微小核糖核酸(micro RNA, miRNA)是一種長度約為22個核苷酸的小型核醣核酸，在細胞中可以藉由剪切信使核糖核酸(messenger RNA, mRNA)或是抑制轉譯作用(translation inhibition)的方式，在轉錄後階段(post-transcriptional level)調控基因表現。現今關於微小核醣核酸的研究大致上可以分成三個方向：辨認新的微小核糖核酸、尋找已知微小核糖核酸標的(miRNA target)以及研究微小核醣核酸表現之調控。本篇研究將涵蓋這三個研究方向，並依照內容分成兩大部分。在辨認新的微小核糖核酸這個部分，雖然已經有一些利用機器學習(machine learning)所開發的預測工具，可以根據高通量次世代定序(high-throughput next generation sequencing)的資料找出可能的微小核糖核酸，但是大多都需要該物種的基因體(genome)序列作為辨認的依據。因此對於基因體尚未定序完成的非模式生物(non-model organism)，這些工具並沒有辦法鑑定出可能的微小核糖核酸。為了要在非模式生物中鑑定出微小核糖核酸，在此篇研究中應用向量支持器演算法(support vector machine, SVM)以及微小核糖核酸的特性（包含5'端的尿嘧啶、微小核糖核酸兩股序列數量差異以及其配對結構）建構出能夠在次世代定序資料中辨識出微小核糖核酸的預測模型。此外，此篇研究中藉由分析阿拉伯芥中微小核糖核酸以及蛋白質的基因，得到共同表現的蛋白質基因以及微小核糖核酸，再根據他們的啟動子(promoter)序列找出可能的轉錄因子(transcription factor)以及轉錄因子結合位(transcription factor binding site)。將這些轉錄因子以及預測或是實驗驗證的微小核糖核酸標的整合成完整的阿拉伯芥微小核糖核酸調控網路，並陳列在名為AtmiRNET (http://atmirnet.itps.ncku.edu.tw/)的網頁上供查詢。

MicroRNAs are endogenous non-coding small RNAs (about 22 nucleotides), which play important roles in post-transcriptional regulation of gene expression via mRNA cleavage or translation inhibition. The major topics of miRNA research can be classified into three parts: novel miRNA identification, miRNA target recognition, and transcriptional regulation of miRNA expression. However, no relevant research comprehensively integrates all these three parts so far. For the discovery of novel miRNAs, although several machine learning-based approaches were developed to identify novel miRNAs from high-throughput next generation sequencing (NGS), most of them essentially require precursor/genomic sequences for reference, especially focusing on pre-miRNA identification. Hence, non-availability of genomic sequences becomes a limitation in miRNA discovery in non-model organisms. It is necessary to develop a systematic approach to identify novel miRNAs without reference sequences. In order to identify miRNAs from non-model organisms, support vector machine (SVM) algorithm was used to build a prediction model for novel miRNA identification from NGS datasets with significant features of mature miRNA, including 5’-uracil, the difference of read count between guide and passenger strand of miRNA precursor, and the paired structure of dicer cleavage site. On the other hand, a web-based resource, AtmiRNET, was established to systematically reconstruct regulatory networks of miRNAs in Arabidopsis. Followed up the series of analytical functions (i.e., promoters, regulators, targets, and networks) in AtmiRNET, reliable miRNA promoters, TF-miRNA relations, and direct and indirect targets are recommended to execute functional enrichment analysis and network reconstruction of Arabidopsis miRNAs. The valuable information that is visually oriented in AtmiRNET recruits the scant understanding of plant miRNAs.

Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T., & Jewell, D. (2003). MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr Biol, 13(10), 807-818.
Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., . . . Tuschl, T. (2003). The small RNA profile during Drosophila melanogaster development. Dev Cell, 5(2), 337-350.
Baigude, H., Ahsanullah, Li, Z., Zhou, Y., & Rana, T. M. (2012). miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew Chem Int Ed Engl, 51(24), 5880-5883.
Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., . . . Soboleva, A. (2013). NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res, 41(D1), D991-D995.
Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2), 281-297.
Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., . . . Lander, E. S. (2005). Genomic maps and comparative analysis of histone modifications in human and mouse. Cell, 120(2), 169-181.
Bernstein, E., Caudy, A. A., Hammond, S. M., & Hannon, G. J. (2001). Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409(6818), 363-366.
