战 昊, 朱 凯, 胡志强, 王鹏程, 代 智, 黄晓武, 周 俭
复旦大学附属中山医院肝癌研究所,上海 200032
环状RNA: 非编码RNA研究新方向
战 昊, 朱 凯, 胡志强, 王鹏程, 代 智, 黄晓武, 周 俭*
复旦大学附属中山医院肝癌研究所,上海 200032
环状RNA(Circular RNAs,circRNAs)是一类新型的非编码RNA,其首尾通过共价键形成闭合的环,表现出与线性RNA不同的特性。circRNA大量存在于真核细胞转录组中,在物种间具有保守性,表达稳定且具有组织及发展阶段特异性。circRNA不易被核酸外切酶RNase R降解,在体液中较线性RNA更稳定,因而具有作为临床诊断及预后标志物的潜在应用价值。目前的研究发现环状RNA能够发挥miRNA分子海绵作用,调控基因转录过程。CircRNA在心血管系统疾病、神经系统疾病、朊蛋白疾病及癌症等疾病中发挥重要作用,有望成为RNA领域研究新的热点。
环状RNA;非编码RNAs;miRNA分子海绵;癌症;生物标记
环状 RNA(Circular RNAs,circRNAs)是一类通过共价键形成的闭合环状非编码 RNA。circRNA不具备5′→3′极性及3′ polyA末端,表现出与线性RNA不同的特性。circRNA不易被核酸外切酶 RNase R 降解。在体液如血浆[1]及唾液[2]里较线性RNA更稳定。大部分circRNA有外显子编码(exonic circular RNA, ecircRNA),主要存在于细胞质中。circRNA分子富含miRNA应答元件(microRNA response elements, MRE)[3-5],能通过这些MRE吸附特定的miRNAs,充当miRNAs的分子“海绵”,从而调控miRNA的功能[5-6];还有一部分circRNA由内含子编码(circular intronic RNA, ciRNA),或外显子与内含子共同编码(circular exon-intron circRNAs, EIciRNAs),位于细胞核内,参与调控基因转录[7-8]。研究发现circRNA在动脉粥样硬化[9]、神经系统紊乱[5]、朊病毒疾病[10]和肿瘤等疾病[11-14]中发挥重要作用。通过研究circRNA与疾病之间的关系能够为疾病诊治提供新的发展方向。
1979 年科学家们利用电子显微镜第一次在真核细胞的细胞质中观察到 RNA以环状的形式存在[15]。随后在酵母的线粒体中也发现了circRNA的存在[16]。1993 年,科学家们在人体细胞的转录本中也发现了一些由外显子编码的circRNA[17]。然而这些circRNA 仅仅被认为是可变剪切过程中产生的中间产物或错误剪切产物[17-19],被归为转录“噪声”,因而没有得到广泛关注。近年来,随着测序技术和生物信息学技术的发展,科学家们通过高通量RNA测序(RNA-sequencing,RNA-seq)对circRNA进行了深入研究。2012年,Salzman等[20]通过 RNA-seq首次证实circRNA在人类体细胞中广泛表达。此后大量研究证实circRNA在哺乳动物细胞内含量丰富,其序列具有进化保守性,通常还具有组织及发育阶段的特异性表达[3-5,7-8,21-22]。Zhang等[7]又在人类细胞内发现了内含子编码的circRNA。Li等[8]还发现了环状外显子-内含子RNA。但是EIciRNA的形成机制目前还不清楚。
在真核细胞内,mRNA前体(pre-mRNA)的外显子区域被内含子隔断。经典剪接通过剪接体(spliceosome)去除pre-mRNA中的内含子并连接外显子。经过5′加帽及3′ polyA等转录及转录后修饰形成具有5′→3′极性的线性RNA转录本[23]。与经典线性剪接不同的是,circRNA的形成通过反向剪接(back-splicing)将下游剪接供体与上游剪接受体反向连接,形成闭合circRNA转录本。Jeck等[4]提出circRNA环化的两种模型。第一种叫做“套索驱动的环化”模型;第二种叫做“内含子配对驱动的环化”模型。先发生经典剪接还是反向剪接是两者的主要区别。“套索驱动的环化”先发生经典剪接,产生一个线性RNA和一个包含外显子的内含子套索,后者通过反向剪接生成circRNA[3-4,20,24]。“内含子配对驱动的环化”则先发生反向剪接,直接生成circRNA[3-4,20,24]。“内含子配对驱动”较“套索驱动”更常见[24]。
