Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/36172
標題: 阿拉伯芥非編碼RNA之研究:生物資訊應用於small RNA序列資料分析
Exploring the Arabidopsis Non-coding RNAs: Inference from the Bioinformatic Analyses of Small RNA Sequencing Data
作者: 陳荷明
Chen, Ho-Ming
關鍵字: Arabidopsis
阿拉伯芥
high-throughput sequencing
bioinformatics
ta-siRNA
snoRNA
大規模定序
生物資訊
反式作用小型干擾核醣核酸 小核仁核醣核酸
出版社: 生物科技學研究所
引用: Addo-Quaye, C., Eshoo, T.W., Bartel, D.P., and Axtell, M.J. (2008). Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18, 758-762. Adenot, X., Elmayan, T., Lauressergues, D., Boutet, S., Bouche, N., Gasciolli, V., and Vaucheret, H. (2006). DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7. Curr Biol 16, 927-932. Allen, E., Xie, Z., Gustafson, A.M., and Carrington, J.C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207-221. Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006). A Two-Hit Trigger for siRNA Biogenesis in Plants. Cell 127, 565-577. Bachellerie, J.P., Cavaille, J., and Huttenhofer, A. (2002). The expanding snoRNA world. Biochimie 84, 775-790. Barneche, F., Steinmetz, F., and Echeverria, M. (2000). Fibrillarin genes encode both a conserved nucleolar protein and a novel small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis thaliana. J Biol Chem 275, 27212-27220. Barneche, F., Gaspin, C., Guyot, R., and Echeverria, M. (2001). Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2''-O-methylation sites. J Mol Biol 311, 57-73. Baumberger, N., and Baulcombe, D.C. (2005). Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A 102, 11928-11933. Bonnet, E., Wuyts, J., Rouze, P., and Van de Peer, Y. (2004). Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A 101, 11511-11516. Borsani, O., Zhu, J., Verslues, P.E., Sunkar, R., and Zhu, J.K. (2005). Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279-1291. Brodersen, P., and Voinnet, O. (2006). The diversity of RNA silencing pathways in plants. Trends Genet 22, 268-280. Brown, J.W., Echeverria, M., and Qu, L.H. (2003a). Plant snoRNAs: functional evolution and new modes of gene expression. Trends Plant Sci 8, 42-49. Brown, J.W., Echeverria, M., Qu, L.H., Lowe, T.M., Bachellerie, J.P., Huttenhofer, A., Kastenmayer, J.P., Green, P.J., Shaw, P., and Marshall, D.F. (2003b). Plant snoRNA database. Nucleic Acids Res 31, 432-435. Chanfreau, G., Legrain, P., and Jacquier, A. (1998). Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J Mol Biol 284, 975-988. Chapman, E.J., and Carrington, J.C. (2007). Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8, 884-896. Chen, C.L., Chen, C.J., Vallon, O., Huang, Z.P., Zhou, H., and Qu, L.H. (2008). Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas reinhardtii reveals an extensive organization into intronic gene clusters. Genetics 179, 21-30. Chen, X. (2005). MicroRNA biogenesis and function in plants. FEBS Lett 579, 5923-5931. Clouet d''Orval, B., Bortolin, M.L., Gaspin, C., and Bachellerie, J.P. (2001). Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. Nucleic Acids Res 29, 4518-4529. Darzacq, X., Jady, B.E., Verheggen, C., Kiss, A.M., Bertrand, E., and Kiss, T. (2002). Cajal body-specific small nuclear RNAs: a novel class of 2''-O-methylation and pseudouridylation guide RNAs. EMBO J 21, 2746-2756. Dunbar, D.A., Wormsley, S., Lowe, T.M., and Baserga, S.J. (2000). Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2''-O-ribose methylation of rRNA. J Biol Chem 275, 14767-14776. Edvardsson, S., Gardner, P.P., Poole, A.M., Hendy, M.D., Penny, D., and Moulton, V. (2003). A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19, 865-873. Ender, C., Krek, A., Friedlander, M.R., Beitzinger, M., Weinmann, L., Chen, W., Pfeffer, S., Rajewsky, N., and Meister, G. (2008). A Human snoRNA with MicroRNA-Like Functions. Mol Cell 32, 519-528. Fahlgren, N., Montgomery, T.A., Howell, M.D., Allen, E., Dvorak, S.K., Alexander, A.L., and Carrington, J.C. (2006). Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA Affects Developmental Timing and Patterning in Arabidopsis. Curr Biol 16, 939-944. Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L., and Carrington, J.C. (2007). High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2, e219. Felippes, F.F., and Weigel, D. (2009). Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Rep 10, 264-270. Ganot, P., Caizergues-Ferrer, M., and Kiss, T. (1997). The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes Dev 11, 941-956. Garcia, D., Collier, S.A., Byrne, M.E., and Martienssen, R.A. (2006). Specification of Leaf Polarity in Arabidopsis via the trans-Acting siRNA Pathway. Curr Biol 16, 933-938. Gasciolli, V., Mallory, A.C., Bartel, D.P., and Vaucheret, H. (2005). Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol 15, 1494-1500. German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R., De Paoli, E., Lu, C., Schroth, G., Meyers, B.C., and Green, P.J. (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26, 941-946. Gregory, B.D., O''Malley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., and Ecker, J.R. (2008). A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14, 854-866. Gustafson, A.M., Allen, E., Givan, S., Smith, D., Carrington, J.C., and Kasschau, K.D. (2005). ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res 33, D637-640. Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J., and Jacobsen, S.E. (2006). Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38, 721-725. Howell, M.D., Fahlgren, N., Chapman, E.J., Cumbie, J.S., Sullivan, C.M., Givan, S.A., Kasschau, K.D., and Carrington, J.C. (2007). Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19, 926-942. Hunter, C., Willmann, M.R., Wu, G., Yoshikawa, M., de la Luz Gutierrez-Nava, M., and Poethig, S.R. (2006). Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis. Development 133, 2973-2981. Jacobsen, S.E., Running, M.P., and Meyerowitz, E.M. (1999). Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development 126, 5231-5243. Jady, B.E., and Kiss, T. (2001). A small nucleolar guide RNA functions both in 2''-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA. EMBO J 20, 541-551. Jady, B.E., Darzacq, X., Tucker, K.E., Matera, A.G., Bertrand, E., and Kiss, T. (2003). Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm. EMBO J 22, 1878-1888. Jones-Rhoades, M.W., and Bartel, D.P. (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14, 787-799. Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., and Carrington, J.C. (2007). Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5, e57. Kawaji, H., Nakamura, M., Takahashi, Y., Sandelin, A., Katayama, S., Fukuda, S., Daub, C.O., Kai, C., Kawai, J., Yasuda, J., Carninci, P., and Hayashizaki, Y. (2008). Hidden layers of human small RNAs. BMC Genomics 9, 157. Kishore, S., and Stamm, S. (2006). The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230-232. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M., and Kiss, T. (1996). Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077-1088. Kiss, A.M., Jady, B.E., Bertrand, E., and Kiss, T. (2004). Human box H/ACA pseudouridylation guide RNA machinery. Mol Cell Biol 24, 5797-5807. Lau, N.C., Seto, A.G., Kim, J., Kuramochi-Miyagawa, S., Nakano, T., Bartel, D.P., and Kingston, R.E. (2006). Characterization of the piRNA Complex from Rat Testes. Science. Lestrade, L., and Weber, M.J. (2006). snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34, D158-162. Lister, R., O''Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H., and Ecker, J.R. