Deep sequencing of small RNAs in plants: Applied bioinformatics

Briefings in Functional Genomics

Volumn 11, Issue 1, 2012, Pages 71-85

  Studholme, David J ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

microRNA; miRNA; Next generation sequencing; RNA; Silencing; siRNA; Small interfering RNA

Indexed keywords

MICRORNA; PLANT RNA; SMALL INTERFERING RNA; SMALL RNA; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; BIOINFORMATICS; CROP; DATA BASE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE MAPPING; GENE SEQUENCE; NONHUMAN; PLANT GENETICS; RNA SEQUENCE; SEQUENCE ALIGNMENT; TREE;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLANTS; RNA, PLANT;

EID: 84857198753     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elr039     Document Type: Article

References (207)

1. Petsko GA. Dog eat dogma. Genome Biol 2000;1: comment1002.1-1002.2.
2. Wirth S, Crespi M. Non-protein-coding RNAs, a diverse class of gene regulators, and their action in plants. RNABiol 2009;6:161-4.
3. Schwach F, Moxon S, Moulton V, et al. Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic 2009;8:472-81.
4. Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999;286:950-2.
5. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. AnnuRev Plant Biol 2006;57: 19-53.
6. Kim VN. Small RNAs: classification, biogenesis, and function. Mol Cells 2005;28:1-15.
7. Mosher RA, Baulcombe DC. Bacterial pathogens encode suppressors of RNA-mediated silencing. Genome Biol 2008; 9:237.
8. Sunkar R, Chinnusamy V, Zhu J, et al. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 2007;12:301-9.
9. Chuck G, O'Connor D. Small RNAs going the distance during plant development. Curr Opin Plant Biol 2010;13: 40-5.
10. Bonnet E, Van de Peer Y, Rouzé P. The small RNA world of plants. New Phytol 2006;171:451-68.
11. Brodersen P, Voinnet O. The diversity of RNA silencing pathways in plants. TrendsGenet 2006;22:268-80.
12. Chuck G, Candela H, Hake S. Big impacts by small RNAs in plant development. Curr Opin Plant Biol 2009;12:81-6.
13. Kanno T, Habu Y. siRNA-mediated chromatin maintenance and its function in Arabidopsis thaliana. Biochim Biophys Acta 2011;1809:444-51.
14. Katiyar-Agarwal S, Jin H. Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 2010;48: 225-46.
15. Mlotshwa S, Pruss GJ, Vance V. Small RNAs in viral infection and host defense. Trends Plant Sci 2008;13:375-82.
16. Pantaleo V. Plant RNA silencing in viral defence. Adv Exp Med Biol 2011;722:39-58.
17. Pikaard CS, Haag JR, Ream T, et al. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 2008;13: 390-7.
18. Ruiz-Ferrer V, Voinnet O. Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 2009;60: 485-510.
19. Simon SA, Meyers BC. Small RNA-mediated epigenetic modifications in plants. CurrOpinPlantBiol 2011;14:148-55.
20. Sontheimer EJ, Carthew RW. Silence from within: endogenous siRNAs and miRNAs. Cell 2005;122:9-12.
21. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 2009;136:642-55.
22. Vaucheret H. Plant argonautes. Trends Plant Sci 2008;13: 350-8.
23. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 2006;20: 759-71.
24. Xie Z, Qi X. Diverse small RNA-directed silencing pathways in plants. Biochim Biophys Acta 2008;1779:720-4.
25. Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell 2011;23:431-42.
26. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97.
27. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat RevMol Cell Biol 2005;6:376-85.
28. Szarzynska B, Sobkowiak L, Pant BD, et al. Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs. Nucleic Acids Res 2009;37:3083-93.
29. Lee Y, Kim M, Han J, et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004;23: 4051-60.
30. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat StructMol Biol 2006; 13:1097-101.
31. Lee Y, Ahn C, Han J, et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003;425: 415-9.
32. Lee Y, Jeon K, Lee JT, et al. MicroRNA maturation: stepwise processing and subcellular localization. EMBOJ 2002; 21:4663-70.