3.1 circRNA的生成主要受circRNA前体中的内含子序列及RNA结合蛋白(RNA binding proteins, RBP)的调控 大量研究证实内含子区域的反向互补序列(如Alu元件)对circRNA的生成起重要作用[25-32]。Liang等[27]对Alu元件进行了研究,发现外显子两侧内含子中30~40 核苷酸的反向重复序列即可有效促进circRNA的产生。特异的互补序列及碱基配对的稳定性对circRNA的生成至关重要。另外一些内含子不含有反向互补序列,也能形成circRNA。这提示除反向互补序列外,还有其他因素影响circRNA的生成[28]。Westholm等[33]研究发现果蝇的circRNA缺乏Alu元件,但是这些circRNA两侧的内含子较一般线性产物长,在哺乳动物[4]及新杆状线虫内亦发现这一现象[28],提示内含子长度也能影响circRNA生成。
3.2 RBP参与circRNA前体剪接过程,也能调控circRNA的生成 研究发现 RBP Quaking(QKI)[34]和Muscleblind(MBL)[30]能够结合外显子两侧的RBP(位于内含子序列)结合模序,通过RBP之间的相互作用拉近外显子的距离,促进反向剪接的形成[30,34]。RBP还可能通过增加互补序列的稳定性或抑制经典剪接,促进环化的发生。Conn等[34]证实,在细胞中敲除RBP QKI后,含有QKI结合模序的circRNA表达发生下调。在某些外显子两侧加入QKI结合模序,可诱导原本不发生环化的基因产生circRNA。Ashwal-Fluss等[30]对果蝇细胞的研究发现MBL能够与其同源pre-mRNA结合,拉近内含子,上调circMbl的表达。此外,Ivanov等[28]发现敲除RBP ADAR1能够上调部分circRNA,提示ADAR1可能抑制circRNA的生成。
4.1 circRNA 充当ceRNA或miRNA sponges ceRNA 全称为“competitive endogenous RNA”,又称 microRNA sponges。 Seitz等[35]于2009 年首次提出了 ceRNA 的概念:“不同蛋白的 mRNA 通过竞争性结合同一种 miRNA,从而调节相互的表达,这些 mRNA 之间互为 ceRNA。” ceRNA(如mRNA,lncRNA)含有共同的MRE,ceRNA通过这些MRE竞争性结合miRNA,从而影响miRNA的活性,进一步影响miRNA靶基因的表达[36]。目前的研究证实circRNA亦含有MRE,能够发挥miRNA sponges 或ceRNA 的作用[5-6,11,37]。如ciRS-7含有70个miR-7结合位点,能与miR-7特异性结合,发挥了天然miRNA sponges的功能[14]。Memczak等[5]发现在斑马鱼体内过表达ciRS-7,其作用效果与miR-7敲除类似,证实了ciRS-7在体内发挥miR-7 sponges的作用。
Y染色体性别决定区 (sex-determining region Y, SRY) 基因在成年小鼠睾丸组织内表达环状转录产物SRY circRNA[19]。SRY circRNA含有16个miR-138结合位点,Hansen等[38]通过荧光素报告酶实验证实SRY circRNA能够抑制miR-138活性。免疫共沉淀实验证实SRY circRNA与miR-138能发生共沉淀特异性结合,由此推断SRY circRNA发挥miR-138 sponges的作用[38]。
4.2 circRNA调控基因表达 Li等[8]发现某些基因编码的circRNA能够通过顺式调节作用,促进其自身基因的表达。研究人员们敲低EIF3J circRNA和PAIP2 circRNA后,发现其自身基因EIF3J和PAIP2的表达相应发生下调[8]。尽管在基因转录的过程中circRNA与其线性RNA(mRNA, lncRNA等)可能发生竞争性抑制,但是细胞核内已存在的circRNA可能同时促进circRNA及mRNA的表达。
Zhang等[7]发现在细胞核内,内含子来源的circRNA ci-ankrd52在其自身基因转录的位置聚集,并对Pol II依赖的转录起促进作用。敲低ci-ankrd52后,其自身基因的表达发生下调。此外,EIciRNA还可能顺式调控其他基因的表达[7]。
4.3 circRNA与RBP相互作用 有研究发现Argonaute[6]、Pol II[7]及MBL[30]等RBP能够与circRNA相互作用。circRNA存贮并转运RBP,与RBP底物竞争其结合位点,从而调节RBP活性。