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536. Lowe, T.M., and Eddy, S.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955-964. Lowe, T.M., and Eddy, S.R. (1999). A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168-1171. Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C., and Green, P.J. (2005). Elucidation of the small RNA component of the transcriptome. Science 309, 1567-1569. Lu, C., Kulkarni, K., Souret, F.F., MuthuValliappan, R., Tej, S.S., Poethig, R.S., Henderson, I.R., Jacobsen, S.E., Wang, W., Green, P.J., and Meyers, B.C. (2006). MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res 16, 1276-1288. Maden, B.E. (1990). The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol 39, 241-303. Mallory, A.C., and Vaucheret, H. (2006). Functions of microRNAs and related small RNAs in plants. Nat Genet 38 Suppl, S31-36. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., and Rothberg, J.M. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380. Marker, C., Zemann, A., Terhorst, T., Kiefmann, M., Kastenmayer, J.P., Green, P., Bachellerie, J.P., Brosius, J., and Huttenhofer, A. (2002). Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana. Curr Biol 12, 2002-2013. Massenet, S., Mougin, A., and Branlant, C. (1998). Posttranscriptional modifications in the U small nuclear RNAs. In Grosjean,H. and Benne,R. (eds), Modification and Editing of RNA. ASM Press, Washington, DC, pp. 201-227 Matera, A.G., Terns, R.M., and Terns, M.P. (2007). Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8, 209-220. Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G.J., and Qi, Y. (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5'' terminal nucleotide. Cell 133, 116-127. Montgomery, T.A., Howell, M.D., Cuperus, J.T., Li, D., Hansen, J.E., Alexander, A.L., Chapman, E.J., Fahlgren, N., Allen, E., and Carrington, J.C. (2008a). Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133, 128-141. Montgomery, T.A., Yoo, S.J., Fahlgren, N., Gilbert, S.D., Howell, M.D., Sullivan, C.M., Alexander, A., Nguyen, G., Allen, E., Ahn, J.H., and Carrington, J.C. (2008b). AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A 105, 20055-20062. Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L., and Poethig, R.S. (2004). SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18, 2368-2379. Piekna-Przybylska, D., Decatur, W.A., and Fournier, M.J. (2007). New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. Rna 13, 305-312. Qi, Y., Denli, A.M., and Hannon, G.J. (2005). Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 19, 421-428. Qu, L.H., Henras, A., Lu, Y.J., Zhou, H., Zhou, W.X., Zhu, Y.Q., Zhao, J., Henry, Y., Caizergues-Ferrer, M., and Bachellerie, J.P. (1999). Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol Cell Biol 19, 1144-1158. Rajagopalan, R., Vaucheret, H., Trejo, J., and Bartel, D.P. (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20, 3407-3425. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520. Richard, P., Darzacq, X., Bertrand, E., Jady, B.E., Verheggen, C., and Kiss, T. (2003). A common sequence motif determines the Cajal body-specific localization of box H/ACA scaRNAs. EMBO J 22, 4283-4293. Rivas, E., and Eddy, S.R. (2001). Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2, 8. Schattner, P., Barberan-Soler, S., and Lowe, T.M. (2006). A computational screen for mammalian pseudouridylation guide H/ACA RNAs. RNA 12, 15-25. Schattner, P., Decatur, W.A., Davis, C.A., Ares, M., Jr., Fournier, M.J., and Lowe, T.M. (2004). Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Res 32, 4281-4296. Stark, B.C., Kole, R., Bowman, E.J., and Altman, S. (1978). Ribonuclease P: an enzyme with an essential RNA component. Proc Natl Acad Sci U S A 75, 3717-3721. Talmor-Neiman, M., Stav, R., Klipcan, L., Buxdorf, K., Baulcombe, D.C., and Arazi, T. (2006). Identification of trans-acting siRNAs in moss and an RNA-dependent RNA polymerase required for their biogenesis. Plant J. Tycowski, K.T., Aab, A., and Steitz, J.A. (2004). Guide RNAs with 5'' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. Curr Biol 14, 1985-1995. Vaucheret, H. (2006). Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20, 759-771. Vazquez, F., Vaucheret, H., Rajagopalan, R., Lepers, C., Gasciolli, V., Mallory, A.C., Hilbert, J.L., Bartel, D.P., and Crete, P. (2004). Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16, 69-79. Wang, B.B., and Brendel, V. (2004). The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol 5, R102. Wang, X.J., Reyes, J.L., Chua, N.H., and Gaasterland, T. (2004). Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 5, R65. Wassenegger, M. (2005). The role of the RNAi machinery in heterochromatin formation. Cell 122, 13-16. Watkins, N.J., Dickmanns, A., and Luhrmann, R. (2002). Conserved stem II of the box C/D motif is essential for nucleolar localization and is required, along with the 15.5K protein, for the hierarchical assembly of the box C/D snoRNP. Mol Cell Biol 22, 8342-8352. Watkins, N.J., Segault, V., Charpentier, B., Nottrott, S., Fabrizio, P., Bachi, A., Wilm, M., Rosbash, M., Branlant, C., and Luhrmann, R. (2000). A common core RNP structure shared between the small nucleoar box C/D RNPs and the spliceosomal U4 snRNP. Cell 103, 457-466. Westin, G., Lund, E., Murphy, J.T., Pettersson, U., and Dahlberg, J.E. (1984). Human U2 and U1 RNA genes use similar transcription signals. EMBO J 3, 3295-3301. Williams, L., Carles, C.C., Osmont, K.S., and Fletcher, J.C. (2005). A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc Natl Acad Sci U S A 102, 9703-9708. Wold, B., and Myers, R.M. (2008). Sequence census methods for functional genomics. Nat Methods 5, 19-21. Xie, Z., Allen, E., Wilken, A., and Carrington, J.C. (2005). DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A 102, 12984-12989. Yang, J.H., Zhang, X.C., Huang, Z.P., Zhou, H., Huang, M.B., Zhang, S., Chen, Y.Q., and Qu, L.H. (2006). snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res 34, 5112-5123. Yoshikawa, M., Peragine, A., Park, M.Y., and Poethig, R.S. (2005). A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19, 2164-2175. Zhang, X., Henderson, I.R., Lu, C., Green, P.J., and Jacobsen, S.E. (2007). Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A 104, 4536-4541. Zhang, Y. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33, W701-704. Zilberman, D., and Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: selective silence. Curr Opin Genet Dev 15, 557-562. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.
摘要: 非編碼RNA在蛋白質轉譯、基因剪接、RNA修飾、RNA加工和調控基因表現扮演重要的角色。隨著分子生物學新技術的發展和新種類非編碼RNA的發現,尋找更多非編碼RNA的方法也不斷革新。高效能定序技術對20-30 nt small regulatory RNA的研究有很大的貢獻。高效能大量定序18-26 nt small RNA所產生的資料中不只包含了small regulatory RNA,也包括了從編碼或非編碼RNA降解而來的小片段產物。在分析大量small RNA序列資料時,選擇適當的計算方法對區分不同來源的small RNA、是否可以發掘新類型的非編碼RNA以及可否揭露其中所隱含的知識有決定性的影響。目前大部分計算方法的發展都集中在尋找microRNA (miRNA)。應用small RNA定序資料在研究其它非編碼RNA的計算方法,尚付之闕如。本論文著重於發展新的生物資訊方法來分析small RNA定序資料,以增進對阿拉伯芥非編碼RNA的了解。 本研究第一部分利用資料庫中大量阿拉伯芥small RNA 序列資料,開發新的生物資訊方法來尋找一種稱為trans-acting siRNA (ta-siRNA)的small regulatory RNA。不同於其它siRNA, 此類siRNA的生合成需要miRNA促成的截切。此外,大部分的ta-siRNA彼此之間和相對於截切點的距離是21的倍數。利用此一特點,本論文開發出第一個計算方法可以從複雜的small RNA序列資料中成功地找到已知和新的會產生ta-siRNA的阿拉伯芥基因。不同於以往發現的ta-siRNAs,其中一群新發現的ta-siRNAs的生合成需要的是另一個ta-siRNA促成的截切,而不是miRNA。本研究結果發現了一條前所未見的small regulatory RNA之連鎖生合成路徑。這路徑從一個miRNA開始,緊接著的是連續兩階層ta-siRNA的產生。 第二部分,則是應用small RNA序列資料去尋找小核仁RNA(small nucleolar RNA)。過去的研究多認為從小核仁RNA來的small RNA是降解而來的產物,所以多予以忽略而未詳加分析。但從分析阿拉伯芥small RNA序列資料中,我發現小核仁RNA的兩端會產生較多的small RNA。利用這樣的特性,本論文得以發展出新的運算方法,來重新註解缺乏明確邊界的小核仁RNA和發掘新的小核仁RNA。而根據這些新找到的小核仁RNA,也得以進一步推論出阿拉伯芥核糖體RNA(rRNA)和剪接體小核內RNA(small nuclear RNA)上存在有先前未鑑定出的RNA修飾點。 本研究顯示,結合生物學已知知識和大量核酸定序資料,可以推衍出嶄新的生物資訊演算法,用於探勘分析small RNA序列資料,對small regulatory RNA或其它非編碼RNA的研究有莫大的助益。