33. Han J, Lee Y, Yeom KH, et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006;125:887-901.
34. Tomari Y, Zamore PD. MicroRNA biogenesis: Drosha can't cut it without a partner. Curr Biol 2005;15: R61-4.
35. Meister G, Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature 2004;431:343-9.
36. Yi R, Qin Y, Macara IG, et al. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003;17:3011-6.
37. Bernstein E, Caudy AA, Hammond SM, et al. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 2001;409:363-6.
38. Grishok A, Pasquinelli AE, Conte D, et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 2001;106:23-34.
39. Hutvágner G, McLachlan J, Pasquinelli AE, et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 2001; 293:834-8.
40. Lee YS, Nakahara K, Pham JW, et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 2004;117:69-81.
41. Sun G. MicroRNAs and their diverse functions in plants. Plant Mol Biol 2011 [Epub ahead of print] PubMed PMID: 21874378.
42. Boutet S, Vazquez F, Liu J, et al. Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance. Curr Biol 2003;13:843-8.
43. Kurihara Y, Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad SciUSA 2004;101:12753-8.
44. Kurihara Y, Takashi Y, Watanabe Y. The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 2006;12:206-12.
45. Park W, Li J, Song R, et al. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 2002;12: 1484-95.
46. Xie Z, Kasschau KD, Carrington JC. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNAguided mRNA degradation. Curr Biol 2003;13:784-9.
47. Reinhart BJ, Weinstein EG, Rhoades MW, et al. MicroRNAs in plants. Genes Dev 2002;16:1616-26.
48. Kasschau KD, Fahlgren N, Chapman EJ, et al. Genomewide profiling and analysis of Arabidopsis siRNAs. PloS Biol 2007;5:e57.
49. Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2004;2:E104.
50. Rajagopalan R, Vaucheret H, Trejo J, et al. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 2006;20:3407-25.
51. Lister R, O'Malley RC, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008;133:523-36.
52. Chan SW, Zhang X, Bernatavichute YV, et al. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol 2006;4:e363.
53. Molnar A, Melnyk CW, Bassett A, et al. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010;328:872-5.
54. Djupedal I, Ekwall K. Epigenetics: heterochromatin meets RNAi. Cell Res 2009;19:282-95.
55. Huettel B, Kanno T, Daxinger L, et al. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBOJ 2006;25:2828-36.
56. Kanno T, Huettel B, Mette MF, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 2005;37:761-5.
57. Pontier D, Yahubyan G, Vega D, et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 2005;19: 2030-40.
58. Henderson IR, Jacobsen SE. Epigenetic inheritance in plants. Nature 2007;447:418-24.
59. Chan SW. Inputs and outputs for chromatin-targeted RNAi. Trends Plant Sci 2008;13:383-9.
60. He XJ, Hsu YF, Zhu S, et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 2009;137:498-508.
61. Wierzbicki AT, Ream TS, Haag JR, et al. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 2009;41:630-4.
62. Axtell MJ, Jan C, Rajagopalan R, et al. A two-hit trigger for siRNA biogenesis in plants. Cell 2006;127:565-77.
63. Yoshikawa M, Peragine A, Park MY, et al. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 2005;19:2164-75.
64. Katiyar-Agarwal S, Morgan R, Dahlbeck D, et al. A pathogen-inducible endogenous siRNA in plant immunity. ProcNatl Acad SciUSA 2006;103:18002-7.
65. Jin H, Vacic V, Girke T, et al. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 2008;9:6.
66. Borsani O, Zhu J, Verslues PE, et al. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005;123: 1279-91.
67. Dunoyer P, Schott G, Himber C, et al. Small RNA duplexes function as mobile silencing signals between plant cells. Science 2010;328:912-6.
68. Mohorianu I, Schwach F, Jing R, et al. Profiling of short RNAs during fleshy fruit development reveals stagespecific sRNAome expression patterns. Plant J 2011;67: 232-46.