4.4 翻译生成蛋白质 基于EcircRNAs具有开放阅读框架(open reading frames, ORF)结构,已有研究证实EcircRNAs可以通过胞内核糖体插入位点(internal ribosome entry sites, IRESs)在体外生成蛋白质[39-40],或通过原核核糖体结合位点(prokaryotic ribosome-binding sites)在体内生成蛋白质[41]。然而,目前尚无证据显示真核细胞来源的circRNAs能够在体内翻译生成蛋白质。
随着研究者对circRNA结构及功能的研究不断深入,越来越多证据显示circRNA可能在人类疾病的发生及发展过程中发挥重要作用。
由于circRNA参与miRNA的调控,circRNA可能通过miRNA参与多种疾病的发生发展[42]。其中研究最多的是ciRS-7及其对应的miR-7。MiR-7涉及帕金森病[43]、糖尿病[44]和肿瘤等多种疾病及相关通路中的关键蛋白,如α-synuclein[43]、mTOR[44]、EGFR、IRS-1、IRS-2[45]、Pak1[46]、Raf1[47]、Ack1[48]及PIK3CD[49]。ciRS-7作为miRNA的sponges,具有募集 miR-7 的能力,通过间接调控 miR-7 靶标的表达,影响疾病的发生和发展[14]。最近的一项研究发现,ciRS-7在阿尔茨海默病(Alzheimer disease,AD)患者的海马区发生下调,导致ciRS-7的sponges效应缺失,导致miR-7表达上调及其靶mRNA的表达下调[50]。
另有研究发现circMbl与肌强直性营养不良的发生发展相关[4]。Hansen等[14]发现在HEK293细胞中高表达朊蛋白 (prion protein, PrPC)可上调 ciRS-7,提示ciRS-7可能与朊病毒相关疾病的发病相关。此外,circRNA cANRIL的表达与动脉硬化性疾病的发病风险相关[9]。
越来越多的研究证实circRNA与肿瘤的发生及发展密切相关。Li等[11]发现Cir-ITCH在食管鳞状细胞癌组织中表达下调,Cir-ITCH通过吸附miR-7、miR-17和miR-124上调ITCH,从而抑制Wnt信号通路,在食管鳞状细胞癌中发挥抑癌作用。Bachmayr-Heyda等[12]在结直肠癌的研究中发现circRNA表达发生广泛下调,且circRNA的表达丰度与细胞增殖呈负相关。最近的一项研究发现血清外泌体中包含大量circRNAs[51]。这些circRNAs的表达受到母细胞内相关miRNA的调控,在外泌体中富集,并向受体细胞传递生物学信息。肿瘤来源的circRNAs随外泌体进入外周循环血,而血清外泌体circRNA表达的差异,能够用来区分结肠癌患者与健康人群。该研究为肿瘤的外周血外泌体-circRNA诊断奠定了基础。另一项研究通过转录组测序发现circRNAs在7种恶性肿瘤与正常组织间存在显著差异。进一步研究发现,circHIPK3在肝癌组织中显著上调。作为miRNA的分子海绵,circHIPK3能够吸附至少9个具有肿瘤抑制作用的miRNA,并且对肿瘤细胞的增殖起到调控作用[52]。circRNAs能够调控肿瘤相关的多种miRNA,并通过circRNA-miRNA-mRNA轴参与肿瘤相关的多种信号通路,从而促进/抑制肿瘤的发生发展及复发转移。
随着高通量测序技术及生物信息学技术的不断发展,circRNA的生成、功能及其与疾病之间的联系逐渐引起科学界的关注[53]。然而与mRNA、miRNA和lncRNA相比,我们对circRNA的认识才刚刚开始。对circRNA的研究将进一步增加我们对基因组非编码序列的认知。基于 circRNA对基因转录的调控作用及其对疾病相关miRNA的吸附作用,circRNA为疾病的治疗提供了新的靶点。由于具有环状闭合结构,circRNAs在体液中具有更高的稳定性,在无创性疾病诊断领域具有巨大的应用前景。环状RNA有望成为非编码RNA研究领域新的热点,未来的研究将进一步揭示环状RNA在人类生理及病理学中发挥的重要作用。
[ 1 ] Koh W, Pan W, Gawad C, et al. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans [J]. Proc Natl Acad Sci U S A, 2014,111(20): 7361-7366.
[ 2 ] Bahn JH, Zhang Q, Li F, et al. The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva [J]. Clin Chem,2015, 61(1): 221-230.
[ 3 ] Salzman J, Chen RE, Olsen MN, et al. Cell-type specific features of circular RNA expression [J]. PLoS Genet, 2013, 9(9): e1003777.
