Skip to main content
SpringerLink
Log in

Nucleus and Genome: Small RNAs

  • Living reference work entry
  • First Online:
Molecular Biology

  • 589 Accesses

Abstract

Small regulatory RNAs 20-30 nucleotides in length guide RNA-mediated silencing processes in eukaryotes in a sequence-specific manner. Based on their biogenesis and precursors, plant small RNAs are classified as miRNAs or siRNAs. Both types of small RNAs are processed from longer precursors by RNase III enzymes and are stabilized by 2’-O-methylation at the 3’ terminal ribose. Mature small RNAs are incorporated into and guide the catalytic action of ARGONAUTE proteins. Small RNAs repress their targets at the posttranscriptional level via mRNA cleavage or translational inhibition or at the transcriptional level via heterochromatin formation. Small RNAs may also originate from exogenous sources such as viruses and transgenes. Consistent with the crucial roles of small RNAs in regulating many biological processes, the homeostasis of these molecules is precisely maintained through the regulation of their biogenesis and turnover.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Similar content being viewed by others

References

  • Allen E, Howell MD. miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin Cell Dev Biol. 2010;21(8):798–804.

    CAS  PubMed  Google Scholar 

  • Azevedo J, Cooke R, Lagrange T. Taking RISCs with ago hookers. Curr Opin Plant Biol. 2011;14(5):594–600.

    CAS  PubMed  Google Scholar 

  • Bazzini AA, Lee MT, Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science. 2012;336(6078):233–7.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Burgyán J, Havelda Z. Viral suppressors of RNA silencing. Trends Plant Sci. 2011;16(5):265–72.

    PubMed  Google Scholar 

  • Castel SE, Martienssen RA. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet. 2013;14(2):100–12.

    CAS  PubMed  Google Scholar 

  • Chan SW, Henderson IR, Jacobsen SE. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet. 2005;6:351–60.

    CAS  PubMed  Google Scholar 

  • Chen X. Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol. 2009;25(1):21–44.

    PubMed  Google Scholar 

  • Ding S-W, Voinnet O. Antiviral immunity directed by small RNAs. Cell. 2007;130(3):413–26.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Djuranovic S, Nahvi A, Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science. 2012;336(6078):237–40.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol. 2011;12(8):483–92.

    CAS  PubMed  Google Scholar 

  • Ishizu H, Siomi H, Siomi MC. Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev. 2012;26(21):2361–73.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ji L, Chen X. Regulation of small RNA stability: methylation and beyond. Cell Res. 2012;22(4):624–36.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol. 2009;10(2):126–39.

    CAS  PubMed  Google Scholar 

  • Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011;39 suppl 1:D152–7.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet. 2010;11(9):597–610.

    CAS  PubMed  Google Scholar 

  • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11(3):204–20.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lisch D. Epigenetic regulation of transposable elements in plants. Annu Rev Plant Biol. 2009;60(1):43–66.

    CAS  PubMed  Google Scholar 

  • Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci. 2008;105(8):3145–50.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8(4):272–85.

    CAS  PubMed  Google Scholar 

  • Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci. 2007;104(11):4536–41.

    CAS  PubMed Central  PubMed  Google Scholar 

Further Readings

  • Allen E, Xie Z, Gustafson AM, Sung G-H, Spatafora JW, Carrington JC. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet. 2004;36(12):1282–90.

    CAS  PubMed  Google Scholar 

  • Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005;121(2):207–21.

    CAS  PubMed  Google Scholar 

  • Aravin AA, Hannon GJ, Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 2007;318:761–4.

    CAS  PubMed  Google Scholar 

  • Aukerman MJ, Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell. 2003;15(11):2730–41.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ausin I, Mockler TC, Chory J, Jacobsen SE. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol. 2009;16(12):1325–7.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ausin I, Greenberg MVC, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee T-F, Feng S, Española SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci. 2012;109(22):8374–81.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Axtell MJ. Evolution of microRNAs and their targets: are all microRNAs biologically relevant? Biochim Biophy Acta (BBA) Gene Regul Mech. 2008;1779(11):725–34.