69. Barakat A, Wall K, Leebens-Mack J, et al. Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants. Plant J 2007;51:991-1003.
70. Martínez G, Forment J, Llave C, et al. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs. PLoS One 2011;6:e19523.
71. Martinez G, Donaire L, Llave C, et al. High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem. Mol Plant Pathol 2010; 11:347-59.
72. Schreiber AW, Shi BJ, Huang CY, et al. Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics 2011;12:129.
73. Zhang W, Gao S, Zhou X, et al. Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. PlantMol Biol 2011;75:93-105.
74. Pantaleo V, Saldarelli P, Miozzi L, et al. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 2010;408:49-56.
75. Navarro B, Pantaleo V, Gisel A, et al. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One 2009;4:e7686.
76. Di Serio F, Gisel A, Navarro B, et al. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 2009;4:e7539.
77. Bolduc F, Hoareau C, St-Pierre P, et al. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMCMol Biol 2010;11:16.
78. Mosher RA, Schwach F, Studholme D, et al. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA 2008; 105:3145-50.
79. Mosher RA, Melnyk CW, Kelly KA, et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009;460:283-6.
80. Szittya G, Moxon S, Pantaleo V, et al. Structural and functional analysis of viral siRNAs. PLoS Pathog 2010;6: e1000838.
81. Brenner S, Johnson M, Bridgham J, et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000;18:630-4.
82. Meyers BC, Souret FF, Lu C, et al. Sweating the small stuff: microRNA discovery in plants. Curr Opin Biotechnol 2006; 17:139-46.
83. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75:843-54.
84. Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993;75: 855-62.
85. Fu H, Tie Y, Xu C, et al. Identification of human fet al liver miRNAs by a novel method. FEBS Lett 2005;579: 3849-54.
86. Llave C, Kasschau KD, Rector MA, et al. Endogenous and silencing-associated small RNAs in plants. Plant Cell 2002; 14:1605-19.
87. Lu J, Getz G, Miska EA, et al. MicroRNA expression profiles classify human cancers. Nature 2009;435:834-8.
88. Berezikov E, Cuppen E, Plasterk RH. Approaches to microRNA discovery. Nat Genet 2006;38:S2-7.
89. Ghosh Z, Chakrabarti J, Mallick B. miRNomics-The bioinformatics of microRNA genes. Biochem Biophys Res Commun 2007;363:6-11.
90. Zhang W, Luo Y, Gong X, et al. Computational identification of 48 potato microRNAs and their targets. Comput Biol Chem 2009;33:84-93.
91. Xie FL, Huang SQ, Guo K, et al. Computational identification of novel microRNAs and targets in Brassica napus. FEBS Lett 2007;581:1464-74.
92. Yin Z, Li C, Han X, Shen F. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 2008;414:60-6.
93. Lim LP, Glasner ME, Yekta S, et al. Vertebrate microRNA genes. Science 2003;299:1540.
94. Li X, Zhang YZ. Computational detection of microRNAs targeting transcription factor genes in Arabidopsis thaliana. Comput Biol Chem 2005;29:360-7.
95. Wang XJ, Reyes JL, Chua NH, et al. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 2004;5:R65.
96. Bonnet E, Wuyts J, Rouzé P, et al. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad SciUSA 2004;101:11511-6.
97. Jones-Rhoades MW, Bartel DP. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004;14:787-99.
98. Song C, Fang J, Li X, et al. Identification and characterization of 27 conserved microRNAs in citrus. Planta 2009;230: 671-85.
99. Khan Barozai MY, Irfan M, Yousaf R, et al. Identification of micro-RNAs in cotton. Plant Physiol Biochem 2008;46: 739-51.
100. Zhang BH, Pan XP, Wang QL, et al. Identification and characterization of new plant microRNAs using EST analysis. Cell Res 2005;15:336-60.
101. Zhang B, Pan X, Stellwag EJ. Identification of soybean microRNAs and their targets. Planta 2008;229:161-82.
102. Sunkar R, Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol 2008;8:37.
103. Qiu CX, Xie FL, Zhu YY, et al. Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 2007;395:49-61.
104. Wen J, Frickey T, Weiller GF. Computational prediction of candidate miRNAs and their targets from Medicago truncatula non-protein-coding transcripts. In Silico Biol 2008;8: 291-306.
