MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Grant Downton, Robert ^a   Le Trionnaire, Gael ^b   Schmid, Ralf ^b   Rodriguez Enriquez, Josefina ^c   Hafidh, Said ^b   Mehdi, Saher ^a   Twell, David ^b   Dickinson, Hugh ^a  

^a Department of Plant Sciences ^*  (United Kingdom)

^b UNIVERSITY OF LEICESTER   (United Kingdom)

^c UNIVERSIDAD DE LA LAGUNA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; SMALL INTERFERING RNA; PLANT RNA;

ARABIDOPSIS; ARTICLE; DNA SYNTHESIS; GENE EXPRESSION; GENE SEQUENCE; GENETIC VARIABILITY; MALE GAMETOPHYTE; MULTIGENE FAMILY; NONHUMAN; PLANT LEAF; POLLEN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA EXTRACTION; BIOLOGY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAGNOLIOPHYTA;

ARABIDOPSIS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLLEN; RNA, PLANT; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, RNA;

EID: 74549162664     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-643     Document Type: Article

References (52)

1. Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet 2006, 38:S31-S36. 10.1038/ng1791, 16736022.
2. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 2006, 20(7):759-771. 10.1101/gad.1410506, 16600909.
3. Fang Y, Spector DL. Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Current Biology 2007, 17(9):818-823. 10.1016/j.cub.2007.04.005, 1950788, 17442570.
4. Song L, Han MH, Lesicka J, Fedoroff N. Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body. Proceedings of the National Academy of Sciences 2007, 104(13):5437-5342.
5. Baumberger N, Baulcombe D. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences 2005, 102(33):11928-11933.
6. 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):1185-1190. 10.1126/science.1159151, 18483398.
7. Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants. Cell 2006, 127(3):565-577. 10.1016/j.cell.2006.09.032, 17081978.
8. Yoshikawa M, Peragine A, Park MY, Poethig RS. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 2005, 19(18):2164-2175. 10.1101/gad.1352605, 1221887,1221887, 16131612.
9. 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):2368-2379. 10.1101/gad.1231804, 522987, 15466488.
10. 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. The Plant Cell Online 2007, 19(3):926-942.
11. Felippes FF, Weigel D. Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173. EMBO Rep 2009, 10(3):264-270. 10.1038/embor.2008.247, 19180117.
12. Ronemus M, Vaughn MW, Martienssen RA. MicroRNA-targeted and small interfering RNA-mediated argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis regulate mRNA degradation. The Plant Cell Online 2006, 18(7):1559-1574.
13. Chan SWL. Inputs and outputs for chromatin-targeted RNAi. Trends Plant Sci 2008, 13(7):383-389. 10.1016/j.tplants.2008.05.001, 18550415.
14. Pikaard CS, Haag JR, Ream T, Wierzbicki AT. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 2008, 13(7):390-397. 10.1016/j.tplants.2008.04.008, 2679257, 18514566.
15. Meyers BC, Souret FF, Lu C, Green PJ. Sweating the small stuff: microRNA discovery in plants. Curr Opin Biotechnol 2006, 17(2):139-146.
16. Pina C, Pinto F, Feijo JA, Becker JD. Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiol 2005, 138(2):744-756. 10.1104/pp.104.057935, 1150393, 15908605.
17. Grant-Downton R, Hafidh S, Twell D, Dickinson HG. Small RNA Pathways Are Present and Functional in the Angiosperm Male Gametophyte. Molecular Plant 2009, 2(3):500-512. 10.1093/mp/ssp003, 19825633.
18. Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijo JA, Becker JD. Comparative transcriptomics of Arabidopsis thaliana sperm cells. Plant Physiol 2008, 1168-1181. 10.1104/pp.108.125229, 2556834, 18667720.
19. Slotkin RK, Vaughn M, Borges F, Tanurdžić M, Becker JD, Feijó JA, Martienssen RA. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009, 136(3):461-472. 10.1016/j.cell.2008.12.038, 19203581.
20. Valoczi A, Varallyay E, Kauppinen S, Burgyan J, Havelda Z. Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant Journal 2006, 47(1):140-151. 10.1111/j.1365-313X.2006.02766.x, 16824182.
21. Sieber P, Wellmer F, Gheyselinck J, Riechmann JL, Meyerowitz EM. Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development 2007, 134(6):1051-1060. 10.1242/dev.02817, 17287247.
22. Linsen SEV, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE. Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods 2009, 6(7):474-476. 10.1038/nmeth0709-474, 19564845.
23. Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ. Criteria for annotation of plant microRNAs. The Plant Cell Online 2008, 20(12):3186-3190.
24. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15(1):78-91. 10.1101/gr.2908205, 540280, 15632092.
25. Warthmann N, Das S, Lanz C, Weigel D. Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae. Mol Biol Evol 2008, 25(5):892-902. 10.1093/molbev/msn029, 18296705.