    CAS  Google Scholar 

  • Azevedo J, Garcia D, Pontier D, Ohnesorge S, Yu A, Garcia S, Braun L, Bergdoll M, Hakimi MA, Lagrange T, Voinnet O. Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev. 2010;24(9):904–15.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136(2):215–33.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Baumberger N, Baulcombe DC. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA. 2005;102(33):11928–33.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ben Amor B, Wirth S, Merchan F, Laporte P, d‘Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M. Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 2009;19(1):57–69.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Brodersen P, Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol. 2009;10(2):141–8.

    CAS  PubMed  Google Scholar 

  • Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O. Widespread translational inhibition by plant miRNAs and siRNAs. Science. 2008;320(5880):1185–90.

    CAS  PubMed  Google Scholar 

  • Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA. Reprogramming of dna methylation in pollen guides epigenetic inheritance via small RNA. Cell. 2012;151(1):194–205.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol. 2003;13(24):2212–7.

    CAS  PubMed  Google Scholar 

  • Chapman EJ, Estelle M. Mechanism of auxin-regulated gene expression in plants. Annu Rev Genet. 2009;43(1):265–85.

    CAS  PubMed  Google Scholar 

  • Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science. 2004;303(5666):2022–5.

    CAS  PubMed  Google Scholar 

  • Chen H-M, Li Y-H, Wu S-H. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci. 2007;104(9):3318–23.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chen H-M, Chen L-T, Patel K, Li Y-H, Baulcombe DC, Wu S-H. 22-nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci. 2010;107(34):15269–74.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chitwood DH, Timmermans MCP. Target mimics modulate miRNAs. Nat Genet. 2007;39(8):935–6.

    CAS  PubMed  Google Scholar 

  • Chitwood DH, Nogueira FTS, Howell MD, Montgomery TA, Carrington JC, Timmermans MCP. Pattern formation via small RNA mobility. Genes Dev. 2009;23(5):549–54.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell. 2002;110(1):33–42.

    CAS  PubMed  Google Scholar 

  • Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452(7184):215–9.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cuperus J, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke R, Takeda A, Sullivan C, Gilbert S, Montgomery T, Carrington J. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol. 2010;17:997–1003.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell Online. 2011;23(2):431–42.

    CAS  Google Scholar 

  • Dong Z, Han M-H, Fedoroff N. The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci. 2008;105(29):9970–5.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell. 2012;151(1):167–80.

    CAS  PubMed Central  PubMed  Google Scholar 

  • El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi M-A, Jacobsen SE, Cooke R, Lagrange T. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 2007;21(20):2539–44.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Eun C, Lorkovic ZJ, Naumann U, Long Q, Havecker ER, Simon SA, Meyers BC, Matzke AJM, Matzke M. AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS ONE. 2011;6(10):e25730.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol: CB. 2006;16(9):939–44.

    CAS  PubMed  Google Scholar 

  • Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE. 2007;2(2):e219.

    PubMed Central  PubMed  Google Scholar 

  • Fenselau de Felippes F, Schneeberger K, Dezulian T, Huson DH, Weigel D. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA. 2008;14(12):2455–9.

    CAS  PubMed Central  Google Scholar 

  • Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet. 2008;9(2):102–14.

    CAS  PubMed  Google Scholar 

  • Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J. Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet. 2007;39(8):1033–7.

    CAS  PubMed  Google Scholar 

  • Fusaro AF, Correa RL, Nakasugi K, Jackson C, Kawchuk L, Vaslin MFS, Waterhouse PM. The Enamovirus P0 protein is a silencing suppressor which inhibits local and systemic RNA silencing through AGO1 degradation. Virology. 2012;426(2):178–87.

    CAS  PubMed  Google Scholar 

  • Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, Huijser P. The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007;49(4):683–93.

