: 4]
Research studies have recently focused on circle RNAs (circRNAs) in relation to their regulatory functions in animals. However, the systematic identification of circRNAs in plants, especially non-model plants, is limited. In addition, raw report on the prediction of the potential role of circRNAs in plant response to pathogen invasion is currently available. We conducted the systematic identification of circRNAs from four materials originating from three species belonging to genusActinidiaunder different situations using ribosomal RNA (rRNA) depleted RNA-Seq data. A total of 3,582 circRNAs were identified inActinidia, of which 64.01, 21.44, and 14.55% were intergenic circRNAs, exonic circRNAs, and intronic circRNAs, respectively. Tissue-specific expression of circRNAs was observed in kiwifruit, and a species-specific response was detected when infected withPseudomonas syringaepv.actinidiae(Psa), which is the causative agent of kiwifruit bacterial canker disease. Furthermore, we found that both exonic and intronic circRNAs were significantly positively correlated to parent protein-coding genes, and intronic circRNAs are a class of highly remarkable regulators the parent genes comparing to that of exonic circRNAs. Expression and weighted gene co-expression network analysis (WGCNA) identified a set of circRNAs that were closely associated with plant defense response. The findings of the presents study suggest that circRNAs exhibit tissue- and species-specific expression, as well as play an important role in plant immune response.
URLPMID:27375638 [本文引用: 4]
RNA circularization made by head-to-tail back-splicing events is involved in the regulation of gene expression from transcriptional to post-translational levels. By exploiting RNA-Seq data and down-stream analysis, we shed light on the importance of circular RNAs in plants. The results introduce circular RNAs as novel interactors in the regulation of gene expression in plants and imply the comprehensiveness of this regulatory pathway by identifying circular RNAs for a diverse set of genes. These genes are involved in several aspects of cellular metabolism as hormonal signaling, intracellular protein sorting, carbohydrate metabolism and cell-wall biogenesis, respiration, amino acid biosynthesis, transcription and translation, and protein ubiquitination. Additionally, these parental loci of circular RNAs, from both nuclear and mitochondrial genomes, encode for different transcript classes including protein coding transcripts, microRNA, rRNA, and long non-coding/microprotein coding RNAs. The results shed light on the mitochondrial exonic circular RNAs and imply the importance of circular RNAs for regulation of mitochondrial genes. Importantly, we introduce circular RNAs in barley and elucidate their cellular-level alterations across tissues and in response to micronutrients iron and zinc. In further support of circular RNAs' functional roles in plants, we report several cases where fluctuations of circRNAs do not correlate with the levels of their parental-loci encoded linear transcripts.
URLPMID:27685607 [本文引用: 6]
A new regulatory class of small endogenous RNAs called circular RNAs (circRNAs) has been described as miRNA sponges in animals. Using 16 Arabidopsis thaliana RNA-Seq data sets, we identified 803 circRNAs in RNase R-/non-RNase R-treated samples. The results revealed the following features: Canonical and non-canonical splicing can generate circRNAs; chloroplasts are a hotspot for circRNA generation; furthermore, limited complementary sequences exist not only in introns, but also in the sequences flanking splice sites. The latter finding suggests that multiple combinations between complementary sequences may facilitate the formation of the circular structure. Our results contribute to a better understanding of this novel class of plant circRNAs. This article is protected by copyright. All rights reserved.
URLPMID:28089131 [本文引用: 1]
Abstract Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia. Using the computational identification, 975 circular RNAs were detected, of which three were validated by experiments. GO and KEGG analyses revealed the biological functions of genes hosting the circRNAs were enriched in the progression of translation initiation, macromolecule metabolism and binding. Notably, we found that many circRNAs in large yellow croaker had abundant microRNA-binding sites. A total of 363 the identified circRNAs had more than five miRNA-binding sites, among which twenty-two had more than ten binding sites for the miRNA-430 and the let-7 family. Our study confirmed the presence of circRNAs in large yellow croaker for the first time, providing a valuable reference for circRNA identification in fish species. Meanwhile, this work confirmed that the RNA-seq data from the traditional linear transcriptome library could be used for preliminary circRNA identification, which may offer an important reference for preliminary circRNA investigations in other species. Copyright 2017. Published by Elsevier B.V.
