生物技术通报 ›› 2016, Vol. 32 ›› Issue (9): 23-31.doi: 10.13560/j.cnki.biotech.bull.1985.2016.09.004
宋娜娜, 柴志欣, 钟金城
收稿日期:
2016-01-19
出版日期:
2016-09-25
发布日期:
2016-10-10
作者简介:
宋娜娜,女,硕士研究生,研究方向:基因组与分子生物学;E-mail:songnana28@126.com
基金资助:
SONG Na-na, CHAI Zhi-xin, ZHONG Jin-cheng
Received:
2016-01-19
Published:
2016-09-25
Online:
2016-10-10
摘要: 人类基因组计划完成证实,人类共有3-3.5万个编码基因,这些基因所涵盖的编码信息仅占人类30亿个碱基对中携带遗传信息的1.5%,其余超过98%的遗传信息并不直接编码蛋白质。近些年来由于测序技术的飞速发展,人们发现这部分遗传信息与调控、剪切、转录等生物过程密切相关,其中长链非编码RNA具有表观遗传学调控、转录调控、疾病调控、细胞分化和个体发育等重要的生命过程的调控等过程,因此如何寻找RAN的功能单元和预测新的长链非编码RNA成为很重要的问题。就非编码RNA的起源与进化进行阐述,综述了长链非编码RNA在癌症上的功能,综合了长链非编码RNA一些常见的数据库及使用最新的生物信息学手段和相关技术预测长链非编码RNA,并进行进一步的功能研究。
宋娜娜, 柴志欣, 钟金城. 长链非编码RAN的研究进展[J]. 生物技术通报, 2016, 32(9): 23-31.
SONG Na-na, CHAI Zhi-xin, ZHONG Jin-cheng. Research Advances on Long Non-coding RNA[J]. Biotechnology Bulletin, 2016, 32(9): 23-31.
[1] ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome[J]. Nature, 2012, 489(7414), 57-74. [2] Morris KV, Mattick JS. The rise of regulatory RNA[J]. Nature Reviews Genetics, 2014, 15(6):423-437. [3] Necsulea A, Soumillon M, Warnefors M, et al. The evolution of lncRNA repertoires and expression patterns in tetrapods[J]. Nature, 2014, 505(7485):635-640. [4] Scotti MM, Swanson MS. RNA mis-splicing in disease[J]. Nature Reviews Genetics, 2016, 17(1):19-32. [5] 陈润生. 关于非编码 RNA 研究的一些思考[C]. 第四届全国生物信息学与系统生物学学术大会论文集, 2010. [6] Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14[J]. Cell, 1993, 75(5):843-854. [7] Fire A, Xu SQ, Montgomery MK, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans[J]. Nature, 1998, 391(6669):806-811. [8] Elbashir SM, Harborth J, Lendeckel W, et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells[J]. Nature, 2001, 411(6836):494-498. [9] Kung JTY, Colognori D, Lee JT. Long noncoding RNAs:past, present, and future[J]. Genetics, 2013, 193(3):651-669. [10] Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60, 770 full-length cDNAs[J]. Nature, 2002, 420(6915):563-573. [11] Rinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs[J]. Cell, 2007, 129(7):1311-1323. [12] Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene[J]. Nature, 1991, 351(6322):153-155. [13] Brockdorff N, Ashworth A, Kay GF, et al. Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome[J]. Nature, 1991, 351(6324):329-331. [14] Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation[J]. Cell, 2010, 143(3):390-403. [15] Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals[J]. Nature, 2009, 458:223-227. [16] Yoon JH, Abdelmohsen K, Srikantan S, et al. LincRNA-p21 suppresses target mRNA translation[J]. Molecular Cell, 2012, 47(4):648-655. [17] Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation[J]. Nature Structural & Molecular Biology, 2013, 20(3):300-307. [18] Tsai MC, Spitale RC, Chang HY. Long intergenic noncoding RNAs:New links in cancer progression[J]. Cancer Res, 2011, 71:3-7. [19] Wapinski O, Chang HY. Long noncoding RNAs and human disease[J]. Trends Cell Biol, 2011, 21:354-361. [20] Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs[J]. Molecular Cell, 2011, 43(6):904-914. [21] Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs[J]. Nature, 2012, 482(7385):339-346. [22] Batista PJ, Chang HY. Long noncoding RNAs:cellular address codes in development and disease[J]. Cell, 2013, 152(6):1298-1307. [23] Kim TK, Hemberg M, Gray JM, et al. Widespread transcription at neuronal activity-regulated enhancers[J]. Nature, 2010, 465(7295):182-187. [24] Salmena L, Poliseno L, Tay Y, et al. A ceRNA hypothesis:the Rosetta Stone of a hidden RNA language?