    CAS  PubMed  Google Scholar 

  • Gao Z, Liu H-L, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJM, Matzke M, Pikaard CS, Zhu J-K. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010;465(7294):106–9.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gasciolli V, Mallory AC, Bartel DP, Vaucheret H. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol: CB. 2005;15(16):1494–500.

    CAS  PubMed  Google Scholar 

  • German MA, Pillay M, Jeong D-H, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotech. 2008;26(8):941–6.

    CAS  Google Scholar 

  • Ghildiyal M, Zamore PD. Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009;10(2):94–108.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Giner A, Lakatos L, García-Chapa M, López-Moya JJ, Burgyán J. Viral protein inhibits RISC activity by Argonaute binding through conserved WG/GW motifs. PLoS Pathog. 2010;6(7):e1000996.

    PubMed Central  PubMed  Google Scholar 

  • Glick E, Zrachya A, Levy Y, Mett A, Gidoni D, Belausov E, Citovsky V, Gafni Y. Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein. Proc Natl Acad Sci. 2008;105(1):157–61.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gutierrez-Marcos JF, Dickinson HG. Epigenetic reprogramming in plant reproductive lineages. Plant Cell Physiol. 2012;53(5):817–23.

    CAS  PubMed  Google Scholar 

  • Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 1999;286(5441):950–2.

    CAS  PubMed  Google Scholar 

  • Han M-H, Goud S, Song L, Fedoroff N. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proc Natl Acad Sci USA. 2004;101(4):1093–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  • He X-J, Hsu Y-F, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu H-L, Wang C-S, Jin H, Zhu J-K. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell. 2009;137(3):498–508.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell Online. 2007;19(3):926–42.

    CAS  Google Scholar 

  • Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. Genome-wide demethylation of Arabidopsis endosperm. Science. 2009;324(5933):1451–4.

    CAS  PubMed  Google Scholar 

  • Huang L, Jones AME, Searle I, Patel K, Vogler H, Hubner NC, Baulcombe DC. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat Struct Mol Biol. 2009;16(1):91–3.

    CAS  PubMed  Google Scholar 

  • Hutvagner G, Simard MJ. Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol. 2008;9:22–32.

    CAS  PubMed  Google Scholar 

  • Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360–4.

    CAS  PubMed  Google Scholar 

  • Isshiki M, Kodama H. Plant RNAi and Crop Improvement. Springer Netherlands: Molecular Techniques in Crop Improvement. S. M. Jain and D. S. Brar; 2009. p. 653–73.

    Google Scholar 

  • Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 2002;416:556–60.

    CAS  PubMed  Google Scholar 

  • Jamous RM, Boonrod K, Fuellgrabe MW, Ali-Shtayeh MS, Krczal G, Wassenegger M. The helper component-proteinase of the Zucchini yellow mosaic virus inhibits the Hua Enhancer 1 methyltransferase activity in vitro. J Gen Virol. 2011;92(9):2222–6.

    CAS  PubMed  Google Scholar 

  • Jeffrey AJ, Trevor LS, Eric JR. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet. 1999;22:94–7.

    Google Scholar 

  • Ji L, Liu X, Yan J, Wang W, Yumul RE, Kim YJ, Dinh TT, Liu J, Cui X, Zheng B, Agarwal M, Liu C, Cao X, Tang G, Chen X. ARGONAUTE10 and ARGONAUTE1 regulate the termination of floral stem cells through two microRNAs in Arabidopsis. PLoS Genet. 2011;7(3):e1001358.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jin H, Zhu J-K. A viral suppressor protein inhibits host RNA silencing by hooking up with Argonautes. Genes Dev. 2010;24(9):853–6.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol. 2006;57(1):19–53.

    CAS  PubMed  Google Scholar 

  • Jullien PE, Mosquna A, Ingouff M, Sakata T, Ohad N, Berger F. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol. 2008;6(8):e194.

    PubMed Central  PubMed  Google Scholar 

  • Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316(5830):1484–8.

