Characterization of target mRNAs for Prunus persica microRNAs using an integrated strategy of PLM-RACE, PPM-RACE and qRT-PCR

Scientia Horticulturae

Volumn 170, Issue , 2014, Pages 8-16

  Zhang, Yanping ^a   Han, Jian ^a   Yu, Mingliang ^b   Ma, Ruijuan ^b   Pervaiz, Tariq ^a   Fang, Jinggui ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Cleavage; Ppe miRNA; PPM RACE; QRT PCR; RLM RACE; Target mRNA

Indexed keywords

BIOCHEMICAL COMPOSITION; FRUIT; GENE EXPRESSION; HORTICULTURE; PHYTOCHEMISTRY; POLYMERASE CHAIN REACTION; RNA;

EID: 84896329821     PISSN: 03044238     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.scienta.2014.02.033     Document Type: Article

References (64)

1. Adai A., Johnson C., Mlotshwa S., Archer-Evans S., Manocha V., Vance V., Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Research 2005, 15:78-91.
2. Addo-Quaye C., Eshoo T.W., Bartel D.P., Axtell M.J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology 2008, 18:758-762.
3. Allison M.C., Bouché N. microRNA-directed regulation: to cleave or not to cleave. Trends in Plant Science 2008, 13:359-367.
4. Allison M.C., Bartel D.P., Bartel B. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 2005, 17:1360-1375.
5. Aukerman M.J., Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741.
6. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
7. Brodersen P., Sakvarelidze-Achard L., Bruun-Rasmussen M., Dunoyer P., Yamamoto Y.Y., Sieburth L., et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 2008, 320:1185.
8. Carra A., Mica E., Gambino G., Pindo M., Moser C., Enrico M.P., Schubert A. Cloning and characterization of small non-coding RNAs from grape. Plant Journal 2009, 59:750-763.
9. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science 2003, 301:336-338.
10. Chekulaeva M., Filipowicz W. Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Current Opinion in Cell Biology 2009, 21:452-460.
11. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
12. Chen X. MicroRNA biogenesis and function in plants. FEBS Letters 2005, 579:5923-5931.
13. Chen X.M. MicroRNA metabolism in plants. Current Topics in Microbiology and Immunology 2008, 320:117-136.
14. Chuck G., Candela H., Hake S. Big impacts by small RNAs in plant development. Current Opinion in Plant Biology 2009, 12:81-86.
15. Colaiacovo M., Bernardo L., Centomani I., Crosatti C., Giusti L., Tacconi L., Orrù G., Lamontanara A., Cattivelli L., Faccioli P. A survey of microRNA length variants contributing to miRNome complexity in peach (Prunus persica L.). Frontiers in Plant Science 2012, 3:165.
16. Czechowski T., Stitt M., Altmann T., Udvardi M.K., Scheible W.R. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiology 2005, 139:5-17.
17. Dai X., Zhao P.X. PsRNATarget: a plant small RNA target analysis server. Nucleic Acids Research 2011, 39:155-159.
18. Elbashir S.M., Lendeckel W., Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes and Development 2001, 15:188-200.
19. Felippes F.F., Schneeberger K., Dezulain T., Huson D.H., Weigel D. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 2008, 14:2455-2459.
20. Gandikota M., Birkenbihl R.P., Höhmann S., Cardon G.H., Saedler H., Huijsr 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 Journal 2007, 49:683-693.
21. Gao Z., Shi X., Luo T., Cai B., Zhang Z., Cheng Z., Zhuang W. Identification and validation of potential conserved micrornas and their targets in peach (Prunus persica). Molecules and Cells 2012, 34:239-249.
22. Garcia D. A miRacle in plant development: role of microRNAs in cell differentiation and patterning. Seminars in Cell and Developmental Biology 2008, 19:586-595.
23. German M.A., Pillay M., Jeong D.H., Hetawal A., Luo S., Janardhanan P., Kannan V., Rymarquis L.A., Nobuta K., German R., Paoli E.D., Lu C., Schroth G., Meyers B.C., Green P.J. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nature Biotechnology 2008, 26:941-946.
24. Guo H.S., Xie Q., Fei J.F., Chua N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 2005, 17:1376-1386.
25. Jones-Rhoades, Bartel D.P. Computational identification of plant micro-RNAs and their targets, including a stress-induced miRNA. Molecular Cell 2004, 14:787-799.
26. Jung J., Seo P.J., Park C.-M. MicroRNA biogenesis and function in higher plants. Plant Biotechnology Reports 2009, 3:111-126.
27. Kasschau K.D., Xie Z., Allen E., Llave C., Chapman E.J., Krizan K.A. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Developmental Cell 2003, 4:205-217.
28. Krol J., Loedige I., Filipowicz W. The widespread regulation of microRNA biogenesis, funcation and decay. Nature Reviews Genetics 2010, 11:597-610.
29. Lanet E., Delannoy E., Sormani R., Floris M., Brodersen P., Patrice C. Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 2009, 21:1762-1768.
30. Lauter N., Kampani A., Carlson S., Goebel M., Moose S.P. microRNA172 down-regulates glossy 15 to promote vegetative phase change in maize. Proceedings of the National Academy of Science of the United States of America 2005, 102:9412-9417.
31. Llave C., Xie Z.X., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056.
32. Mallory A.C., Vaucheret H. MicroRNAs: something important between the genes. Current Opinion in Plant Biology 2004, 7:120-125.