URLPMID:27739910 [本文引用: 1]
Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.
URLPMID:28717203 [本文引用: 2]
Abstract Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.
URLPMID:27493192 [本文引用: 2]
Motivation:Recent studies reveal an important role of non-coding circular RNA (circRNA) in the control of cellular processes. Because of differences in the organization of plant and mammal genomes, the sensitivity and accuracy of circRNA prediction programs using algorithms developed for animals and humans perform poorly for plants. Results:A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer), Based on analysis of simulated and real rRNA-/RNAase R RNA-Seq data fromArabidopsis thalianaand rice PcircRNA_finder provides a more comprehensive sensitive, precise prediction method for plants circRNAs. Availability and Implementation:http://ibi.zju.edu.cn/bioinplant/tools/manual.htm. Contact:fanlj@zju.edu.cn Supplementary information:Supplementary dataare available atBioinformaticsonline.
URLPMID:4279448 [本文引用: 2]
Circularization was recently recognized to broadly expand transcriptome complexity. Here, we exploit massive Drosophila total RNA-sequencing data, >5 billion paired-end reads from >100 libraries covering diverse developmental stages, tissues, and cultured cells, to rigorously annotate >2,500 fruit fly circular RNAs. These mostly derive from back-splicing of protein-coding genes and lack poly(A) tails, and the circularization of hundreds of genes is conserved across multiple Drosophila species. We elucidate structural and sequence properties of Drosophila circular RNAs, which exhibit commonalities and distinctions from mammalian circles. Notably, Drosophila circular RNAs harbor >1,000 well-conserved canonical miRNA seed matches, especially within coding regions, and coding conserved miRNA sites reside preferentially within circularized exons. Finally, we analyze the developmental and tissue specificity of circular RNAs and note their preferred derivation from neural genes and enhanced accumulation in neural tissues. Interestingly, circular isoforms increase substantially relative to linear isoforms during CNS aging and constitute an aging biomarker.
URLPMID:4316645 [本文引用: 1]
Abstract Recent studies reveal that circular RNAs (circRNAs) are a novel class of abundant, stable and ubiquitous noncoding RNA molecules in animals. Comprehensive detection of circRNAs from high-throughput transcriptome data is an initial and crucial step to study their biogenesis and function. Here, we present a novel chiastic clipping signal-based algorithm, CIRI, to unbiasedly and accurately detect circRNAs from transcriptome data by employing multiple filtration strategies. By applying CIRI to ENCODE RNA-seq data, we for the first time identify and experimentally validate the prevalence of intronic/intergenic circRNAs as well as fragments specific to them in the human transcriptome.
URLPMID:28334140 [本文引用: 1]
Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage.
URLPMID:20802226 [本文引用: 1]
Abstract The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads ( 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
URLPMID:24039610 [本文引用: 1]
Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.
URLPMID:26076956 [本文引用: 1]
Background The pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover, discovering biological contexts where circular RNAs are regulated will shed light on potential functional roles they may play. Results We present a new algorithm that increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries, including intergenic regions of the genome, with high statistical confidence. Unlike approaches that rely on read count and exon homology to determine confidence in prediction of circular RNA expression, our algorithm uses a statistical approach. Using our algorithm, we unveiled striking induction of general and tissue-specific circular RNAs, including in the heart and lung, during human fetal development. We discover regions of the human fetal brain, such as the frontal cortex, with marked enrichment for genes where circular RNA isoforms are dominant. Conclusions The vast majority of circular RNA production occurs at major spliceosome splice sites; however, we find the first examples of developmentally induced circular RNAs processed by the minor spliceosome, and an enriched propensity of minor spliceosome donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, these results suggest a potentially significant role for circular RNA in human development.
