Identification and characterization of small RNAs from vernalizedArabidopsis thaliana

Abstract

MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two major classes of small non-coding RNAs with important roles in the regulation of gene expression, such as mRNA degradation and translational repression, heterochromatin formation, genome defense against transposons and viruses in eukaryotes. MiRNA- and siRNA-directed processes have emerged as a regulatory mechanism for growth and development in both animals and plants. To identify small RNAs that might be involved in vernalization, a process accelerating flowering brought on by a long period of cold, we generated a library of small RNAs from Arabidopsis that had been subject to vernalization. From the analysis of the library, 277 small RNAs were identified. They were distributed throughout all the five chromosomes. While the vast majority of small RNA genes locate on intergenic regions, others locate on repeat-rich regions, centromeric regions, transposon-related genes, and protein-coding genes. Five of them were mapped to convergent overlapping gene pairs. Two-hundred and forty of them were novel endogenous small RNAs that have not been cloned yet from plants grown under normal conditions and other environmental stresses. Seven putative miRNAs were up- or down-regulated by vernalization. In conclusion, many small RNAs were identified from vernalized Arabidopsis and some of these identified small RNAs may play roles in plant responses to vernalization.

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Liteature cited

  1. Arhard R, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral developmenl by a gibberelIin-regulated microRNA. Development131: 3357–3365

    Article  Google Scholar 

  2. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Garrington JC (2004) Evolution of microRNA genes by inverted duplica-Genel36: 1282–1290

    CAS  Google Scholar 

  3. Allen E, Xie Z, Custafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acling siRNA biogenesis in plants. Cell121: 207–221

    PubMed  Article  CAS  Google Scholar 

  4. Aravin A, Tuschl T (2005) Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett579(26): 5830–5840

    PubMed  Article  CAS  Google Scholar 

  5. Aufsatz W, Mette MF, van der Winden J, Matzke M., Matzke AJM (2002) HDA6, a putative hislone deacelylase needed to enhance DNA melhylation induced by double-stranded RNA. EMBO J21: 6812–6841

    Article  Google Scholar 

  6. Aukerman MJ, Sakai H (2003) Regulation of (lowering lime and gel genes. Plant Cell15: 2730–2741

    PubMed  Article  CAS  Google Scholar 

  7. Bartel B, Bartel DP (2003) MicroRNAs: Al the rool of plant developmenl Plant Physiol132: 709–717

    PubMed  Article  CAS  Google Scholar 

  8. Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism. and function. Cell116: 281–297

    PubMed  Article  CAS  Google Scholar 

  9. Baulcombe D (2004) RNA silencing in plants. Nature431: 156–363

    Article  Google Scholar 

  10. Boi S, Solda G, Tenchini ML (2004) Shedding light on the dark side of the genome: Overlapping genes in higher eukaryoles. Curr Genomics5: 509–524

    Article  CAS  Google Scholar 

  11. Bonnet E, Van de Peer Y, Rouze P (2006) The small RNA world of plants. New Phylol171: 451–468

    CAS  Google Scholar 

  12. Borsani O, Jhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-anlisense transcripts regulate salt tolerance in Arabidopsis. Cell7: 1279–1291

    Article  Google Scholar 

  13. Bouche N, Lauressergues D, Gasciolli V, Vaucheret H (2006) An antagonistic Function fro Arabidopsis DCL2 in developmenl and a new Function (or DCL4 in generaling viral siRNAs. EMBO J25: 3347–3356

    PubMed  Article  CAS  Google Scholar 

  14. Denli AM, Hannon GJ (2001) RNAi: an ever-growing puzzle. Trends Biochem Sci4: 196–201

    Google Scholar 

  15. Fagard M, Boutet S, Morel JB, Bellini C, Vaucheret H (2000) AGO1, QDE-2. and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi. and RNA interference in animals. Proc Nail Acad Sci USA97: 11650–11654

    Article  CAS  Google Scholar 

  16. Casciolli V, Mallory AC, Barlel DR Vaucheret H (2005) Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. Curr Biol15: 1494–1500