105. Zhang B, Pan X, Anderson TA. Identification of 188 conserved maize microRNAs and their targets. FEBSLett 2006; 580:3753-62.
106. Adai A, Johnson C, Mlotshwa S, et al. Computational prediction of miRNAs in Arabidopsis thaliana. GenomeRes 2005; 15:78-91.
107. Lindow M, Krogh A. Computational evidence for hundreds of non-conserved plant microRNAs. BMCGenomics 2005; 6:119.
108. Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2010;11:31-46.
109. Axtell MJ, Bartel DP. Antiquity of microRNAs and their targets in land plants. Plant Cell 2005;17:1658-73.
110. Lu C, Tej SS, Luo S, et al. Elucidation of the small RNA component of the transcriptome. Science 2005;309:1567-9.
111. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-80.
112. Grant-Downton R, Le Trionnaire G, Schmid R, et al. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. BMCGenomics 2009;10:643.
113. Zhang X, Henderson IR, Lu C, et al. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad SciUSA 2007;104:4536-41.
114. Lu C, Kulkarni K, Souret FF, MuthuValliappan R, et al. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res 2006;16:1276-88.
115. Legrand S, Valot N, Nicolé F, et al. One-step identification of conserved miRNAs, their targets, potential transcription factors and effector genes of complete secondary metabolism pathways after 454 pyrosequencing of calyx cDNAs from the Labiate Salvia sclarea L. Gene 2010;450:55-62.
116. Qi Y, He X, Wang XJ, et al. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 2006;443:1008-12.
117. Howell MD, Fahlgren N, Chapman EJ, et al. Genomewide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 2007;19:926-42.
118. Klevebring D, Street NR, Fahlgren N, et al. Genome-wide profiling of Populus small RNAs. BMC Genomics 2009;10:620.
119. Molnár A, Schwach F, Studholme DJ, et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 2007;447:1126-9.
120. Zhao T, Li G, Mi S, et al. A complex system of small RNAs in the unicellular green alga Chlamydomonasreinhardtii. Genes Dev 2007;21:1190-203.
121. Hafner M, Landgraf P, Ludwig J, et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 2008;44:3-12.
122. Galan M, Guivier E, Caraux G, et al. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 2010;11:296.
123. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:53-9.
124. Montgomery TA, Yoo SJ, Fahlgren N, et al. AGO1-miR173 complex initiates phased siRNA formation in plants. ProcNatl Acad SciUSA 2008;105:20055-62.
125. Montgomery TA, Howell MD, Cuperus JT, et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 2008;133:128-41.
126. Zhu QH, Spriggs A, Matthew L, et al. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 2008;18:1456-65.
127. Nobuta K, Lu C, Shrivastava R, et al. Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA 2008;105:14958-63.
128. German MA, Pillay M, Jeong DH, et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008;26:941-6.
129. Gregory BD, O'Malley RC, Lister R, et al. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 2008;14:854-66.
130. Mi S, Cai T, Hu Y, et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 50 terminal nucleotide. Cell 2008;133:116-27.
131. Szittya G, Moxon S, Santos DM, et al. High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 2008;9:593.
132. Valouev A, Ichikawa J, Tonthat T, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008;18: 1051-63.
133. Mitrovich QM, Tuch BB, De La Vega FM, et al. Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science 2010;330: 838-41.
134. Li SC, Chan WC, Hu LY, et al. Identification of homologous microRNAs in 56 animal genomes. Genomics 2010;96: 1-9.
135. Li S, Wang Y, Wang H, et al. MicroRNAs as participants in cytotoxicity of CdTe quantum dots in NIH/3T3 cells. Biomaterials 2011;32:3807-14.
136. Schopman NC, Willemsen M, Liu YP, et al. Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. Nucleic Acids Res 2011 Sep 12. [Epub ahead of print] PubMed PMID: 21911362.