URL [本文引用: 1]
URLPMID:29338875 [本文引用: 1]
Recent studies have demonstrated that circular RNAs (circRNAs) are ubiquitous and have diverse functions and mechanisms of biogenesis. In these studies, computational profiling of circRNAs has been prevalently used as an indispensable method to provide high-throughput approaches to detect and analyze circRNAs. However, without an overall understanding of the underlying strategies, these computational methods may not be appropriately selected or used for a specific research purpose, and some misconceptions may result in biases in the analyses. In this review we attempt to illustrate the key steps and summarize tradeoff of different strategies, covering all popular algorithms for circRNA detection and various downstream analyses. We also clarify some common misconceptions and put emphasis on the fields of application for these computational methods.
URLPMID:4824091 [本文引用: 1]
Abstract CircRNAs are novel members of the non-coding RNA family. For several decades circRNAs have been known to exist, however only recently the widespread abundance has become appreciated. Annotation of circRNAs depends on sequencing reads spanning the backsplice junction and therefore map as non-linear reads in the genome. Several pipelines have been developed to specifically identify these non-linear reads and consequently predict the landscape of circRNAs based on deep sequencing datasets. Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance. By this approach, we observe surprisingly dramatic differences between the algorithms specifically regarding the highly expressed circRNAs and the circRNAs derived from proximal splice sites. Collectively, this study emphasizes that circRNA annotation should be handled with care and that several algorithms should ideally be combined to achieve reliable predictions. The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
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URLPMID:3857533
No abstract available.
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URLPMID:29036403
Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background. We constructed acancer-specificcircRNAdatabase (CSCD,http://gb.whu.edu.cn/CSCD). To understand the functional effects of circRNAs, we predicted the microRNA response element sites and RNA binding protein sites for each circRNA. We further predicted potential open reading frames to highlight translatable circRNAs. To understand the association between the linear splicing and the back-splicing, we also predicted the splicing events in linear transcripts of each circRNA. As the first comprehensive cancer-specific circRNA database, we believe CSCD could significantly contribute to the research for the function and regulation of cancer-associated circRNAs.
URLPMID:27725737
Abstract It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb.
URLPMID:28315753
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URLPMID:5727401
Circular RNA (circRNA) is a novel type of endogenous noncoding RNA with covalently closed loop structures, which are widely expressed in various tissues and have functional implications in cellular processes. Acting as competing endogenous RNAs (ceRNAs), circRNAs are important regulators of miRNA activities. The identification of these circRNAs underlines the increasing complexity of ncRNA-mediated regulatory networks. However, more biological evidence is required to infer direct circRNA–miRNA associations while little attention has been paid to circRNAs in plants as compared to the abundant research in mammals. PlantCircNet is presented as an integrated database that provides visualized plant circRNA–miRNA–mRNA regulatory networks containing identified circRNAs in eight model plants. The bioinformatics integration of data from multiple sources reveals circRNA–miRNA–mRNA regulatory networks and helps identify mechanisms underlying metabolic effects of circRNAs. An enrichment analysis tool was implemented to detect significantly overrepresented Gene Ontology categories of miRNA targets. The genomic annotations, sequences and isoforms of circRNAs were also investigated. PlantCircNet provides a user-friendly interface for querying detailed information of specific plant circRNAs. The database may serve as a resource to facilitate plant circRNA research. Several circRNAs were identified to play potential regulatory roles in flower development and response to environmental stress from regulatory networks related with miR156a and AT5G59720, respectively. This present research indicated that circRNAs could be involved in diverse biological processes. Database URL:http://bis.zju.edu.cn/plantcircnet/index.php
URLPMID:28968841
react-text: 162 Hybrids occasionally exhibit genetic interactions resulting in reduced fitness in comparison to their parents. Studies of Arabidopsis thaliana have highlighted the role of immune conflicts, but less is known about the role of other factors in hybrid incompatibility in plants. Here, we present a new hybrid incompatibility phenomenon in this species. We have characterized a new case of F1 hybrid... /react-text react-text: 163 /react-text [Show full abstract]
URLPMID:25558066 [本文引用: 1]
Ivanov et02al. study the biogenesis of circRNAs and reveal its conserved features. Moreover, they show that circRNAs can be predicted based on the genomic sequence of their flanking introns. Finally, they demonstrate that the circRNA formation mechanism depends on the RNA-editing enzyme ADAR.
