Identification of microRNAs potentially involved in male sterility of Brassica campestris ssp. chinensis using microRNA array and quantitative RT-PCR assays

• Autorzy: Jiang J. , Jiang J. , Yang Y. , Cao J.
• Języki publikacji: EN

Abstrakty

EN

microRNAs (miRNAs) are a class of newly identified, noncoding, small RNA molecules that negatively regulate gene expression. Many miRNAs are reportedly involved in plant growth, development and stress response processes. However, their roles in the sexual reproduction mechanisms in flowering plants remain unknown. Pollen development is an important process in the life cycle of a flowering plant, and it is closely related to the yield and quality of crop seeds. This study aimed to identify miRNAs involved in pollen development. A microarray assay was conducted using the known complementary sequences of plant miRNAs as probes on inflorescences of a sterile male line (Bcajh97-01A) and a fertile male line (Bcajh97-01B) of the Brassica campestris ssp. chinensis cv. ‘Aijiaohuang’ genic male sterility sister line system (Bcajh97-01A/B). The results showed that 44 miRNAs were differently expressed in the two lines. Of these, 15 had over 1.5-fold changes in their transcript levels, with 9 upregulated and 6 downregulated miRNAs in inflorescences of ‘Bcajh97-01A’ sterile line plants. We then focused on 3 of these 15 miRNAs (miR158, miR168 and miR172). Through computational methods, 13 family members were predicted for these 3 miRNAs and 22 genes were predicted to be their candidate target genes. By using 5’ modified RACE, 2 target genes of miR168 and 5 target genes of miR172 were identified. Then, qRT-PCR was applied to verify the existence and expression patterns of the 3 miRNAs in the flower buds at five developmental stages. The results were generally consistent with those of the microarray. Thus, this study may give a valuable clue for further exploring the miRNA group that may function during pollen development.

• Wydawca: -
• Czasopismo: Cellular and Molecular Biology Letters
• Rocznik: 2013
• Tom: 18
• Numer: 3
• Opis fizyczny: p.416-432,fig.,ref.

Twórcy

autor

Jiang J.

• Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China

autor

Jiang J.

• Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China

autor

Yang Y.

• Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China

autor

Cao J.

• Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China

Bibliografia

• 1. Sun, G. MicroRNAs and their diverse functions in plants. Plant Mol. Biol. 80 (2012) 17-36.
• 2. He, S., Yang, Z., Skogerbo, G., Ren, F., Cui, H., Zhao, H., Chen, R. and Zhao, Y. The properties and functions of virus encoded microRNA, siRNA and other small noncoding RNAs. Crit. Rev. Microbiol. 34 (2008) 175-188.
• 3. Pfeffer, S., Zavolan, M., Grasser, F.A., Chien, M., Russo, J.J., Ju, J., John, B., Enright, A.J., Marks, D., Sander, C. and Tuschl, T. Identification of virusencoded microRNAs. Science 304 (2004) 734-736.
• 4. Siomi, H. and Siomi, M.C. Posttranscriptional regulation of microRNA biogenesis in animals. Mol. Cell. 38 (2010) 323-332.
• 5. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism and function. Cell 116 (2004) 281-297.
• 6. Chen, X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303 (2004) 2022-2025.
• 7. Voinnet, O. Origin, biogenesis and activity of plant microRNAs. Cell 136 (2009) 669-687.
• 8. Lee, R.C., Feinbaum, R.L. and Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854.
• 9. Floyd, S.K. and Bowman, J.L. Gene regulation: ancient microRNA target sequences in plants. Nature 428 (2004) 485-486.
• 10. Guo, H.S., Xie, Q., Fei, J.F. and Chua, N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. Plant Cell 17 (2005) 1376-1386.
• 11. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B. and Bartel, D.P. Prediction of plant microRNA targets. Cell 110 (2002) 513-520.
• 12. Yamasaki, H., Abdel-Ghany, S.E., Cohu, C.M., Kobayashi, Y., Shikanai, T. and Pilon, M. Regulation of copper homeostasis by micro-RNA in Arabidopsis. J. Biol. Chem. 282 (2007) 16369-16378.
• 13. Sunkar, R., Chinnusamy, V., Zhu, J. and Zhu, J.K. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 12 (2007) 301-309.
• 14. Ruiz-Ferrer, V. and Voinnet, O. Roles of plant small RNAs in biotic stress responses. Annu. Rev. Plant Biol. 60 (2009) 485-510.
• 15. Katiyar-Agarwal, S. and Jin, H. Role of small RNAs in host-microbe interactions. Annu. Rev. Phytopathol. 48 (2010) 225-246.
• 16. Grant-Downton, R., Le Trionnaire, G., Schmid, R., Rodriguez-Enriquez, J., Hafidh, S., Mehdi, S., Twell, D. and Dickinson, H. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana. BMC Genomics 10 (2009) 643-658. DOI:10.1186/1471-2164-10-643.
• 17. Chambers, C. and Shuai, B. Profiling microRNA expression in Arabidopsis pollen using microRNA array and real-time PCR. BMC Plant Biol. 9 (2009) 87-96. DOI:10.1186/1471-2229-9-87.
• 18. Slotkin, R.K., Vaughn, M., Borges, F., Tanurdzic, M., Becker, J.D., Feijo, J.A. and Martienssen, R.A. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136 (2009) 461-472.
• 19. Borges, F., Pereira, P.A., Slotkin, R.K., Martienssen, R.A. and Becker, J.D. MicroRNA activity in the Arabidopsis male germline. J. Exp. Bot. 62 (2011) 1611-1620.
• 20. Sunkar, R. and Jagadeeswaran, G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 8 (2008) 37-49. DOI:10.1186/1471-2229-8-37.
• 21. Glowacki, S., Macioszek, V.K. and Kononowicz, A. R proteins as fundamentals of plant innate immunity. Cell. Mol. Biol. Lett. 16 (2011) 373-396.
• 22. He, X.F., Fang, Y.Y., Feng, L. and Guo, H.S. Characterization of conserved and novel microRNAs and their targets, including a TuMV-induced TIR- NBS-LRR class R gene-derived novel miRNA in Brassica. FEBS Lett. 582 (2008) 2445-2452.
• 23. Wang, L., Wang, M.B., Tu, J.X., Helliwell, C.A., Waterhouse, P.M., Dennis, E.S., Fu, T.D. and Fan, Y.L. Cloning and characterization of microRNAs from Brassica napus. FEBS Lett. 581 (2007) 3848-3856.
• 24. Huang, L., Cao, J., Ye, W., Liu, T., Jiang, L. and Ye, Y. Transcriptional differences between the male-sterile mutant bcms and wild-type Brassica campestris ssp.chinensis reveal genes related to pollen development. Plant Biol. 10 (2008) 342-355.
• 25. Huang, L., Ye, W., Liu, T. and Cao, J. Characterization of the male-sterile line ‘Bcajh97-01A/B’ and identification of candidate genes for genic male sterility in Chinese cabbage-pak-choi. J. Am. Soc. Hortic. Sci. 134 (2009) 632-640.
• 26. Bolstad, B.M., Irizarry, R.A., Astrandand, M. and Speed, T.P. A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias. Bioinfo 19 (2003) 185-193.
• 27. Gao, X., Gulari, E. and Zhou, X. In situ synthesis of oligonucleotide microarrays. Biopolymers 73 (2004) 579-596.
• 28. Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.Y., Srivannavit, O., Gulari, E., Gao, X. and Zhou, X. Microfluidic biochip for nucleic acid and protein analysis. Methods Mol. Biol. 382 (2007) 287-312.
• 29. Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940.
• 30. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415.
• 31. Zhang, B.H., Pan, X.P., Cox, S.B., Cobb, G.P. and Anderson, T.A. Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci. 63 (2006) 246-254.
• 32. Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., GriffithsJones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D. and Zhu, J.K. Criteria for annotation of plant MicroRNAs. Plant Cell 20 (2008) 3186-3190.
• 33. Dai, X. and Zhao, P.X. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res. 39 (2011) W155-159. DOI:10.1093/nar/gkr319.
• 34. Livak, K.J. and Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta CT) method. Methods 25 (2001) 402-408.
• 35. Wu, M.F., Tian, Q. and Reed, J.W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression and regulates both female and male reproduction. Development 133 (2006) 4211-4218.
• 36. Wei, L.Q., Yan, L.F. and Wang, T. Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol. 12 (2011) R53. DOI: 10.1186/gb-2011-12-6-r53.
• 37. Moxon, S., Schwach, F., Dalmay, T., Maclean, D., Studholme, D.J. and Moulton, V. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics 24 (2008) 2252-2253.
• 38. Xie, F. and Zhang, B. Target-align: a tool for plant microRNA target identification. Bioinformatics 26 (2010) 3002-3003.
• 39. Bonnet, E., He, Y., Billiau, K. and Van de Peer, Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26 (2010) 1566-1568.
• 40. Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Sys. 23 (1992) 263-286.
• 41. San, M.D. and Agorreta, A. Molecular systematics: A synthesis of the common methods and the state of knowledge. Cell. Mol. Biol. Lett. 15 (2010) 311-341.
• 42. Aukerman, M.J. and Sakai, H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15 (2003) 2730-2741.
• 43. Jones-Rhoades, M.W. and Bartel, D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 (2004) 787-799.
• 44. Song, C., Jia, Q., Fang, J., Li, F., Wang, C. and Zhang, Z. Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biol. (Stuttgart) 12 (2010) 927-934.

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