    CAS  PubMed  Google Scholar 

  • Kasschau K, Fahlgren N, Chapman E, Sullivan C, Cumbie J, Givan S, Carrington J. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007;5:e57.

    PubMed Central  PubMed  Google Scholar 

  • Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. Role of CG and Non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol. 2003;13(5):421–6.

    CAS  PubMed  Google Scholar 

  • Khraiwesh B, Zhu J-K, Zhu J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta (BBA) Gene Regul Mech. 2012;1819(2):137–48.

    CAS  Google Scholar 

  • Kim YJ, Zheng B, Yu Y, Won SY, Mo B, Chen X. The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana. EMBO J. 2011;30(5):814–22.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science. 2004;303(5657):521–3.

    CAS  PubMed  Google Scholar 

  • Kurihara Y, Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc Natl Acad Sci U S A. 2004;101(34):12753–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  • 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(2):206–12.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lakatos L, Szittya G, Silhavy D, Burgyan J. Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses. EMBO J. 2004;23(4):876–84.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lares MR, Rossi JJ, Ouellet DL. RNAi and small interfering RNAs in human disease therapeutic applications. Trends Biotechnol. 2010;28(11):570–9.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu J-K, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol: CB. 2010;20(10):951–6.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 2011;7(7):e1002195.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee JT. Epigenetic regulation by long noncoding RNAs. Science. 2012;338(6113):1435–9.

    CAS  PubMed  Google Scholar 

  • 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(5):843–54.

    CAS  PubMed  Google Scholar 

  • Lee Y, Kim M, Han J, Yeom K-H, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004;23(20):4051–60.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Li J, Yang Z, Yu B, Liu J, Chen X. Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol. 2005;15(16):1501–7.

    CAS  PubMed  Google Scholar 

  • Li S, Liu L, Zhuang X, Yu Y, Liu X, Cui X, Ji L, Pan Z, Cao X, Mo B, Zhang F, Raikhel N, Jiang L, Chen X. MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell. 2013;153(3):562–74.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 2001;292(5524):2077–80.

    CAS  PubMed  Google Scholar 

  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133(3):523–36.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science. 2002;297(5589):2053–6.

    CAS  PubMed  Google Scholar 

  • Lobbes D, Rallapalli G, Schmidt DD, Martin C, Clarke J. SERRATE: a new player on the plant microRNA scene. EMBO Rep. 2006;7(10):1052–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Luo Z, Chen Z. Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-Mediated RNA silencing in Arabidopsis. Plant Cell Online. 2007;19(3):943–58.

    CAS  Google Scholar 

  • Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette M-L, Mireau H, Peeters N, Renou J-P, Szurek B, Taconnat L, Small I. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell Online. 2004;16(8):2089–103.

    CAS  Google Scholar 

  • Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 2006;16(4):510–9.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Malik S, Roeder RG. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet. 2010;11(11):761–72.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet. Suppl:S31-6, 2006.

    Google Scholar 

  • Manavella PA, Koenig D, Weigel D Plant secondary siRNA production determined by microRNA-duplex structure. Proc Nat Acad Sci. 2012;109(7):2461–6.

    Google Scholar 

  • Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol. 2013;20(3):300–7.

    CAS  PubMed  Google Scholar 

  • Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu J-K. Criteria for annotation of plant microRNAs. Plant Cell Online. 2008;20(12):3186–90.

    CAS  Google Scholar 

  • Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature. 2001;411(6834):212–4.

    CAS  PubMed  Google Scholar 

  • Montgomery T, Howell M, Cuperus J, Li D, Hansen J, Alexander A, Chapman E, Fahlgren N, Allen E, Carrington J. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell. 2008;133:128–41.

    CAS  PubMed  Google Scholar 

  • Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell Online. 1990;2(4):279–89.

    CAS  Google Scholar 

  • Olmedo-Monfil V, Duran-Figueroa N, Arteaga-Vazquez M, Demesa-Arevalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA, Vielle-Calzada J-P. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature. 2010;464(7288):628–32.