[本文引用: 2]
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URLPMID:27068474 [本文引用: 1]
Zhang et al. study the link between circRNA processing and transcription using 4sUDRB-seq. They find that circRNA production from pre-mRNA back-splicing is slow and largely occurs post-transcriptionally. The authors argue that circRNAs that are abundant at a steady-state level tend to be transcribed quickly and accumulate.
URL [本文引用: 1]
URLPMID:23446346 [本文引用: 4]
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs1. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants(2-7). We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain(8). Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry)(9), serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.
URLPMID:24811520 [本文引用: 3]
Circular RNA transcripts were first identified in the early 1990s but knowledge of these species has remained limited, as their study through traditional methods of RNA analysis has been difficult. Now, novel bioinformatic approaches coupled with biochemical enrichment strategies and deep sequencing have allowed comprehensive studies of circular RNA species. Recent studies have revealed thousands of endogenous circular RNAs in mammalian cells, some of which are highly abundant and evolutionarily conserved. Evidence is emerging that some circRNAs might regulate microRNA (miRNA) function, and roles in transcriptional control have also been suggested. Therefore, study of this class of noncoding RNAs has potential implications for therapeutic and research applications. We believe the key future challenge for the field will be to understand the regulation and function of these unusual molecules.
URLPMID:28418376 [本文引用: 1]
Abstract Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life 1 , yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS 2-4 . This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
URLPMID:20074138 [本文引用: 1]
Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development,spread of infectious agents and plant defense responses.The fundamental questions being pursued at the forefronts revolve around function,mechanism and evolution.In the present review,we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA.We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking.We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants,as well as the promise for new insights in the years ahead.Finally.we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function,mechanism and evolution.
URL [本文引用: 1]
URLPMID:16181802 [本文引用: 1]
RNA trafficking has broad implications in the systemic spread of infectious agents, plant defense, and the systemic regulation of gene expression. The mechanisms that regulate trafficking remain poorly understood. The non-coding, infectious viroid RNAs are emerging as highly tractable model systems for the investigation of the basic mechanisms of RNA trafficking. Recent studies on viroids have led to new insights into the direct role of RNAs in intracellular and systemic trafficking, and to the identification of cellular proteins that might play a role in RNA trafficking. Here, we discuss these areas of progress, emphasizing on the unifying principles that control the trafficking of viroid, viral and endogenous RNAs.
URLPMID:23463100 [本文引用: 1]
Circular (circ) RNAs are to transcriptomics what the famous hidden musical theme is to Elgar's Enigma Variations: woven into the entire composition but not unambiguously identified or understood by scholars to this day. Now, two studies (Hansen et al, 2013; Memczak et al, 2013) have made substantial progress in both, identifying thousands of circRNAs and beginning to crack the enigma of their cellular function, by demonstrating that the circRNAs CiRS-7/CDR1as and SRY function as natural and highly stable sponges for specific microRNAs.
URLPMID:29158818 [本文引用: 1]
Circular RNAs have been identified as naturally occurring RNAs that are highly represented in the eukaryotic transcriptome. Although a large number of circRNAs have been reported, circRNA functions remain largely unknown. CircRNAs can function as miRNA sponges, thereby reducing their ability to target mRNAs. We hypothesize that circRNAs may bind, store, sort, and sequester proteins to particular subcellular locations, and act as dynamic scaffolding molecules that modulate protein-protein interactions. Here, we review the biological implication and function of circRNA-protein interaction, and reveal a dynamic model of the interaction in various tissues, development stages and physiological conditions. Improved techniques to identify and characterize the dynamic RNA-protein interactions may elucidate the molecular mechanisms associated with the expression and functional diversity of circRNAs.
URLPMID:28080204 [本文引用: 1]
HuR influences gene expression programs and hence cellular phenotypes by binding to hundreds of coding and noncoding linear RNAs. However, whether HuR binds to circular RNAs (circRNAs) and impacts on their function is unknown. Here, we have identified en masse circRNAs binding HuR in human cervical carcinoma HeLa cells. One of the most prominent HuR target circRNAs was hsa_circ_0031288, renamed CircPABPN1 as it arises from the PABPN1 pre-mRNA. Further analysis revealed that HuR did not influence CircPABPN1 abundance; interestingly, however, high levels of CircPABPN1 suppressed HuR binding to PABPN1 mRNA. Evaluation of PABPN1 mRNA polysomes indicated that PABPN1 translation was modulated positively by HuR and hence negatively by CircPABPN1. We propose that the extensive binding of CircPABPN1 to HuR prevents HuR binding to PABPN1 mRNA and lowers PABPN1 translation, providing the first example of competition between a circRNA and its cognate mRNA for an RBP that affects translation.