137. Li SC, Chan WC, Ho MR, et al. Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMCGenomics 2010;11(Suppl 4):S8.
138. Hanina SA, Mifsud W, Down TA, et al. Genome-wide identification of targets and function of individual MicroRNAs in mouse embryonic stem cells. PLoS Genet 2010;6:e1001163.
139. Fehniger TA, Wylie T, Germino E, et al. Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res 2010;20:1590-604.
140. Ribeiro-dos-Santos Â, Khayat AS, Silva A, et al. Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach. PLoS One 2010;5:e13205.
141. Lin YT, Kincaid RP, Arasappan D, et al. Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA 2010;16: 1540-58.
142. Johansen SD, Karlsen BO, Furmanek T, et al. RNA deep sequencing of the Atlantic cod transcriptome. CompBiochem Physiol PartDGenomics Proteomics 2011;6:18-22.
143. Schulte JH, Marschall T, Martin M, et al. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavourable neuroblastoma. Nucleic Acids Res 2010; 38:5919-28.
144. Qi Y, Tu J, Cui L, et al. High-throughput sequencing of microRNAs in adenovirus type 3 infected human laryngeal epithelial cells. J Biomed Biotechnol 2010;2010: 915980.
145. Marques JT, Kim K, Wu PH, et al. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat StructMol Biol 2010;17:24-30.
146. Goff LA, Davila J, Swerdel MR, et al. Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors. PLoS One 2009;4: e7192.
147. Guo L, Yang Q, Lu J, et al. A comprehensive survey of miRNA repertoire and 30 addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing. PLoS One 2011;6:e21072.
148. Wu Q, Lu Z, Li H, et al. Next-generation sequencing of microRNAs for breast cancer detection. J Biomed Biotechnol 2011;2011:597145.
149. Ma Z, Coruh C, Axtell MJ. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 2010;22:1090-103.
150. Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475:348-52.
151. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011;11:759-69.
152. Cock PJ, Fields CJ, Goto N, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/ Illumina FASTQ variants. Nucleic Acids Res 2010;38: 1767-71.
153. Chan PP, Lowe TM. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009;37:D93-7.
154. Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 2009;37:D141-5.
155. Griffiths-Jones S, Moxon S, Marshall M, et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005;33:D121-4.
156. Salmela L, Schröder J. Correcting errors in short reads by multiple alignments. Bioinformatics 2011;27:1455-61.
157. Nakamura K, Oshima T, Morimoto T, et al. Sequencespecific error profile of Illumina sequencers. Nucleic Acids Res 2011;39:e90.
158. Brockman W, Alvarez P, Young S, et al. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008;18:763-70.
159. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008;18:1851-8.
160. Kircher M, Stenzel U, Kelso J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 2009;10:R83.
161. Kim YK, Heo I, Kim VN. Modifications of small RNAs and their associated proteins. Cell 2010;143:703-9.
162. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 2006;20: 759-71.
163. Pilcher RL, Moxon S, Pakseresht N, et al. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 2007;226:709-17.
164. Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 2010;11: 473-83.
165. de Hoon MJ, Taft RJ, Hashimoto T, et al. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 2010; 20:257-64.
166. Smeds L, Künstner A. ConDeTri-A content dependent read trimmer for Illumina data. PLoS One 2011;6: e26314.
167. Fahlgren N, Sullivan CM, Kasschau KD, et al. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 2009;15: 992-1002.
168. Hardcastle T, Kelly K, Baulcombe DC. Identifying small interfering RNA loci from high-throughput sequencing data. Bioinformatics. In press.
169. MacLean D, Moulton V, Studholme DJ. Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics 2010;11:93.
170. Guo L, Lu Z. Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data. Comput Biol Chem 2010;34:165-71.
171. Morin RD, O'Connor MD, Griffith M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. GenomeRes 2008; 18:610-21.
172. McCormick KP, Willmann MR, Meyers BC. Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. Silence 2011;2:2.
173. Moxon S, Schwach F, Dalmay T, et al. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 2008; 24:2252-3.
174. Bagnall A, Moxon S, Studholme DJ, et al. Time series data mining algorithms for identifying short RNA in. Arabidopsis thaliana. BIOCOMP 2008: 182-8.