    Article  Google Scholar 

  17. Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell111: 803–814

    PubMed  Article  CAS  Google Scholar 

  18. Hamilton A, Baulcombe D (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science286: 950–952

    PubMed  Article  CAS  Google Scholar 

  19. Hamilton A, VoinneL O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J21: 4671–4679

    PubMed  Article  CAS  Google Scholar 

  20. Jen CH, Michalopoulos I, Westhead DR, Meyer P (2005) Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. Genome Biol6: R51

    PubMed  Article  Google Scholar 

  21. Jones-Rhoades MW, BarLel DP, Barlel B (2006) MicroRNA and regulatory roles in Plants. Annu Rev Cell Dev Biol18: 707–746

    Google Scholar 

  22. Kasschau KD, Fahlqren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carringlon JC (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol5: e57

    PubMed  Article  Google Scholar 

  23. Kim JH, Lee BH (2006) GROWTH-REGULATING FACTOR4 ofArabidopsis thaliana is required for development of leaves, cotyledons, and shoot apical meristem. J Plant Biol49(6): 463–468

    CAS  Google Scholar 

  24. Kim VN, Nam JW (2006) Genomics of miRNA. TRENDS in Genetics 22(3)

  25. Lau NC, Lim PL, WeinsLein EG, Barlel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditiselegans. Science294: 858–862

    PubMed  Article  CAS  Google Scholar 

  26. Lindow M, Krogh A (2005) Computational evidence for hundreds of non-conserved plant miRNAs. BMC Genomics6: 1999

    Article  Google Scholar 

  27. Liu J, He Y, Amasino R, Chen X (2004) SiRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev18: 2873–2878

    PubMed  Article  CAS  Google Scholar 

  28. Llave C, Kasschau KD, RecLor MA, Carringlon JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell14: 1605–1619

    PubMed  Article  CAS  Google Scholar 

  29. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL (2005) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell17: 2186–2203

    PubMed  Article  CAS  Google Scholar 

  30. Maher C, SLein L, Ware D (2006) Evolution of Arabidopsis microRNA families through duplication events. Genome Res16: 510–519

    PubMed  Article  CAS  Google Scholar 

  31. Meisler G, Tuschl T (2004) Mechanisms of gene silencing by double stranded RNA. Nature431: 343–349.

    Article  Google Scholar 

  32. MeLLe MF, Aufslaz W, van der Winden J, Matzke M, Matzke A (2000) Transcriptional gene silencing and promoter methylation triggered by double-stranded RNA. EMBO J19: 5194–5201.

    Article  Google Scholar 

  33. Michaels SD, Amasino RM (1999) FLOWERINGLOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell11: 949–956

    PubMed  Article  CAS  Google Scholar 

  34. Michaels SD, Amasino RM (2001) Loss ofFLOWERING LOCUS C activity eliminates the late-flowering phenotype ofFRIGIDA and autonomous pathway mutations but ot responsiveness to vernalization. Plant Cell13: 935–942

    PubMed  Article  CAS  Google Scholar 

  35. Onodera Y, Haaq JR, Ream T, Nunes PC, Pontes O, Pikaard CS (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell120: 613–622

    PubMed  Article  CAS  Google Scholar 

  36. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carringlon JC, Weigel D (2003) Control of leaf morphogenesis by microR-NAs. Nature425: 257–263

    PubMed  Article  CAS  Google Scholar 

  37. Papp L, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M, Matzke AJM (2003) Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant physiol132: 1382–1390

    PubMed  Article  CAS  Google Scholar 

  38. 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 inArabidopsis thaliana. Curr Biol12: 1484–1495

    PubMed  Article  CAS  Google Scholar 

  39. Peragine A, Yoshikawa M, Wu G, AlbrechL HL, Poelhig RS (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev18: 2368–2379

    PubMed  Article  CAS  Google Scholar 

  40. Ponles O, Li CF, Nunes PC, Haaq J, Ream U, Vilins A, Jacobson SE, Pikaard CS (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nuclear RNA processing center. Cell126: 79–92