Bracht J Fau - Bracht, J., Hunter S Fau - Hunter, S., Eachus R Fau - Eachus, R., Weeks P Fau - Weeks, P., & Pasquinelli Ae Fau - Pasquinelli, A. E. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts.
Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., & Cohen, S. M. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell, 113(1), 25-36.
Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y. Y., Sieburth, L., & Voinnet, O. (2008). Widespread translational inhibition by plant miRNAs and siRNAs. Science, 320(5880), 1185-1190.
Cai X Fau - Cai, X., Hagedorn Ch Fau - Hagedorn, C. H., & Cullen Br Fau - Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs.
Cai, X. Z., Hagedorn, C. H., & Cullen, B. R. (2004). Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. Rna-a Publication of the Rna Society, 10(12), 1957-1966.
Chang, C. C., & Lin, C. J. (2011). LIBSVM: A Library for Support Vector Machines. Acm Transactions on Intelligent Systems and Technology, 2(3), 27.
Chang, W. C., Lee, T. Y., Shien, D. M., Hsu, J. B., Horng, J. T., Hsu, P. C., . . . Pan, R. L. (2009). Incorporating support vector machine for identifying protein tyrosine sulfation sites. J Comput Chem, 30(15), 2526-2537.
Chaudhuri, K., & Chatterjee, R. (2007). MicroRNA detection and target prediction: integration of computational and experimental approaches. DNA Cell Biol, 26(5), 321-337.
Chavez Montes, R. A., de Fatima Rosas-Cardenas, F., De Paoli, E., Accerbi, M., Rymarquis, L. A., Mahalingam, G., . . . de Folter, S. (2014). Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nat Commun, 5, 3722.
Chen, C. Z., Li, L., Lodish, H. F., & Bartel, D. P. (2004). MicroRNAs modulate hematopoietic lineage differentiation. Science, 303(5654), 83-86.
Chendrimada, T. P., Finn, K. J., Ji, X. J., Baillat, D., Gregory, R. I., Liebhaber, S. A., . . . Shiekhattar, R. (2007). MicroRNA silencing through RISC recruitment of eIF6. Nature, 447(7146), 823-U821.
Chien, C. H., Chiang-Hsieh, Y. F., Chen, Y. A., Chow, C. N., Wu, N. Y., Hou, P. F., & Chang, W. C. (2015). AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. Database (Oxford), 2015(1758-0463 (Electronic)), bav042.
Chien, C. H., Chiang-Hsieh, Y. F., Tsou, A. P., Weng, S. L., Chang, W. C., & Huang, H. D. (2014). Large-scale investigation of human TF-miRNA relations based on coexpression profiles. Biomed Res Int, 2014, 623078.
Coleman J Fau - Green, P. J., Green Pj Fau - Inouye, M., & Inouye, M. The use of RNAs complementary to specific mRNAs to regulate the expression of individual bacterial genes.
Coleman J Fau - Hirashima, A., Hirashima A Fau - Inokuchi, Y., Inokuchi Y Fau - Green, P. J., Green Pj Fau - Inouye, M., & Inouye, M. A novel immune system against bacteriophage infection using complementary RNA (micRNA).
Crowley Te Fau - Nellen, W., Nellen W Fau - Gomer, R. H., Gomer Rh Fau - Firtel, R. A., & Firtel, R. A. Phenocopy of discoidin I-minus mutants by antisense transformation in Dictyostelium.
Cuellar, T. L., & McManus, M. T. (2005). MicroRNAs and endocrine biology. J Endocrinol, 187(3), 327-332.
Cuperus, J. T., Fahlgren, N., & Carrington, J. C. (2011). Evolution and functional diversification of MIRNA genes. Plant Cell, 23(2), 431-442.
Dai, X., & Zhao, P. X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res, 39(Web Server issue), W155-159.
Dai, X., Zhuang, Z., & Zhao, P. X. (2011). Computational analysis of miRNA targets in plants: current status and challenges. Brief Bioinform, 12(2), 115-121.
Ding, Y., Tao, Y., & Zhu, C. (2013). Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot, 64(11), 3077-3086.
Ding, Z., Li, S., An, X., Liu, X., Qin, H., & Wang, D. (2009). Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thaliana. J Genet Genomics, 36(1), 17-29.
Doench, J. G., Petersen, C. P., & Sharp, P. A. (2003). siRNAs can function as miRNAs. Genes Dev, 17(4), 438-442.