33. Mallory A.C., Bouché N. MicroRNA-directed regulation: to cleave or not to cleave. Trends in Plant Science 2008, 13:359-367.
34. Mallory A.C., Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nature Genetics 2006, 38(Suppl):S31-S36.
35. Mica E., Piccolo V., Delledonne M., Ferrarini A., Pezzotti M., Casati C. Correction: high throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 2010, 11:9.
36. Moxon S., Jing R., Szittya G., Schwach F., Pilcher R.L., Moulton V. Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Research 2008, 18:1602-1609.
37. Nag A., Jack T. Chapter twelve-sculpting the flower; the role of microRNAs in flower development. Current Topics in Developmental Biology 2010, 91:349-378.
38. Nag A., King S., Jack T. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. Proceedings of the National Academy of Science of the United States of America 2009, 106:22534-22539.
39. Navarro L., Dunoyer P., Jay F., Arnold B., Dharmasiri N., Estelle M., Voinnet O., Jones J.D.G. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312:436-439.
40. Palatnik J.F., Allen E., Wu X., Schommer C., Schwab R., Carrington J.C., Weigel D. Control of leaf morphogenesis by microRNAs. Nature 2003, 425:257-263.
41. Palatnik J.F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Husan D., Carrington J.C., Weigel D. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Developmental Cell 2007, 13:115-125.
42. Pantaleo V., Szittya G., Moxon S., Miozzi L., Moulton V., Dalmay T. Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant Journal 2010, 62:960-976.
43. Phillips J.R., Dalmay T., Bartels D. The role of small RNAs in abiotic stress. FEBS Letters 2007, 581:3592-3597.
44. Ramakers C., Ruijter J.M., Deprez R.H., Moorman A.F.M. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neuroscience Letters 2003, 33:62-66.
45. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell 2002, 110:513-520.
46. Shi R., Chiang V.L. Facile means for quantifying microRNA expression by real-time PCR. BioTechniques 2005, 39:519-525.
47. Song C.N., Fang J.G., Wang C., Guo L., Nicholas K.K., Ma Z. miR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs. PLoS ONE 2010, 5:e10861.
48. Song C.N., Jia Q.D., Fang J.G., Li F., Wang C., Zhang Z. Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biology 2010, 12:927-934.
49. Sunkar R., Chinnusamy V., Zhu J., Zhu J.K. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends in Plant Science 2007, 12:301-309.
50. Sunkar R., Girke T., Jain P.K., Zhu J.K. Cloning and characterization of microRNAs from rice. Plant Cell 2005, 17:1397-1411.
51. Thomson D.W., Bracken C.P., Goodal G.J. Experimental strategies for microRNA target identification. Nucleic Acids Research 2011, 39:6845-6853.
52. Vaucheret H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes and Development 2006, 20:759-771.
53. Verde I., Abbott A.G., Scalabrin S., Jung S., Shu S., Marroni F., Zhebentyayeva T., Dettori M.T., Grimwood J., Cattonaro F., Zuccolo A., Rossini L., Jenkins J., Vendramin E., Meisel L.A., Decroocq V., Sosinski B., Prochnik S., Mitros T., Policriti A., Cipriani G., Dondini L., Ficklin S., Goodstein D.M., Xuan P., Del Fabbro C., Aramini V., Copetti D., Gonzalez S., Horner D.S., Falchi R., Lucas S., Mica E., Maldonado J., Lazzari B., Bielenberg D., Pirona R., Miculan M., Barakat A., Testolin R., Stella A., Tartarini S., Tonutti P., Arús P., Orellana A., Wells C., Main D., Vizzotto G., Silva H., Salamini F., Schmutz J., Morgante M., Rokhsar D.S. The high quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics 2013, 45:487-496.
54. Vierstra R.D. The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends in Plant Science 2003, 8:135-142.
55. Wang C., Shangguan L.F., Kibet K.N., Wang X.C., Han J., Song C.N., Fang J.G. Characterization of microRNAs identified in a table grapevine cultivar with validation of computationally predicted grapevine miRNAs by miR-RACE. PLoS ONE 2011, 6:e21259.
56. Wang J.W., Schwab R., Czech B., Mica E., Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 2008, 20:1231-1243.
57. Willmann M.R., Poethig R.S. Time to grow up: the temporal role of smallRNAs in plants. Current Opinion in Plant Biology 2005, 8:548-552.
58. Wu G., Park M.Y., Conway S.R., Wang J.W., Weigel D., Poethig R.S. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009, 138:750-759.
59. Xie Z., Kasschau K.D., Carrington J.C. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Current Biology 2003, 13:784-789.
60. Xu L., Yang L., Hang H. Transcriptional, post-transcriptional and post-translational regulations of gene expression during leaf polarity formation. Cell Research 2007, 17:512-519.
61. Yang L., Wu G., Poethig R.S. Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proceedings of the National Academy of Science of the United States of America 2012, 109:315.
62. Zhang Y., Bai Y., Han J., Chen M., Kayesh E., Jiang W., Fang J. Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE. Journal of Plant Physiology 2013, 170:80-92.
63. Zhang Y.P., Yu M.L., Yu H.P., Han J., Song C.N., Ma R.J., Fang J.G. Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE. Molecular Biology Reports 2012, 39:1975-1987.
64. Zhu H., Xia R., Zhao B., An Y., Dardick C.D., Callahan A.M., Liu Z. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biology 2012, 12:149.