[J]. Cell, 2011, 146(3):353-358. [25] Djebali S, Davis CA, Merkel A, et al. Landscape of transcription in human cells[J]. Nature, 2012, 489(7414):101-108. [26] Li A, Zhang J, Zhou Z. PLEK:a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme[J]. BMC Bioinformatics, 2014, 15(1):311. [27] Yang JH, Li JH, Jiang S, et al. ChIPBase:a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data[J]. Nucleic Acids Research, 2013, 41(D1):D177-D187. [28] Volders PJ, Verheggen K, Menschaert G, et al. An update on LNCipedia:a database for annotated human lncRNA sequences[J]. Nucleic Acids Research, 2015, 43(D1):D174-D180. [29] Amaral PP, Clark MB, Gascoigne DK, et al. lncRNAdb:a reference database for long noncoding RNAs[J]. Nucleic Acids Research, 2011, 39(Suppl 1):D146-D151. [30] Chen G, Wang Z, Wang D, et al. LncRNADisease:a database for long-non-coding RNA-associated diseases[J]. Nucleic Acids Research, 2013, 41(D1):D983-D986. [31] Xie C, Yuan J, Li H, et al. NONCODEv4:exploring the world of long non-coding RNA genes[J]. Nucleic Acids Research, 2014, 42(D1):D98-D103. [32] Dinger ME, Pang KC, Mercer TR, et al. NRED:a database of long noncoding RNA expression[J]. Nucleic Acids Research, 2009, 37(suppl 1):D122-D126. [33] Erdmann VA, Szymanski M, Hochberg A, et al. Non-coding, mRNA-like RNAs database Y2K[J]. Nucleic Acids Research, 2000, 28(1):197-200. [34] Li A, Zhang J, Zhou Z, et al. ALDB:a domestic-animal long noncoding RNA database[J]. PLoS One, 2015, 10(4):e0124003. [35] Bhartiya D, Pal K, Ghosh S, et al. lncRNome:a comprehensive knowledgebase of human long noncoding RNAs[J]. Database, 2013, 2013:bat034. [36] Szymanski M, Erdmann VA, Barciszewski J. Noncoding RNAs database(ncRNAdb)[J]. Nucleic Acids Research, 2007, 35 (Suppl 1):D162-D164. [37] Gardner PP, Daub J, Tate JG, et al. Rfam:updates to the RNA families database[J]. Nucleic Acids Research, 2009, 37(Suppl 1):D136-D140. [38] Nawrocki EP, Burge SW, Bateman A, et al. Rfam 12. 0:updates to the RNA families database[J]. Nucleic Acids Research, 2014:gku1063. [39] Panzitt K, Tschernatsch MMO, Guelly C, et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA[J]. Gastroenterology, 2007, 132(1):330-342. [40] Romanuik TL, Wang G, Morozova O, et al. LNCaP Atlas:gene expression associated with in vivo progression to castration-recurrent prostate cancer[J]. BMC Medical Genomics, 2010, 3(1):43. [41] Castle JC, Armour CD, Löwer M, et al. Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification[J]. 2010, 5(7):e11779. [42] Poirier F, Chan CT, Timmons PM, et al. The murine H19 gene is activated during embryonic stem cell differentiation in vitro and at the time of implantation in the developing embryo[J]. Development, 1991, 113(4):1105-1114. [43] Lustig O, Ariel I, Ilan J, et al. Expression of the imprinted gene H19 in the human fetus[J]. Molecular Reproduction and Development, 1994, 38(3):239-246. [44] Matouk I, DeGroot N, Mezan S, et al. The H19 non-coding RNA is essential for human tumor growth and may serve as an anti-tumor target[C]//Human Gene Therapy. 140 Huguenot Street, 3rd FL, New Rochelle, NY 10801 USA:Mary Ann Liebert INC, 2007, 18(10):1034-1034. [45] Barsyte-Lovejoy D, Lau SK, Boutros PC, et al. The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis[J]. Cancer Research, 2006, 66(10):5330-5337. [46] Berteaux N, Lottin S, Monté D, et al. H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1[J]. Journal of Biological Chemistry, 2005, 280(33):29625-29636. [47] Dugimont T, Montpellier C, Adriaenssens E, et al. The H19 TATA-less promoter is efficiently repressed by wild-type tumor suppressor gene product p53[J]. Oncogene, 1998, 16(18):2395-2401. [48] Farnebo M, Bykov VJN, Wiman KG. The p53 tumor suppressor:a master regulator of diverse cellular processes and therapeutic target in cancer[J]. Biochemical and Biophysical Research Communications, 2010, 396(1):85-89. [49] Cai X, Cullen BR. The imprinted H19 noncoding RNA is a primary microRNA precursor[J]. RNA, 2007, 13(3):313-316. [50] Tsang WP, Ng EKO, Ng SSM, et al. Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer[J]. Carcinogenesis, 2010, 31(3):350-358. [51] Baniol M, Hagege H, Petit JS, et al. Long-range chromatin interactions at the mouse Igf2/H19 locus reveal a novel paternally expressed long non-coding RNA[J]. Nucleic Acids Research, 2011, 39(14):5893-5906. [52] Rinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs[J]. Cell, 2007, 129(7):1311-1323. [53] Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis[J]. Nature, 2010, 464(7291):1071-1076. [54] Tsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes[J]. Science, 2010, 329(5992):689-693. [55] Simon JA, Kingston RE. Occupying chromatin:Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put[J]. Molecular Cell, 2013, 49(5):808-824. [56] Hayami S, Kelly JD, Cho HS, et al. Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers[J]. International Journal of Cancer, 2011, 128(3):574-586. [57] Ling H, Spizzo R, Atlasi Y, et al. CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer[J]. Genome Research, 2013, 23(9):1446-1461. [58] Redis RS, Sieuwerts AM, Look MP, et al. CCAT2, a novel long non-coding RNA in breast cancer:expression study and clinical correlations[J]. Oncotarget, 2013, 4(10):1748. [59] Hung T, Chang HY. Long noncoding RNA in genome regulation:prospects and mechanisms[J]. RNA Biology, 2010, 7(5):582-585. [60] Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs:analysis of their gene structure, evolution, and expression[J]. Genome Research, 2012, 22(9):1775-1789. [61] Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals[J]. Nature, 2009, 458(7235):223-227. [62] Gibb EA, Vucic EA, Enfield KS, et al. Human cancer long non-coding RNA transcriptomes[J]. PLoS One, 2011, 6(10):e25915. [63] Lee TL, Xiao A, Rennert OM. Identification of novel long noncoding RNA transcripts in male germ cells[M]//Germline Development. Springer New York, 2012:105-114. [64] Nam JW, Bartel DP. Long noncoding RNAs in C. elegans[J]. Genome Research, 2012, 22(12):2529-2540. [65] Prensner JR, Iyer MK, Balbin OA, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression[J]. Nature Biotechnology, 2011, 29(8):742-749. [66] Zhao J, Sun BK, Erwin JA, et al. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome[J]. Science, 2008, 322(5902):750-756. [67] Liu J, Gough J, Rost B. Distinguishing protein-coding from non-coding RNAs through support vector machines[J]. PLoS Genet, 2006, 2(4):e29. [68] Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST:a new generation of protein database search programs[J]. Nucleic Acids Research, 1997, 25(17):3389-3402. [69] Kong L, Zhang Y, Ye ZQ, et al. CPC:assess the protein-coding potential of transcripts using sequence features and support vector machine[J]. Nucleic Acids Research, 2007, 35(Suppl 2):W345-W349. [70] Lu ZJ, Yip KY, Wang G, et al. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data[J]. Genome Research, 2011, 21(2):276-285. [71] Chinwalla AT, Cook LL, Delehaunty KD, et al. Initial sequencing and comparative analysis of the mouse genome[J]. Nature, 2002, 420(6915):520-562. [72] Gorodkin J, Cirera S, Hedegaard J, et al. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1, 021, 891 expressed sequence tags[J]. Genome Biology, 2007, 8(4):R45. [73] Andersen ES, Rosenblad MA, Larsen N, et al. The tmRDB and SRPDB resources[J]. Nucleic Acids Research, 2006, 34(Suppl 1):D163-D168. [74] Brown JW. The ribonuclease P database[J]. Nucleic Acids Research, 1999, 27(1):314-314. [75] Weinberg Z, Ruzzo WL. Faster genome annotation of non-coding RNA families without loss of accuracy[C]//Proceedings of the eighth annual international conference on Resaerch in computational molecular biology. ACM, 2004:243-251. [76] Nawrocki EP, Eddy SR. Query-dependent banding(QDB)for faster RNA similarity searches[J]. PLoS Comput Biol, 2007, 3:e56. [77] Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1. 0:inference of RNA alignments[J]. Bioinformatics, 2009, 25(10):1335-1337. [78] Ellis JC, Brown JW. The evolution of RNase P and its RNA[M]//Ribonuclease P. Springer New York, 2010:17-40. [79] Xie M, Mosig A, Qi X, et al. Structure and function of the smallest vertebrate telomerase RNA from teleost fish[J]. Journal of Biological Chemistry, 2008, 283(4):2049-2059. [80] Yang L, Duff MO, Graveley BR, et al. Genomewide characterization of non-polyadenylated RNAs[J]. Genome Biol, 2011, 2:R16. |
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