Ecker, J. R., & Davis, R. W. (1986). Inhibition of gene expression in plant cells by expression of antisense RNA. Proc Natl Acad Sci U S A, 83(15), 5372-5376.
Edgar, R., Domrachev, M., & Lash, A. E. (2002). Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res, 30(1), 207-210.
Elbashir, S. M., Lendeckel, W., & Tuschl, T. (2001). RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev, 15(2), 188-200.
Fahlgren, N., & Carrington, J. C. (2010). miRNA Target Prediction in Plants. Methods Mol Biol, 592(1940-6029 (Electronic)), 51-57.
Fahlgren, N., Jogdeo, S., Kasschau, K. D., Sullivan, C. M., Chapman, E. J., Laubinger, S., . . . Carrington, J. C. (2010). MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell, 22(4), 1074-1089.
Filipowicz, W., Bhattacharyya, S. N., & Sonenberg, N. (2008). Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet, 9(2), 102-114.
Finkelstein, R. R., & Lynch, T. J. (2000). The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor. Plant Cell, 12(4), 599-609.
Fire, A., Xu, S., Montgomery, M. K., Kostas, S. A., Driver, S. E., & Mello, C. C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391(6669), 806-811.
Friedlander, M. R., Chen, W., Adamidi, C., Maaskola, J., Einspanier, R., Knespel, S., & Rajewsky, N. (2008). Discovering microRNAs from deep sequencing data using miRDeep. Nature Biotechnology, 26(4), 407-415.
Gkirtzou, K., Tsamardinos, I., Tsakalides, P., & Poirazi, P. (2010). MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors. Plos One, 5(8).
Grad, Y., Aach, J., Hayes, G. D., Reinhart, B. J., Church, G. M., Ruvkun, G., & Kim, J. (2003). Computational and experimental identification of C. elegans microRNAs. Molecular Cell, 11(5), 1253-1263.
Gregory, R. I., Chendrimada, T. P., & Shiekhattar, R. (2006). MicroRNA biogenesis: isolation and characterization of the microprocessor complex. Methods Mol Biol, 342(1064-3745 (Print)), 33-47.
Griffiths-Jones, S. (2004). The microRNA Registry. Nucleic Acids Res, 32(Database issue), D109-111.
Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A., & Enright, A. J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res, 34(Database issue), D140-144.
Griffiths-Jones, S., Saini, H. K., van Dongen, S., & Enright, A. J. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res, 36(Database issue), D154-158.
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007). A chromatin landmark and transcription initiation at most promoters in human cells. Cell, 130(1), 77-88.
Guleria, P., Mahajan M Fau - Bhardwaj, J., Bhardwaj J Fau - Yadav, S. K., & Yadav, S. K. Plant small RNAs: biogenesis, mode of action and their roles in abiotic stresses.
Ha, M., Ng, D. W. K., Li, W. H., & Chen, Z. J. (2011). Coordinated histone modifications are associated with gene expression variation within and between species. Genome Research, 21(4), 590-598.
Hall, I. M., Shankaranarayana, G. D., Noma, K., Ayoub, N., Cohen, A., & Grewal, S. I. (2002). Establishment and maintenance of a heterochromatin domain. Science, 297(5590), 2232-2237.
Hamilton, A., Voinnet, O., Chappell, L., & Baulcombe, D. (2002). Two classes of short interfering RNA in RNA silencing. Embo Journal, 21(17), 4671-4679.
Harfe, B. D., McManus Mt Fau - Mansfield, J. H., Mansfield Jh Fau - Hornstein, E., Hornstein E Fau - Tabin, C. J., & Tabin, C. J. The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb.
Harland R Fau - Weintraub, H., & Weintraub, H. Translation of mRNA injected into Xenopus oocytes is specifically inhibited by antisense RNA.
Houbaviy Hb Fau - Houbaviy, H. B., Dennis L Fau - Dennis, L., Jaenisch R Fau - Jaenisch, R., & Sharp Pa Fau - Sharp, P. A. Characterization of a highly variable eutherian microRNA gene.
Hsu, S. D., Tseng, Y. T., Shrestha, S., Lin, Y. L., Khaleel, A., Chou, C. H., . . . Huang, H. D. (2014). miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res, 42(Database issue), D78-85.
Hutvagner, G., & Zamore, P. D. (2002). A microRNA in a multiple-turnover RNAi enzyme complex. Science, 297(5589), 2056-2060.
Jenuwein, T., & Allis, C. D. (2001). Translating the histone code. Science, 293(5532), 1074-1080.