    CAS  PubMed  Google Scholar 

  • Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol. 2002;12(17):1484–95.

    CAS  PubMed  Google Scholar 

  • Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS. Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci U S A. 2005;102(10):3691–6.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pekker I, Alvarez JP, Eshed Y. Auxin response factors mediate Arabidopsis organ asymmetry via modulation of KANADI activity. Plant Cell Online. 2005;17(11):2899–910.

    CAS  Google Scholar 

  • Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 2004;18(19):2368–79.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pulido A, Laufs P. Co-ordination of developmental processes by small RNAs during leaf development. J Exp Bot. 2010;61(5):1277–91.

    CAS  PubMed  Google Scholar 

  • Qi Y, Denli AM, Hannon GJ. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell. 2005;19(3):421–8.

    CAS  PubMed  Google Scholar 

  • Qi Y, He X, Wang X-J, Kohany O, Jurka J, Hannon GJ. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature. 2006;443(7114):1008–12.

    PubMed  Google Scholar 

  • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 2006;20(24):3407–25.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ramachandran V, Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science. 2008;321(5895):1490–2.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu J-K, Hagen G, Guilfoyle TJ, Paša-Tolić L, Pikaard CS. Subunit COmpositions of the RNA-silencing enzymes pol IV and pol V reveal their origins as specialized forms of RNA polymerase II. Mol Cell. 2009;33(2):192–203.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev. 2002;16(13):1616–26.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ren G, Chen X, Yu B. Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis. Curr Biol. 2012;22(8):695–700.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rymarquis LA, Souret FF, Green PJ. Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories. RNA. 2011;17(3):501–11.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Shen B, Goodman HM. Uridine addition after microRNA-directed cleavage. Science. 2004;306(5698):997.

    CAS  PubMed  Google Scholar 

  • Siomi MC, Sato K, Pezic D, Aravin AA. PIWI-interacting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol. 2011;12(4):246–58.

    CAS  PubMed  Google Scholar 

  • Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, FeijÛ JA, Martienssen RA. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009;136(3):461–72.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell Online. 2007;19(5):1507–21.

    CAS  Google Scholar 

  • Song M-G, Kiledjian M. 3′ terminal oligo U-tract-mediated stimulation of decapping. RNA. 2007;13(12):2356–65.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Soppe WJJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJM. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell. 2000;6(4):791–802.

    CAS  PubMed  Google Scholar 

  • Souret FF, Kastenmayer JP, Green PJ. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell. 2004;15(2):173–83.

    CAS  PubMed  Google Scholar 

  • Spitz F, Furlong EEM. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13(9):613–26.

    CAS  PubMed  Google Scholar 

  • Sunkar R, Zhu J-K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell Online. 2004;16(8):2001–19.

    CAS  Google Scholar 

  • Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T. Bursts of retrotransposition reproduced in Arabidopsis. Nature. 2009;461(7262):423–6.

    CAS  PubMed  Google Scholar 

  • van der Krol AR, Mur LA, Beld M, Mol JN, Stuitje AR. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell Online. 1990;2(4):291–9.

    Google Scholar 

  • Vaucheret H. Plant ARGONAUTES. Trends Plant Sci. 2008;13:350–8.

    CAS  PubMed  Google Scholar 

  • Vaucheret H, Vazquez F, Crété P, Bartel DP. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 2004;18(10):1187–97.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Vazquez F, Gasciolli V, CrÈtÈ P, Vaucheret H. The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr Biol: CB. 2004a;14(4):346–51.

    CAS  PubMed  Google Scholar 

  • Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert J-L, Bartel DP, Crété P. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell. 2004b;16(1):69–79.

    CAS  PubMed  Google Scholar 

  • Vongs A, Kakutani T, Martienssen RA, Richards EJ. Arabidopsis thaliana DNA methylation mutants. Science. 1993;260:1926–8.