URLPMID:27539542 [本文引用: 1]
Abstract Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. Here we show that circular antisense non-coding RNA in the INK4 locus (circANRIL), which is transcribed at a locus of atherosclerotic cardiovascular disease on chromosome 9p21, confers atheroprotection by controlling ribosomal RNA (rRNA) maturation and modulating pathways of atherogenesis. CircANRIL binds to pescadillo homologue 1 (PES1), an essential 60S-preribosomal assembly factor, thereby impairing exonuclease-mediated pre-rRNA processing and ribosome biogenesis in vascular smooth muscle cells and macrophages. As a consequence, circANRIL induces nucleolar stress and p53 activation, resulting in the induction of apoptosis and inhibition of proliferation, which are key cell functions in atherosclerosis. Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring atheroprotection, thereby showing that circularization of long non-coding RNAs may alter RNA function and protect from human disease.
URLPMID:4444809 [本文引用: 1]
URLPMID:4824104 [本文引用: 1]
Most RNAs generated by the human genome have no protein-coding ability and are termed non-coding RNAs. Among these include circular RNAs, which include exonic circular RNAs (circRNA), mainly found in the cytoplasm, and intronic RNAs (ciRNA), predominantly detected in the nucleus. The biological functions of circular RNAs remain largely unknown, although ciRNAs have been reported to promote gene transcription, while circRNAs may function as microRNA sponges. We demonstrate that the circular RNA circ-Foxo3 was highly expressed in non-cancer cells and were associated with cell cycle progression. Silencing endogenous circ-Foxo3 promoted cell proliferation. Ectopic expression of circ-Foxo3 repressed cell cycle progression by binding to the cell cycle proteins cyclin-dependent kinase 2 (also known as cell division protein kinase 2 or CDK2) and cyclin-dependent kinase inhibitor 1 (or p21), resulting in the formation of a ternary complex. Normally, CDK2 interacts with cyclin A and cyclin E to facilitate cell cycle entry, while p21works to inhibit these interactions and arrest cell cycle progression. The formation of this circ-Foxo3-p21-CDK2 ternary complex arrested the function of CDK2 and blocked cell cycle progression.
URLPMID:27886165 [本文引用: 1]
Cell death and differentiation is a monthly research journal focused on the exciting field of programmed cell death and apoptosis. It provides a single accessible source of information for both scientists and clinicians, keeping them up-to-date with advances in the field. It encompasses programmed cell death, cell death induced by toxic agents, differentiation and the interrelation of these with cell proliferation.
URLPMID:28622299 [本文引用: 1]
Circular RNAs (circRNAs) are a subclass of noncoding RNAs widely expressed in mammalian cells. We report here the tumorigenic capacity of a circRNA derived from angiomotin-like1 (circ-Amotl1). Circ-Amotl1 is highly expressed in patient tumor samples and cancer cell lines. Single-cell inoculations using circ-Amotl1-transfected tumor cells showed a 30-fold increase in proliferative capacity relative to control. Agarose colony-formation assays similarly revealed a 142-fold increase. Tumor-take rate in nude mouse xenografts using 6-day (219 cells) and 3-day (9 cells) colonies were 100%, suggesting tumor-forming potential of every cell. Subcutaneous single-cell injections led to the formation of palpable tumors in 41% of mice, with tumor sizes >1 m(3) in 1 month. We further found that this potent tumorigenicity was triggered through interactions between circ-Amotl1 and c-myc. A putative binding site was identified in silico and tested experimentally. Ectopic expression of circ-Amotl1 increased retention of nuclear c-myc, appearing to promote c-myc stability and upregulate c-myc targets. Expression of circ-Amotl1 also increased the affinity of c-myc binding to a number of promoters. Our study therefore reveals a novel function of circRNAs in tumorigenesis, and this subclass of noncoding RNAs may represent a potential target in cancer therapy.Cell Death and Differentiation advance online publication, 16 June 2017; doi:10.1038/cdd.2017.86.
