Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)

Addo-Quaye C, Miller W, Axtell MJ (2009). CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics, 25: 130–131

Addo-Quaye C, Eshoo TW, Bartel D P, Axtell M J (2008). Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol, 18: 758–762

Allen E, Xie Z, Gustafson A M, Carrington J C (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 121: 207–221

Archak S, Nagaraju J (2007). Computational prediction of rice (Oryza sativa) miRNA targets. Genomics Proteomics Bioinformatics, 5: 196–206

Axtell M J, Snyder J A, Bartel D P (2007). Common functions for diverse small RNAs of land plants. Plant Cell, 19: 1750–1769

Bartel D P (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116: 281–297

Bartel D P (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136: 215–233

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: 1185–1190

German M A, Luo S, Schroth G, Meyers B C, Green P J (2009). Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc, 4: 356–362

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, Green P J (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol, 26: 941–946

Goff S A, Ricke D, Lan T H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange B M, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W L, Chen L, Cooper B, Park S, Wood T C, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller R M, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296: 92–100

Gregory B D, O’Malley R C, Lister R, Urich M A, Tonti-Filippini J, Chen H, Millar A H, Ecker J R (2008). A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell, 14: 854–866

Griffiths-Jones S, Saini H K, van Dongen S, Enright A J (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res, 36: D154–158

Hock J, Meister G (2008). The Argonaute protein family. Genome Biol, 9: 210

Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan G L,Walbot V, Sundaresan V, Vance V, Bowman L H (2009). Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res, 19: 1429–1440

Jones-Rhoades M W, Bartel D P (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell, 14: 787–799

Jones-Rhoades M W, Bartel D P, Bartel B (2006). MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol, 57: 19–53

Kawashima C G, Yoshimoto N, Maruyama-Nakashita A, Tsuchiya Y N, Saito K, Takahashi H, Dalmay T (2009). Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J, 57: 313–321

Lacombe S, Nagasaki H, Santi C, Duval D, Piegu B, Bangratz M, Breitler J C, Guiderdoni E, Brugidou C, Hirsch J, Cao X, Brice C,Panaud O, Karlowski W M, Sato Y, Echeverria M (2008). Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice. BMC Plant Biol, 8: 123

Li R, Li Y, Kristiansen K, Wang J (2008). SOAP: short oligonucleotide alignment program. Bioinformatics, 24: 713–714

Liu B, Li P, Li X, Liu C, Cao S, Chu C, Cao X (2005). Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol, 139: 296–305

Liu B, Chen Z, Song X, Liu C, Cui X, Zhao X, Fang J, Xu W, Zhang H, Wang X, Chu C, Deng X, Xue Y, Cao X (2007a). Oryza sativa dicerlike4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell, 19: 2705–2718

Liu P P, Montgomery T A, Fahlgren N, Kasschau K D, Nonogaki H, Carrington J C (2007b). Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J, 52: 133–146

Liu Q, Zhang Y C, Wang C Y, Luo Y C, Huang Q J, Chen S Y, Zhou H, Qu L H, Chen Y Q (2009). Expression analysis of phytohormoneregulated microRNAs in rice, implying their regulation roles in plant hormone signaling. FEBS Lett, 583: 723–728

Llave C, Xie Z, Kasschau K D, Carrington J C (2002a). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297: 2053–2056

Llave C, Kasschau K D, Rector M A, Carrington J C (2002b). Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14: 1605–1619

Lu C, Jeong D H, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher S R, Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers B C, Green P J (2008). Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A, 105: 4951–4956

Luo Y C, Zhou H, Li Y, Chen J Y, Yang J H, Chen Y Q, Qu L H (2006). Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development. FEBS Lett, 580: 5111–5116

Maere S, Heymans K, Kuiper M (2005). BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics, 21: 3448–3449

Mallory A C, Bartel D P, Bartel B (2005). MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell, 17: 1360–1375

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, Qi Y (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5’ terminal nucleotide. Cell. 133: 116–127

Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek R L, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell C R (2007). The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res, 35: D883–887

Park W, Li J, Song R, Messing J, Chen X (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol, 12: 1484–1495

Peragine A, Yoshikawa M, Wu G, Albrecht H L, 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

Reinhart B J, Weinstein E G, Rhoades M W, Bartel B, Bartel D P (2002). MicroRNAs in plants. Genes Dev, 16: 1616–1626

Rhoades M W, Reinhart B J, Lim L P, Burge C B, Bartel B, Bartel D P (2002). Prediction of plant microRNA targets. Cell, 110: 513–520

Rice P, Longden I, Bleasby A (2000). EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet, 16: 276–277

Rubio-Somoza I, Cuperus J T, Weigel D, Carrington J C (2009). Regulation and functional specialization of small RNA-target nodes during plant development. Curr Opin Plant Biol, 12(5): 622–627

Song J J, Smith S K, Hannon G J, Joshua-Tor L (2004). Crystal structure of Argonaute and its implications for RISC slicer activity. Science, 305: 1434–1437

Sunkar, R., and Zhu, J.K. (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell16, 2001–2019.

Sunkar R, Jagadeeswaran G (2008). In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol, 8: 37

Sunkar R, Girke T, Jain P K, Zhu J K (2005). Cloning and characterization of microRNAs from rice. Plant Cell, 17: 1397–1411

Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J K (2008). Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol, 8: 25

Vaucheret H (2008). Plant ARGONAUTES. Trends Plant Sci, 13: 350–358

Vaucheret H, Vazquez F, Crete P, Bartel D P (2004). The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev, 18: 1187–1197

Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory A C, Hilbert J L, Bartel D P, Crete P (2004). Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell, 16: 69–79

Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, Tang K, Han B, Tao Y (2007). Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene, 394: 13–24

Wang J W, Wang L J, Mao Y B, Cai W J, Xue H W, Chen X Y (2005). Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell, 17: 2204–2216

Warthmann N, Chen H, Ossowski S, Weigel D, Herve P (2008). Highly specific gene silencing by artificial miRNAs in rice. PLoS One, 3: e1829

Wu M F, Tian Q, Reed J W (2006). Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development, 133: 4211–4218

Xie K, Wu C, Xiong L (2006). Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiol, 142: 280–293

Xie Z, Kasschau K D, Carrington J C (2003). Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol, 13: 784–789

Xie Z, Allen E, Fahlgren N, Calamar A, Givan S A, Carrington J C (2005). Expression of Arabidopsis MIRNA genes. Plant Physiol, 138: 2145–2154

Xue L J, Zhang J J, Xue H W (2009). Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res, 37: 916–930

Yang J H, Han S J, Yoon E K, Lee, W S (2006). Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells’. Nucleic Acids Res, 34: 1892–1899

Yu J, Hu S, Wang J, Wong G K, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296: 79–92

Zhu Q H, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C (2008). A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res, 18: 1456–1465