[ 4 ] Jeck WR, Sorrentino JA, Wang K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats [J]. RNA, 2013, 19(2): 141-157.
[ 5 ] Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency [J]. Nature, 2013, 495(7441): 333-338.
[ 6 ] Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges [J]. Nature, 2013, 495(7441): 384-388.
[ 7 ] Zhang Y, Zhang XO, Chen T, et al. Circular intronic long noncoding RNAs [J]. Mol Cell, 2013, 51(6): 792-806.
[ 8 ] Li Z, Huang C, Bao C, et al. Exon-intron circular RNAs regulate transcription in the nucleus [J]. Nat Struct Mol Biol, 2015, 22(3): 256-264.
[ 9 ] Burd CE, Jeck WR, Liu Y, et al. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk [J]. PLoS Genet, 2010, 6(12): e1001233.
[10] Satoh J, Yamamura T. Gene expression profile following stable expression of the cellular prion protein [J]. Cell Mol Neurobiol, 2004, 24(6): 793-814.
[11] Li F, Zhang L, Li W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/beta-catenin pathway [J]. Oncotarget, 2015, 6(8): 6001-6013.
[12] Bachmayr-Heyda A, Reiner AT, Auer K, et al. Correlation of circular RNA abundance with proliferation-exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues [J]. Sci Rep, 2015, 5: 8057.
[13] Li P, Chen S, Chen H, et al. Using circular RNA as a novel type of biomarker in the screening of gastric cancer [J]. Clin Chim Acta, 2015, 444: 132-136.
[14] Hansen TB, Kjems J, Damgaard CK. Circular RNA and miR-7 in cancer [J]. Cancer Res, 2013,73(18): 5609-5612.
[15] Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells [J]. Nature, 1979, 280(5720): 339-340.
[16] Arnberg AC, Van Ommen GJ, Grivell LA, et al. Some yeast mitochondrial RNAs are circular [J]. Cell, 1980, 19(2): 313-319.
[17] Cocquerelle C, Mascrez B, Hétuin D, et al. Mis-splicing yields circular RNA molecules [J]. FASEB J, 1993, 7(1): 155-160.
[18] Nigro JM, Cho KR, Fearon ER, et al. Scrambled exons [J]. Cell, 1991, 64(3): 607-613.