URLPMID:28676341 [本文引用: 1]
Delayed or impaired wound healing is a major health issue worldwide, especially in patients with diabetes and atherosclerosis. Here we show that expression of the circular RNA circ-Amotl1 accelerated healing process in a mouse excisional wound model. Further studies showed that ectopic circ-Amotl1 increased protein levels of Stat3 and Dnmt3a. The increased Dnmt3a then methylated the promoter of microRNA miR-17, decreasing miR-17-5p levels but increasing fibronectin expression. We found that Stat3, similar to Dnmt3a and fibronectin, was a target of miR-17-5p. Decreased miR-17-5p levels would increase expression of fibronectin, Dnmt3a, and Stat3. All of these led to increased cell adhesion, migration, proliferation, survival, and wound repair. Furthermore, we found that circ-Amotl1 not only increased Stat3 expression but also facilitated Stat3 nuclear translocation. Thus, the ectopic expressed circ-Amotl1 and Stat3 were mainly translocated to nucleus. In the presence of circ-Amotl1, Stat3 interacted with Dnmt3a promoter with increased affinity, facilitating Dnmt3a transcription. Ectopic application of circ-Amotl1 accelerating wound repair may shed light on skin wound healing clinically.
URLPMID:25714049 [本文引用: 1]
Abstract Circular RNAs (circRNAs) have re-emerged as an interesting RNA species. Using deep RNA profiling in different mouse tissues, we observed that circRNAs were substantially enriched in brain and a disproportionate fraction of them were derived from host genes that encode synaptic proteins. Moreover, on the basis of separate profiling of the RNAs localized in neuronal cell bodies and neuropil, circRNAs were, on average, more enriched in the neuropil than their host gene mRNA isoforms. Using high-resolution in situ hybridization, we visualized circRNA punctae in the dendrites of neurons. Consistent with the idea that circRNAs might regulate synaptic function during development, many circRNAs changed their abundance abruptly at a time corresponding to synaptogenesis. In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibited substantial up- or downregulation. Together, our data indicate that brain circRNAs are positioned to respond to and regulate synaptic function.
URLPMID:26669964
Circular RNAs (circRNAs) are widely expressed in animal cells, but their biogenesis and functions are poorly understood. CircRNAs have been shown to act as sponges for miRNAs and may also potentially sponge RNA-binding proteins (RBPs) and are thus predicted to function as robust posttranscriptional regulators of gene expression. The joint analysis of large-scale transcriptome data coupled with computational analyses represents a powerful approach to elucidate possible biological roles of ribonucleoprotein (RNP) complexes. Here, we present a new web tool, CircInteractome (circRNA interactome), for mapping RBP- and miRNA-binding sites on human circRNAs. CircInteractome searches public circRNA, miRNA, and RBP databases to provide bioinformatic analyses of binding sites on circRNAs and additionally analyzes miRNA and RBP sites on junction and junction-flanking sequences. CircInteractome also allows the user the ability to (1) identify potential circRNAs which can act as RBP sponges, (2) design junction-spanning primers for specific detection of circRNAs of interest, (3) design siRNAs for circRNA silencing, and (4) identify potential internal ribosomal entry sites (IRES). In sum, the web tool CircInteractome, freely accessible at http://circinteractome.nia.nih.gov, facilitates the analysis of circRNAs and circRNP biology.