Non-coding RNAs (ncRNAs) play vital roles in translation, splicing, RNA processing, RNA modification and regulation of gene expression. The advancement in ncRNA discovery is evolving along with the finding of new classes of ncRNAs and the invention of revolutionary sequencing platforms. High-throughput sequencing technologies greatly facilitate the study of small regulatory RNAs which are 20 to 30 nt in length. High-throughput sequencing data of 18-26 nt small RNA fragments are a mixture of small regulatory RNAs and degraded products from coding RNAs or ncRNAs. The proper choice of computational approaches in analyzing small RNA sequencing data is crucial for the dissection of small RNAs derived from distinct origins, for making discovery of new ncRNAs and for revealing embedded knowledge in these ncRNAs. To date, the development of computational approaches mostly focused on the discovery of microRNAs (miRNAs). Computational approaches which use small RNA sequencing data for the studies of other ncRNAs are much in need. This dissertation presents the development of novel bioinformatics approaches to analyze small RNA sequencing data and showed that the analyses have increased the understandings of Arabidopsis ncRNAs. In first part, by the use of abundant small RNA sequencing data from the public domain, a new bioinformatics approach was developed for the finding of trans-acting small interfering RNAs (ta-siRNAs), a new class of small regulatory RNAs. Different from that of other siRNAs, the biogenesis of ta-siRNAs is dependent on the cleavage directed by miRNAs. Moreover, most ta-siRNAs are clustered in 21-nt increments relative to the cleavage site. Based on this characteristic, this study developed the first computational algorithm which successfully recovered both known and novel Arabidopsis loci producing ta-siRNAs from complex small RNA sequencing data. A group of newly identified ta-siRNAs was produced by the cleavage directed by a ta-siRNA instead of by miRNAs as was reported previously. The results indicate the existence of a small RNA regulatory cascade initiated by miRNA-directed cleavage and followed by the consecutive production of ta-siRNAs. The second part focuses on the use of small RNA sequencing data in the annotation of small nucleolar RNAs (snoRNAs). Small RNAs from snoRNAs are often considered to be degraded products of snoRNAs and were filtered out without further analysis in previous studies. However, the analysis of Arabidopsis small RNA sequencing data revealed an enrichment of small RNAs at the termini of snoRNAs. With the use of this feature, this study developed a new method which was able to re-annotate known snoRNAs lacking well defined termini and to discover novel snoRNA species. The finding of new snoRNAs also supported that there are additional RNA modification sites on Arabidopsis ribosomal RNAs and spliceosomal small nuclear RNAs. This research demonstrates that, by combining pre-existing biological knowledge and appropriate mining approaches, small RNA sequencing data represent a wealth treasure for the studies of small regulatory RNAs as well as other ncRNAs.
URI: http://hdl.handle.net/11455/36172
其他識別: U0005-1803200914014800
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-1803200914014800
Appears in Collections:生物科技學研究所

文件中的檔案:

取得全文請前往華藝線上圖書館

Show full item record
 
TAIR Related Article
 
Citations:


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.