    CAS  PubMed  Google Scholar 

  • Wierzbicki A, Haag J, Pikaard C. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell. 2008;135:635–48.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet. 2009;41:630–4.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wu H-J, Wang Z-M, Wang M, Wang X-J. Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiol. 2013;161(4):1875–84.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Xie Z, Kasschau KD, Carrington JC. Negative feedback regulation of Dicer-like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr Biol. 2003;13(9):784–9.

    CAS  PubMed  Google Scholar 

  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004;2(5):e104.

    PubMed Central  PubMed  Google Scholar 

  • Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC. Expression of Arabidopsis MIRNA genes. Plant Physiol. 2005a;138(4):2145–54.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Xie Z, Allen E, Wilken A, Carrington JC. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2005b;102(36):12984–9.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yan J, Gu Y, Jia X, Kang W, Pan S, Tang X, Chen X, Tang G. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell. 2012;24:415.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yang L, Liu Z, Lu F, Dong A, Huang H. SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J. 2006;47(6):841–50.

    CAS  PubMed  Google Scholar 

  • Yang L, Wu G, Poethig RS. Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proc Natl Acad Sci. 2012;109(1):315–20.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ye K, Patel DJ. RNA silencing suppressor p21 of beet yellows virus forms an RNA binding octameric ring structure. Structure. 2005;13(9):1375–84.

    CAS  PubMed  Google Scholar 

  • Ye R, Wang W, Iki T, Liu C, Wu Y, Ishikawa M, Zhou X, Qi Y. Cytoplasmic assembly and selective nuclear import of Arabidopsis ARGONAUTE4/siRNA complexes. Mol Cell. 2012;46(6):859–70.

    CAS  PubMed  Google Scholar 

  • Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev. 2005;19(18):2164–75.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X. Methylation as a crucial step in plant microRNA biogenesis. Science. 2005;307(5711):932–5.

    CAS  PubMed  Google Scholar 

  • Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC, Chen X. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci. 2008;105(29):10073–8.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang X, Yuan Y-R, Pei Y, Lin S-S, Tuschl T, Patel DJ, Chua N-H. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 2006;20(23):3255–68.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang C, Ng DWK, Lu J, Chen ZJ. Roles of target site location and sequence complementarity in trans-acting siRNA formation in Arabidopsis. Plant J. 2012a;69(2):217–26.

    CAS  PubMed  Google Scholar 

  • Zhang C-J, Ning Y-Q, Zhang S-W, Chen Q, Shao C-R, Guo Y-W, Zhou J-X, Li L, Chen S, He X-J. IDN2 and its paralogs form a complex required for RNA–directed DNA methylation. PLoS Genet. 2012b;8(5):e1002693.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh TT, Meyers BC, Mo B, Chen X. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr Biol. 2012;22(8):689–94.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zheng X, Zhu J, Kapoor A, Zhu J-K. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO. 2007;J26(6):1691–701.

    Google Scholar 

  • Zheng B, Wang Z, Li S, Yu B, Liu J-Y, Chen X. Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 2009;23:2850–60.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhu H, Hu F, Wang R, Zhou X, Sze S-H, Liou LW, Barefoot A, Dickman M, Zhang X. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell. 2011;145(2):242–56.

    CAS  PubMed  Google Scholar 

  • Zilberman D, Cao X, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716–9.

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA

    So Youn Won, Rae Eden Yumul & Xuemei Chen

  2. Howard Hughes Medical Institute, University of California, Riverside, CA, 92521, USA

    Xuemei Chen

Authors
  1. So Youn Won
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rae Eden Yumul
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xuemei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xuemei Chen .

Editor information

Editors and Affiliations

  1. Ames, Iowa, USA

    Stephen H. Howell

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this entry

Cite this entry

Won, S.Y., Yumul, R.E., Chen, X. (2013). Nucleus and Genome: Small RNAs. In: Howell, S. (eds) Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0263-7_3-1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0263-7_3-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4939-0263-7

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics

Search

Navigation