26. Mallory AC, Vaucheret H. ARGONAUTE 1 homeostasis invokes the coordinate action of the microRNA and siRNA pathways. EMBO Rep 2009, 10(5):521-526. 10.1038/embor.2009.32, 19343050.
27. Kidner CA, Martienssen RA. The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol 2005, 280(2):504-517. 10.1016/j.ydbio.2005.01.031, 15882589.
28. Honys D, Twell D. Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol 2003, 132(2):640-652. 10.1104/pp.103.020925, 167004, 12805594.
29. Honys D, Twell D. Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol 2004, 5(11):R85. 10.1186/gb-2004-5-11-r85, 545776, 15535861.
30. Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD. The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proceedings of the National Academy of Sciences 2002, 99(17):11519-11524.
31. Lechner E, Achard P, Vansiri A, Potuschak T, Genschik P. F-box proteins everywhere. Curr Opin Plant Biol 2006, 9(6):631-638. 10.1016/j.pbi.2006.09.003, 17005440.
32. Kim HJ, Oh SA, Brownfield L, Hong SH, Ryu H, Hwang I, Twell D, Nam HG. Control of plant germline proliferation by SCFFBL17 degradation of cell cycle inhibitors. Nature 2008, 455(7216):1134-1137. 10.1038/nature07289, 18948957.
33. Saha D, Prasad A, Srinivasan R. Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Physiology et Biochemistry 2007, 45(8):521-534.
34. Schmitz-Linneweber C, Small I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 2008, 13(12):663-670. 10.1016/j.tplants.2008.10.001, 19004664.
35. Koizuka N, Imai R, Fujimoto H, Hayakawa T, Kimura Y, Kohno-Murase J, Sakai T, Kawasaki S, Imamura J. Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish. Plant Journal 2003, 34(4):407-415. 10.1046/j.1365-313X.2003.01735.x, 12753581.
36. Beick S, Schmitz-Linneweber C, Williams-Carrier R, Jensen B, Barkan A. The pentatricopeptide repeat protein PPR5 stabilizes a specific tRNA precursor in maize chloroplasts. Mol Cell Biol 2008, 28(17):5337-5347. 10.1128/MCB.00563-08, 2519714, 18591259.
37. de Longevialle AF, Hendrickson L, Taylor NL, Delannoy E, Lurin C, Badger M, Millar AH, Small I. The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana. Plant Journal 2008, 56(1):157-168. 10.1111/j.1365-313X.2008.03581.x, 18557832.
38. Mogensen H. The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany 1996, 83:383-404.
39. Alves-Junior L, Niemeier S, Hauenschild A, Rehmsmeier M, Merkle T. Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana. Nucleic Acids Res 2009, 37(12):4010-4021. 10.1093/nar/gkp272, 2709567, 19417064.
40. Ebbs ML, Bartee L, Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 2005, 25(23):10507-10515. 10.1128/MCB.25.23.10507-10515.2005, 1291251, 16287862.
41. Ebbs ML, Bender J. Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. The Plant Cell Online 2006, 18(5):1166-1176.
42. Arteaga-Vazquez M, Caballero-Perez J, Vielle-Calzada JP. A family of microRNAs present in plants and animals. The Plant Cell Online 2006, 18(12):3355-3369.
43. Rotman N, Durbarry A, Wardle A, Yang WC, Chaboud A, Faure JE, Berger F, Twell D. A novel class of MYB factors controls sperm-cell formation in plants. Curr Biol 2005, 15(3):244-248. 10.1016/j.cub.2005.01.013, 15694308.
44. Boavida LC, Shuai B, Yu HJ, Pagnussat G, Sundaresan V, McCormick S. A Collection of Ds Insertional Mutants Associated With Defects in Male Gametophyte Development and Function in Arabidopsis thaliana. Genetics 2009, 181:1369-1385. 10.1534/genetics.108.090852, 2666506, 19237690.
45. Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crete P, Voinnet O, Robaglia C. Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs. The Plant Cell 2009, 21:1762-1768. 10.1105/tpc.108.063412, 19531599.
46. Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, Lukowitz W. Paternal Control of Embryonic Patterning in Arabidopsis thaliana. Science 2009, 323(5920):1485-1488. 10.1126/science.1167784, 19286558.
47. Gou X, Yuan T, Wei X, Russell SD. Gene expression in the dimorphic sperm cells of Plumbago zeylanica: Transcript profiling, diversity, and relationship to cell type. The Plant journal 2009, 15:33-47.
48. Ramachandran V, Chen X. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 2008, 321(5895):1490-1492. 10.1126/science.1163728, 2570778, 18787168.
49. Moxon S, Schwach F, Dalmay T, MacLean D, Studholme DJ, Moulton V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 2008, 24(19):2252-2253. 10.1093/bioinformatics/btn428, 18713789.
50. Dupl'akova N, Renak D, Hovanec P, Honysova B, Twell D, Honys D. Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. BMC Plant Biol 2007, 7:39. 10.1186/1471-2229-7-39, 1963329, 17645793.
51. Dai X, Zhao PX. pssRNAMiner: a plant short small RNA regulatory cascade analysis server. Nucleic Acids Res 2008, W114-118. 10.1093/nar/gkn297, 2447807, 18474525.
52. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29(9):e45. 10.1093/nar/29.9.e45, 55695, 11328886.