URLPMID:29194536
Despite their lack of protein-coding potential, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These noncoding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum, as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels. While a handful of publicly available databases have been reported, existing tools do not fully capture, from a network perspective, the functional implications of lncRNAs or circRNAs of interest. Through an integrated and streamlined design, circlncRNAnet aims to broaden the understanding of ncRNA candidates by testingin silicoseveral hypotheses of ncRNA-based functions, on the basis of large-scale RNA-seq data. This web server is implemented with several features that represent advances in the bioinformatics of ncRNAs: (1) a flexible framework that accepts and processes user-defined next-generation sequencing ased expression data; (2) multiple analytic modules that assign and productively assess the regulatory networks of user-selected ncRNAs by cross-referencing extensively curated databases; (3) an all-purpose, information-rich workflow design that is tailored to all types of ncRNAs. Outputs on expression profiles, co-expression networks and pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria. In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on circRNAs/lncRNAs of their interest. In summary, circlncRNAnet provides a ne-stop resource for in-depth analyses of ncRNA biology. circlncRNAnet is freely available athttp://app.cgu.edu.tw/circlnc/.
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URLPMID:4702864
Abstract SomamiR 2.0 (http://compbio.uthsc.edu/SomamiR) is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). Here, we describe the recent major updates to the SomamiR database. We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. Recently, a large number of miRNA target sites have been discovered by newly emerged high-throughput technologies for mapping the miRNA interactome. We have mapped 388 247 somatic mutations to the experimentally identified miRNA target sites. The updated database also includes a list of somatic mutations in the miRNA seed regions, which contain the most important guiding information for miRNA target recognition. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA-ceRNA interactions. The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
URLPMID:27365365
Abstract Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines. Compared with their linear cognate RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket alternative back-splice sites. In addition, all four basic types of alternative splicing that have been identified in the (linear) mRNA process were found within circRNAs, and many exons were predominantly spliced in circRNAs. Unexpectedly, thousands of previously unannotated exons were detected in circRNAs from the examined cell lines. Although these novel exons had similar splice site strength, they were much less conserved than known exons in sequences. Finally, both alternative back-splicing and circRNA-predominant alternative splicing were highly diverse among the examined cell lines. All of the identified alternative back-splicing and alternative splicing in circRNAs are available in the CIRCpedia database (http://www.picb.ac.cn/rnomics/circpedia). Collectively, the annotation of alternative back-splicing and alternative splicing in circRNAs provides a valuable resource for depicting the complexity of circRNA biogenesis and for studying the potential functions of circRNAs in different cells. 2016 Zhang et al.; Published by Cold Spring Harbor Laboratory Press.
URLPMID:28344082 [本文引用: 1]
Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here weperformed expression profiling of circRNAs during invitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy. A high-content functional genomic screen allowed the study of their functionalrole in muscle differentiation. One of them, circ-ZNF609, resulted in specifically controlling myoblast proliferation. Circ-ZNF609 contains an open reading frame spanning from the start codon, in common with the linear transcript, and terminating at an in-frame STOP codon, created upon circularization. Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes.
[本文引用: 1]
URLPMID:19239892 [本文引用: 1]
Translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease. We describe recent advances in our understanding of the molecular structures and biochemical functions of the translation initiation machinery and summarize key strategies that mediate general or gene-specific translational control, particularly in mammalian systems.
URLPMID:25253891 [本文引用: 1]
Abstract The highly structured (64% GC) covalently closed circular (CCC) RNA (220 nt) of the virusoid associated with rice yellow mottle virus codes for a 16-kDa highly basic protein using novel modalities for coding, translation, and gene expression. This CCC RNA is the smallest among all known viroids and virusoids and the only one that codes proteins. Its sequence possesses an internal ribosome entry site and is directly translated through two (or three) completely overlapping ORFs (shifting to a new reading frame at the end of each round). The initiation and termination codons overlap UGAUGA (underline highlights the initiation codon AUG within the combined initiation-termination sequence). Termination codons can be ignored to obtain larger read-through proteins. This circular RNA with no noncoding sequences is a unique natural supercompact "nanogenome."
URL [本文引用: 1]
Many proteins with unusual structural properties are comprised of multiple repeating amino acid sequences and are often fractious to expression in recombinant systems. To facilitate recombinant production of such proteins for structural and engineering studies, we have produced circular messenger RNAs with infinite open reading frames. We show that a circular mRNA containing a simple green fluorescent protein (GFP) open reading frame can direct GFP expression in Escherichia coli. A circular mRNA with an infinite GFP open reading frame produces extremely long protein chains, proving that bacterial ribosomes can internally initiate and repeatedly transit a circular mRNA. Only the monomeric forms of GFP produced from circular mRNA are fluorescent. Analysis of the translation initiation region shows that multiple sequences contribute to maximal translation from circular mRNA. This technology provides a unique means of producing a very long repeating-sequence protein, and may open the way for development of proteinaceous materials with novel properties.