    Article  Google Scholar 

  41. Reinharl BJ, Weinslein EG, Rhoades MW, Barlel B, BarLel DP (2002) MicroRNAs in plants. Genes Dev16: 1616–1626

    Article  Google Scholar 

  42. Schwab R, Palatnik JF, Riesler M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transciptome. Dev Cell8: 517–527

    PubMed  Article  CAS  Google Scholar 

  43. Sheldon CC, Rouse DT, Finnegan EJ, Peacock WJ, Dennis ES (2000) The molecular basis of vernalization: the central role ofFLOWERING LOCUS C (FLC). Proc Natl Acad Sci USA97: 3753–3758

    PubMed  Article  CAS  Google Scholar 

  44. Sigova A, Rhind N, Zamore PDA (2004) single Argonaute protein mediates both transcriptional and posttranscriptional silencing in chizosaccharomyces pombe. Genes Dev18: 2359–2367

    PubMed  Article  CAS  Google Scholar 

  45. Sonlheimer EJ, Carlhew RW (2005) Silence from with: endogenous siRNAs and miRNAs. Cell122: 9–12

    Article  Google Scholar 

  46. Sunkar R, Girke T, Jain PK, Zhu JK (2005a) Cloning and characterization of microRNAs from rice. Plant Cell17: 1397–1411

    Article  CAS  Google Scholar 

  47. Sunkar R, Girke T, Zhu JK (2005b) Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res33: 4443–4454

    Article  CAS  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

  49. Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C, (2007) Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC. PNAS104: 3633–3638

    PubMed  Article  CAS  Google Scholar 

  50. Tang G, Reinharl BJ, Barlel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev17: 49–63

    PubMed  Article  CAS  Google Scholar 

  51. Tomari Y, Zamore PD (2005) Perspective: Machines for RNAi. Genes Dev19: 517–529

    PubMed  Article  CAS  Google Scholar 

  52. Vaucherel H, Vazquez F, Crele P, Barlel DP (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev18: 1187–1197

    Article  Google Scholar 

  53. Vaucherel H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev20: 759–771

    Article  Google Scholar 

  54. Vazquez F, Vaucherel H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilberl JL, Barlel DP, andCrele P (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell16: 69–79

    PubMed  Article  CAS  Google Scholar 

  55. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S et al. (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science303: 672–676

    PubMed  Article  CAS  Google Scholar 

  56. Voinnet O (2001) RNA silencing as a plant immune system against viruses. Trends Genet17: 449–459

    PubMed  Article  CAS  Google Scholar 

  57. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Marlienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science297: 1833–1837

    PubMed  Article  CAS  Google Scholar 

  58. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell17: 2204–2216

    PubMed  Article  CAS  Google Scholar 

  59. Walerhouse PM, Wang MB, Lough T (2001) Gene silencing as an adaptive defense against viruses. Nature411: 834–842

    Article  Google Scholar 

  60. Xie Z, Allen E, Wilken A, Carringlon JC (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA102: 12984–1289

    PubMed  Article  CAS  Google Scholar 

  61. Xie Z, Johansen LK, Guslafson AM, Kasschau KD, Lellis AD, et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol2: E104

    PubMed  Article  Google Scholar 

  62. Yoshikawa M, Peragine A, Park MY, Poelhig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev19: 2164–2175

    PubMed  Article  CAS  Google Scholar 

  63. Yu B, Yang Z, Li J, Minakhina S, Yang M, et al. (2005) Methylation as a crucial step in plant microRNA biogenesis. Science307: 932–935

    PubMed  Article  CAS  Google Scholar 

  64. Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histon methylation. Science299: 716–719

    PubMed  Article  CAS  Google Scholar 

  65. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res31: 3406–3415

    PubMed  Article  CAS  Google Scholar 

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Correspondence to Mijin Oh or Horim Lee or Young-Kook Kim or Jin-Wu Nam or Je-Keun Rhee or Byoung-Tak Zhang or V. Narry Kim or Ilha Lee.

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Oh, M., Lee, H., Kim, YK. et al. Identification and characterization of small RNAs from vernalizedArabidopsis thaliana . J. Plant Biol. 50, 562–572 (2007). https://doi.org/10.1007/BF03030710

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Key words

  • microRNA
  • small interference RNA
  • vernalization