Jha, A., Chauhan, R., Mehra, M., Singh, H. R., & Shankar, R. (2012). miR-BAG: bagging based identification of microRNA precursors. Plos One, 7(9), e45782.
Jha, A., & Shankar, R. (2013). miReader: Discovering Novel miRNAs in Species without Sequenced Genome. Plos One, 8(6).
Jones-Rhoades, M. W., Bartel, D. P., & Bartel, B. (2006). MicroRNAs and their regulatory roles in plants. Annual Review of Plant Biology, 57(1543-5008 (Print)), 19-53.
Kasschau, K. D., Xie, Z., Allen, E., Llave, C., Chapman, E. J., Krizan, K. A., & Carrington, J. C. (2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev Cell, 4(2), 205-217.
Kawahara, Y., de la Bastide, M., Hamilton, J. P., Kanamori, H., McCombie, W. R., Ouyang, S., . . . Matsumoto, T. (2013). Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice, 6(1939-8425 (Print)).
Kersey, P. J., Allen, J. E., Christensen, M., Davis, P., Falin, L. J., Grabmueller, C., . . . Staines, D. M. (2014). Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res, 42(Database issue), D546-552.
Kozomara, A., & Griffiths-Jones, S. (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res, 39(Database issue), D152-157.
Kozomara, A., & Griffiths-Jones, S. (2014). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res, 42(D1), D68-D73.
Lagos-Quintana, M., Rauhut, R., Lendeckel, W., & Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science, 294(5543), 853-858.
Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W., & Tuschl, T. (2002). Identification of tissue-specific microRNAs from mouse. Curr Biol, 12(9), 735-739.
Lau, N. C., Lim, L. P., Weinstein, E. G., & Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294(5543), 858-862.
Lee, R. C., & Ambros, V. (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science, 294(5543), 862-864.
Lee, R. C., Feinbaum, R. L., & Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5), 843-854.
Lee, Y., Ahn, C., Han, J., Choi, H., Kim, J., Yim, J., . . . Kim, V. N. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature, 425(6956), 415-419.
Lee Y Fau - Lee, Y., Jeon K Fau - Jeon, K., Lee Jt Fau - Lee, J.-T., Kim S Fau - Kim, S., & Kim Vn Fau - Kim, V. MicroRNA maturation: stepwise processing and subcellular localization.
Lee, Y., Kim, M., Han, J., Yeom, K. H., Lee, S., Baek, S. H., & Kim, V. N. (2004). MicroRNA genes are transcribed by RNA polymerase II. EMBO J, 23(20), 4051-4060.
Lelandais-Briere, C., Sorin, C., Declerck, M., Benslimane, A., Crespi, M., & Hartmann, C. (2010). Small RNA diversity in plants and its impact in development. Curr Genomics, 11(1), 14-23.
Leuschner, P. J., Ameres, S. L., Kueng, S., & Martinez, J. (2006). Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep, 7(3), 314-320.
Li, B., Carey, M., & Workman, J. L. (2007). The role of chromatin during transcription. Cell, 128(4), 707-719.
Li, L., Xu, J., Yang, D., Tan, X., & Wang, H. (2010). Computational approaches for microRNA studies: a review. Mamm Genome, 21(1-2), 1-12.
Light J Fau - Molin, S., & Molin, S. The sites of action of the two copy number control functions of plasmid R1.
Light, J., & Molin, S. (1983). Post-transcriptional control of expression of the repA gene of plasmid R1 mediated by a small RNA molecule. EMBO J, 2(1), 93-98.
Lisse, T. S., Chun, R. F., Rieger, S., Adams, J. S., & Hewison, M. (2013). Vitamin D activation of functionally distinct regulatory miRNAs in primary human osteoblasts. J Bone Miner Res, 28(6), 1478-1488.
Liu, H. H., Tian, X., Li, Y. J., Wu, C. A., & Zheng, C. C. (2008). Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA, 14(5), 836-843.
Llave, C., Xie, Z., Kasschau, K. D., & Carrington, J. C. (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297(5589), 2053-2056.
Matranga, C., Tomari, Y., Shin, C., Bartel, D. P., & Zamore, P. D. (2005). Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell, 123(4), 607-620.