URLPMID:28281539 [本文引用: 1]
Cell death and differentiation is a monthly research journal focused on the exciting field of programmed cell death and apoptosis. It provides a single accessible source of information for both scientists and clinicians, keeping them up-to-date with advances in the field. It encompasses programmed cell death, cell death induced by toxic agents, differentiation and the interrelation of these with cell proliferation.
URLPMID:28854373 [本文引用: 1]
Abstract N 6 -methyladenosine (m 6 A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m 6 A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m 6 A immunoprecipitation, defined thousands of m 6 A circRNAs with cell-type-specific expression. The presence of m 6 A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m 6 A sites in mRNAs, and by reduced m 6 A levels upon depletion of METTL3, the m 6 A writer. Despite sharing m 6 A readers and writers, m 6 A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m 6 A circRNAs exhibit less stability in a0002process regulated by YTHDF2. These results expand our understanding of the breadth of m 6 A modifications and uncover regulation of circRNAs through m 6 A modification. Copyright 0008 2017 The Authors. Published by Elsevier Inc. All rights reserved.
URLPMID:24713629 [本文引用: 1]
Abstract N(6)-methyladenosine (m(6)A) is a modified base that has long been known to be present in non-coding RNAs, ribosomal RNA, polyadenylated RNA and at least one mammalian mRNA. However, our understanding of the prevalence of this modification has been fundamentally redefined by transcriptome-wide m(6)A mapping studies, which have shown that m(6)A is present in a large subset of the transcriptome in specific regions of mRNA. This suggests that mRNA may undergo post-transcriptional methylation to regulate its fate and function, which is analogous to methyl modifications in DNA. Thus, the pattern of methylation constitutes an mRNA 'epitranscriptome'. The identification of adenosine methyltransferases ('writers'), m(6)A demethylating enzymes ('erasers') and m(6)A-binding proteins ('readers') is helping to define cellular pathways for the post-transcriptional regulation of mRNAs.
[本文引用: 1]
URLPMID:26667818 [本文引用: 1]
Background m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, differential m6A patterns between organs have not...
URLPMID:28358055 [本文引用: 1]
The RNA binding protein FUS functions in several RNA biosynthetic processes and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS).
URLPMID:28223408 [本文引用: 1]
Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing back-splicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task. Coexpression of Csy4 and the circRNA switch allows for the removal of downstream competitive splice sites and stabilization of the 5' cleavage product. This subsequently results in back-splicing of the 5' cleavage product into a circRNA that can translate a reporter protein from an internal ribosomal entry site (IRES). Our platform outlines a straightforward approach toward regulating splicing and could find potential applications in synthetic biology as well as in studying the properties of different circRNAs.
URLPMID:28439031 [本文引用: 1]
Kin selection theory predicts that, where kin discrimination is possible, animals should typically act more favorably toward closer genetic relatives and direct aggression toward less closely related individuals. Contrary to this prediction, we present data from an 18-y study of wild banded mongooses, Mungos mungo, showing that females that are more closely related to dominant individuals are specifically targeted for forcible eviction from the group, often suffering severe injury, and sometimes death, as a result. This pattern cannot be explained by inbreeding avoidance or as a response to more intense local competition among kin. Instead, we use game theory to show that such negative kin discrimination can be explained by selection for unrelated targets to invest more effort in resisting eviction. Consistent with our model, negative kin discrimination is restricted to eviction attempts of older females capable of resistance; dominants exhibit no kin discrimination when attempting to evict younger females, nor do they discriminate between more closely or less closely related young when carrying out infanticidal attacks on vulnerable infants who cannot defend themselves. We suggest that in contexts where recipients of selfish acts are capable of resistance, the usual prediction of positive kin discrimination can be reversed. Kin selection theory, as an explanation for social behavior, can benefit from much greater exploration of sequential social interactions.