175. Chen HM, Li YH, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad SciUSA 2007;104:3318-23.
176. Berninger P, Gaidatzis D, van Nimwegen E, et al. Computational analysis of small RNA cloning data. Methods 2008;44:13-21.
177. Yang X, Li L. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics 2011;27:2614-5.
178. Yang X, Zhang H, Li L. Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics 2011;98:40-6.
179. Ronen R, Gan I, Modai S, et al. miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics 2010; 26:2615-6.
180. Gustafson AM, Allen E, Givan S, et al. ASRP: the Arabidopsis small RNA project database. Nucleic Acids Res 2005;33:D637-40.
181. Backman TW, Sullivan CM, Cumbie JS, et al. Update of ASRP: the Arabidopsis small RNA project database. Nucleic Acids Res 2008;36:D982-5.
182. Zhang Z, Yu J, Li D, et al. PMRD: plant microRNA database. Nucleic Acids Res 2010;38:D806-13.
183. Yang JH, Shao P, Zhou H, et al. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 2010;38:D123-30.
184. Bateman A, Agrawal S, Birney E, et al. RNAcentral: A vision for an international database of RNA sequences. RNA 2011;17:1941-6.
185. Uni Prot Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011;39: D214-9.
186. Prüfer K, Stenzel U, Dannemann M, et al. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics 2008;24:1530-1.
187. Hofacker IL, Fekete M, Stadler PF. Secondary structure prediction for aligned RNA sequences. J Mol Biol 2002; 319:1059-66.
188. Ronen R, Gan I, Modai S, et al. miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics 2010; 26:2615-6.
189. Hackenberg M, Sturm M, Langenberger D, et al. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res 2009;37:W68-76.
190. Pantano L, Estivill X, Martí E. SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells. Nucleic Acids Res 2010;38:e34.
191. Huang PJ, Liu YC, Lee CC, et al. DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res 2010;38: W385-91.
192. Zhu E, Zhao F, Xu G, et al. mirTools: microRNA profiling and discovery based on high-throughput sequencing. Nucleic Acids Res 2010;38:W392-7.
193. Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Brief Bioinform 2009;10:490-7.
194. Fang Z, Cui X. Design and validation issues in RNA-seq experiments. Brief Bioinform 2011;12:280-7.
195. Hansen KD, Wu Z, Irizarry RA, et al. Sequencing technology does not eliminate biological variability. Nat Biotechnol 2011;29:572-3.
196. Hardcastle TJ, Kelly KA. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010;11:422.
197. Rhoades MW, Reinhart BJ, Lim LP, et al. Prediction of plant microRNA targets. Cell 2002;110:513-20.
198. Allen E, Xie Z, Gustafson AM, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005;121:207-21.
199. Xie F, Zhang B. Target-align: a tool for plant microRNA target identification. Bioinformatics 2010;26:3002-3.
200. Bonnet E, He Y, Billiau K, Van de Peer Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 2010;26:1566-8.
201. Alves L, Jr, Niemeier S, Hauenschild A, et al. Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res 2009;37:4010-21.
202. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 2005;33:W701-4.
203. Maragkakis M, Reczko M, Simossis VA, et al. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 2009;37: W273-6.
204. Joung JG, Fei Z. Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information. BMCBioinformatics 2009; 10:S34.
205. MacLean D, Elina N, Havecker ER, et al. Evidence for large complex networks of plant short silencing RNAs. PLoSOne 2010;5:e9901.
206. Su WL, Kleinhanz RR, Schadt EE. Characterizing the role of miRNAs within gene regulatory networks using integrative genomics techniques. Mol Syst Biol 2011; 7:490.
207. Baulcombe DC. Short silencing RNA: the dark matter of genetics? Cold SpringHarb Symp Quant Biol 2006;71:13-20.