Matys, V., Fricke E Fau - Geffers, R., Geffers R Fau - Gossling, E., Gossling E Fau - Haubrock, M., Haubrock M Fau - Hehl, R., Hehl R Fau - Hornischer, K., . . . Wingender, E. TRANSFAC: transcriptional regulation, from patterns to profiles. (1362-4962 (Electronic)). doi: D - NLM: PMC165555 EDAT- 2003/01/10 04:00 MHDA- 2003/03/15 04:00 CRDT- 2003/01/10 04:00 PST - ppublish
Melton, D. A. (1985). Injected anti-sense RNAs specifically block messenger RNA translation in vivo. Proc Natl Acad Sci U S A, 82(1), 144-148.
Mette, M. F., Aufsatz, W., van der Winden, J., Matzke, M. A., & Matzke, A. J. (2000). Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J, 19(19), 5194-5201.
Mizuno T Fau - Chou, M. Y., Chou My Fau - Inouye, M., & Inouye, M. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA).
Mochizuki, K., Fine, N. A., Fujisawa, T., & Gorovsky, M. A. (2002). Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell, 110(6), 689-699.
Mraz, M., Dolezalova, D., Plevova, K., Kozubik, K. S., Mayerova, V., Cerna, K., . . . Pospisilova, S. (2012). MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia. Blood, 119(9), 2110-2113.
Murchison, E. P., & Hannon, G. J. (2004). miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Cell Biol, 16(3), 223-229.
Ohler, U., Yekta, S., Lim, L. P., Bartel, D. P., & Burge, C. B. (2004). Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA, 10(9), 1309-1322.
Ozsolak, F., Poling, L. L., Wang, Z., Liu, H., Liu, X. S., Roeder, R. G., . . . Fisher, D. E. (2008). Chromatin structure analyses identify miRNA promoters. Genes Dev, 22(22), 3172-3183.
Park, J. E., Heo, I., Tian, Y., Simanshu, D. K., Chang, H., Jee, D., . . . Kim, V. N. (2011). Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature, 475(7355), 201-205.
Pasquinelli, A. E., Reinhart, B. J., Slack, F., Martindale, M. Q., Kuroda, M. I., Maller, B., . . . Ruvkun, G. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature, 408(6808), 86-89.
Pestka S Fau - Daugherty, B. L., Daugherty Bl Fau - Jung, V., Jung V Fau - Hotta, K., Hotta K Fau - Pestka, R. K., & Pestka, R. K. Anti-mRNA: specific inhibition of translation of single mRNA molecules.
Petersen, C. P., Bordeleau, M. E., Pelletier, J., & Sharp, P. A. (2006). Short RNAs repress translation after initiation in mammalian cells. Molecular Cell, 21(4), 533-542.
Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., Lee, T. I., . . . Young, R. A. (2005). Genome-wide map of nucleosome acetylation and methylation in yeast. Cell, 122(4), 517-527.
Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., . . . Stoffel, M. (2004). A pancreatic islet-specific microRNA regulates insulin secretion. Nature, 432(7014), 226-230.
Pratt, A. J., & MacRae, I. J. (2009). The RNA-induced silencing complex: a versatile gene-silencing machine. J Biol Chem, 284(27), 17897-17901.
Reinhart, B. J., & Bartel, D. P. (2002). Small RNAs correspond to centromere heterochromatic repeats. Science, 297(5588), 1831.
Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., . . . Ruvkun, G. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403(6772), 901-906.
Rhee, S. Y., Beavis, W., Berardini, T. Z., Chen, G., Dixon, D., Doyle, A., . . . Zhang, P. (2003). The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res, 31(1), 224-228.
Ritchie, W., Theodule, F. X., & Gautheret, D. (2008). Mireval: a web tool for simple microRNA prediction in genome sequences. Bioinformatics, 24(11), 1394-1396.
Rock, C. D., & Sun, X. (2005). Crosstalk between ABA and auxin signaling pathways in roots of Arabidopsis thaliana (L.) Heynh. Planta, 222(1), 98-106.
Ronen, R., Gan, I., Modai, S., Sukacheov, A., Dror, G., Halperin, E., & Shomron, N. (2010). miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics, 26(20), 2615-2616.
Rosenberg Ub Fau - Preiss, A., Preiss A Fau - Seifert, E., Seifert E Fau - Jackle, H., Jackle H Fau - Knipple, D. C., & Knipple, D. C. Production of phenocopies by Kruppel antisense RNA injection into Drosophila embryos.
Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C. T., . . . Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature, 419(6905), 407-411.