[19] Capel B, Swain A, Nicolis S, et al. Circular transcripts of the testis-determining gene Sry in adult mouse testis [J]. Cell, 1993, 73(5): 1019-1030.
[20] Salzman J, Gawad C, Wang PL, et al. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types [J]. PloS one, 2012, 7(2): e30733.
[21] Rybak-Wolf A, Stottmeister C, Glažar P, et al. Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed [J]. Mol Cell, 2015, 58(5): 870-885.
[22] Guo JU, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs [J]. Genome Biol, 2014, 15(7): 409.
[23] Matera AG, Wang Z. A day in the life of the spliceosome [J]. Nat Rev Mol Cell Biol, 2014, 15(2): 108-121.
[24] Jeck WR, Sharpless NE. Detecting and characterizing circular RNAs [J]. Nat Biotechnol, 2014, 32(5): 453-461.
[25] Dubin RA, Kazmi MA, Ostrer H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript [J]. Gene, 1995, 167(1-2): 245-248.
[26] Zhang XO, Wang HB, Zhang Y, et al. Complementary sequence-mediated exon circularization [J]. Cell, 2014, 159(1): 134-147.
[27] Liang D, Wilusz JE. Short intronic repeat sequences facilitate circular RNA production [J]. Genes Dev, 2014, 28(20): 2233-2247.
[28] Ivanov A, Memczak S, Wyler E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals [J]. Cell Rep, 2015, 10(2): 170-177.
[29] Starke S, Jost I, Rossbach O, et al. Exon circularization requires canonical splice signals [J]. Cell Rep, 2015, 10(1): 103-111.
[30] Ashwal-Fluss R, Meyer M, Pamudurti NR, et al. circRNA biogenesis competes with pre-mRNA splicing [J]. Mol Cell, 2014, 56(1): 55-66.
[31] Vicens Q, Westhof E. Biogenesis of Circular RNAs [J]. Cell, 2014, 159(1): 13-14.
[32] Petkovic S, Muller S. RNA circularization strategies in vivo and in vitro [J]. Nucleic Acids Res, 2015, 43(4): 2454-2465.
[33] Westholm JO, Miura P, Olson S, et al. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation [J]. Cell Rep, 2014, 9(5): 1966-1980.
[34] Conn SJ, Pillman KA, Toubia J, et al. The RNA binding protein quaking regulates formation of circRNAs [J]. Cell, 2015, 160(6): 1125-1134.
[35] Seitz H. Redefining microRNA targets [J]. Curr Biol, 2009,19(10): 870-873.
[36] Shi X, Sun M, Liu H, et al. Long non-coding RNAs: a new frontier in the study of human diseases [J]. Cancer Lett, 2013, 339(2): 159-166.
[37] Taulli R, Loretelli C, Pandolfi PP. From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition [J]. Nat Struct Mol Biol, 2013, 20(5): 541-543.
[38] Hansen TB, Wiklund ED, Bramsen JB, et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA [J]. EMBO J, 2011, 30(21): 4414-4422.
[39] Chen CY, Sarnow P. Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs[J]. Science, 1995, 268(5209): 415-417.
[40] AbouHaidar MG, Venkataraman S, Golshani A, et al. Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt[J]. Proc Natl Acad Sci USA, 2014, 111(40): 14542-14547.
[41] Perriman R, Ares M Jr. Circular mRNA can direct translation of extremely long repeating-sequence proteins in vivo[J]. RNA, 1998, 4(9): 1047-1054.
[42] Yu X, Li Z. The role of MicroRNAs expression in laryngeal cancer [J]. Oncotarget, 2015,6(27):23297-23305.
[43] Junn E, Lee KW, Jeong BS, et al. Repression of alpha-synuclein expression and toxicity by microRNA-7 [J]. Proc Natl Acad Sci U S A, 2009, 106(31): 13052-13057.