Schneider, R., Bannister, A. J., Myers, F. A., Thorne, A. W., Crane-Robinson, C., & Kouzarides, T. (2004). Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat Cell Biol, 6(1), 73-77.
Seitz, H., Youngson, N., Lin, S. P., Dalbert, S., Paulsen, M., Bachellerie, J. P., . . . Cavaille, J. (2003). Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet, 34(3), 261-262.
Simons Rw Fau - Kleckner, N., & Kleckner, N. Translational control of IS10 transposition.
Siomi, H., & Siomi, M. C. (2009). On the road to reading the RNA-interference code. Nature, 457(7228), 396-404.
Terai, G., Okida, H., Asai, K., & Mituyama, T. (2012). Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features. Plos One, 7(9).
Tsutsumi, A., Kawamata, T., Izumi, N., Seitz, H., & Tomari, Y. (2011). Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol, 18(10), 1153-1158.
Turner, B. M. (2002). Cellular memory and the histone code. Cell, 111(3), 285-291.
Vermeulen, A., Behlen, L., Reynolds, A., Wolfson, A., Marshall, W. S., Karpilow, J., & Khvorova, A. (2005). The contributions of dsRNA structure to Dicer specificity and efficiency. RNA, 11(5), 674-682.
Voinnet, O. (2009). Origin, biogenesis, and activity of plant microRNAs. Cell, 136(4), 669-687.
Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., & Martienssen, R. A. (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297(5588), 1833-1837.
Wakiyama, M., Takimoto, K., Ohara, O., & Yokoyama, S. (2007). Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev, 21(15), 1857-1862.
Wang, W. C., Lin, F. M., Chang, W. C., Lin, K. Y., Huang, H. D., & Lin, N. S. (2009). miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. Bmc Bioinformatics, 10(1471-2105 (Electronic)), 328.
Wang, X. J., Reyes, J. L., Chua, N. H., & Gaasterland, T. (2004). Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology, 5(9).
Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., . . . Plasterk, R. H. (2005). MicroRNA expression in zebrafish embryonic development. Science, 309(5732), 310-311.
Wilfred, B. R., Wang, W. X., & Nelson, P. T. (2007). Energizing miRNA research: A review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways. Molecular Genetics and Metabolism, 91(3), 209-217.
Wu, Y. G., Wei, B., Liu, H. Z., Li, T. X., & Rayner, S. (2011). MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. Bmc Bioinformatics, 12(1471-2105 (Electronic)).
Xie, F. L., Huang, S. Q., Guo, K., Xiang, A. L., Zhu, Y. Y., Nie, L., & Yang, Z. M. (2007). Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett, 581(7), 1464-1474.
Xie, Z., Allen, E., Fahlgren, N., Calamar, A., Givan, S. A., & Carrington, J. C. (2005). Expression of Arabidopsis MIRNA genes. Plant Physiol, 138(4), 2145-2154.
Xuan, P., Guo, M. Z., Huang, Y. C., Li, W. B., & Huang, Y. F. (2011). MaturePred: Efficient Identification of MicroRNAs within Novel Plant Pre-miRNAs. Plos One, 6(11).
Xue, C. H., Li, F., He, T., Liu, G. P., Li, Y. D., & Zhang, X. G. (2005). Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. Bmc Bioinformatics, 6(1471-2105 (Electronic)).
Yamamoto, Y. Y., Yoshitsugu, T., Sakurai, T., Seki, M., Shinozaki, K., & Obokata, J. (2009). Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis. Plant J, 60(2), 350-362.
Zamore, P. D., Tuschl, T., Sharp, P. A., & Bartel, D. P. (2000). RNAi: Double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101(1), 25-33.
Zeng, Y., Wagner, E. J., & Cullen, B. R. (2002). Both natural and designed micro RNAs technique can inhibit the expression of cognate mRNAs when expressed in human cells. Molecular Cell, 9(6), 1327-1333.
Zeng, Y., Yi, R., & Cullen, B. R. (2003). MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci U S A, 100(17), 9779-9784.
Zhang, B., Pan, X., Cannon, C. H., Cobb, G. P., & Anderson, T. A. (2006). Conservation and divergence of plant microRNA genes. Plant J, 46(2), 243-259.
Zhang, Y. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Res, 33(Web Server issue), W701-704.
Zhou, X., Ruan, J., Wang, G., & Zhang, W. (2007). Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol, 3(3), e37.
Zilberman, D., Cao, X., & Jacobsen, S. E. (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science, 299(5607), 716-719.