[44] Wang Y, Liu J, Liu C, et al. MicroRNA-7 regulates the mTOR pathway and proliferation in adult pancreatic beta-cells [J]. Diabetes, 2013, 62(3): 887-895.
[45] Kefas B, Godlewski J, Comeau L, et al. microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down-regulated in glioblastoma [J]. Cancer Res, 2008, 68(10): 3566-3572.
[46] Reddy SD, Ohshiro K, Rayala SK, et al. MicroRNA-7, a homeobox D10 target, inhibits p21-activated kinase 1 and regulates its functions [J]. Cancer Res, 2008, 68(20): 8195-8200.
[47] Webster RJ, Giles KM, Price KJ, et al. Regulation of epidermal growth factor receptor signaling in human cancer cells by microRNA-7 [J]. J Biol Chem, 2009, 284(9): 5731-5741.
[48] Saydam O, Senol O, Wurdinger T, et al. miRNA-7 attenuation in Schwannoma tumors stimulates growth by upregulating three oncogenic signaling pathways [J]. Cancer Res, 2011, 71(3): 852-861.
[49] Fang Y, Xue JL, Shen Q, et al. MicroRNA-7 inhibits tumor growth and metastasis by targeting the phosphoinositide 3-kinase/Akt pathway in hepatocellular carcinoma [J]. Hepatology, 2012, 55(6): 1852-1862.
[50] Lukiw WJ. Circular RNA (circRNA) in Alzheimer′s disease (AD) [J]. Front Genet, 2013, 4: 307.
[51] Li Y, Zheng Q, Bao C, et al. Circular RNA is enriched and stable in exosomes: a promising biomarker for cancer diagnosis [J]. Cell Res, 2015, 25(8): 981-984.
[52] Zheng Q, Bao C, Guo W, et al. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs [J]. Nat Commun, 2016, 7: 11215.
[53] Fang XY, Pan HF, Leng RX, et al. Long noncoding RNAs: novel insights into gastric cancer [J]. Cancer Lett, 2015, 356 (2 Pt B): 357-366.
[本文编辑] 叶 婷, 贾泽军
Circular RNA: a new research trend of noncoding RNAs
ZHAN Hao, ZHU Kai, HU Zhi-qiang, WANG Peng-cheng, DAI Zhi, HUANG Xiao-wu, ZHOU Jian*
Department of Liver Cancer Institute, Zhongshan Hospital,Fudan University, Shanghai 200032, China
Circular RNAs (circRNAs) are the new type of noncoding RNAs characterized by their circular shape resulting from covalently closed continuous loops and they showed different characteristic with linear RNAs. The majority of circRNAs is conserved across species and with stable expression, and often exhibit tissue and specificity in developmental stage. They are resistant to RNase R, and thus more stable than linear RNAs in fluid. They have significant potential in clinical diagnosis and prognosis biomarker of different diseases. Recent research has revealed that circRNAs can function as microRNA (miRNA) sponges, and modifiers of genetic transcription. Emerging evidence indicates that circRNAs might play important roles in disease of cardiovascular system, neurological disorders, prion diseases and cancer. CircRNA is becoming a new star in the research of RNAs.
circular RNA; noncoding RNAs;miRNA sponge; cancer; biomarker
2016-03-22 [接受日期] 2016-08-11
十二五国家肝病重大专项课题(2012ZX10002-016),国家自然科学杰出青年基金(81225019),国家重点研发计划精准医学研究专项(2016YFC0902400),国家自然科学基金青年科学基金项目(81402376). Supported by the National Key Sci-Tech Special Project of China (2012ZX10002-016), National Science Fund for Distinguished Young Scholar (81225019), National Key Research and Development Plan(2016YFC0902400) and Youth Science Fund Project(81402376).
战 昊,博士生. E-mail: zhanhao860930@hotmail.com
*通信作者(Corresponding author). Tel: 021-64041990, E-mail: zhou.jian@zs-hospital.sh.cn
10.12025/j.issn.1008-6358.2016.20160316
综 述
Q 522
A