Dynamic expression of novel and conserved microRNAs and their targets in diploid and tetraploid of Paulownia tomentosa

Biochimie

Volumn 102, Issue 1, 2014, Pages 68-77

  Fan, Guoqiang ^a   Zhai, Xiaoqiao ^b   Niu, Suyan ^a   Ren, Yuanyuan ^b  

^a HENAN AGRICULTURAL UNIVERSITY   (China)

^b Henan Academy of Forestry   (China)

Author keywords

Diploid; MicroRNA; Paulownia tomentosa; Targets; Tetraploid

Indexed keywords

MICRORNA; PEPTIDE TRANSPORTER 2; PEPTIDE TRANSPORTER 4; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOLOGICAL ACTIVITY; DIPLOIDY; ECONOMIC ASPECT; GENE EXPRESSION; GENE IDENTIFICATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC TRAIT; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PAULOWNIA TOMENTOSA; PLANT DEVELOPMENT; PLANT GROWTH; REGULATORY MECHANISM; SEQUENCE ANALYSIS; TETRAPLOIDY; TREE; BIOSYNTHESIS; CHINA; GENE EXPRESSION REGULATION; GENETICS; NUCLEOTIDE SEQUENCE; POPULUS;

PAULOWNIA TOMENTOSA; PAULOWNIACEAE;

CHINA; CONSERVED SEQUENCE; DIPLOIDY; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; POPULUS; TETRAPLOIDY;

EID: 84901794596     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2014.02.008     Document Type: Article

References (37)

1. D.P. Bartel MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2004 281 297
2. A.C. Mallory, and H. Vaucheret Functions of microRNAs and related small RNAs in plants Nat. Genet. 38 Suppl. 2006 S31 S36
3. O. Voinnet Origin, biogenesis, and activity of plant microRNAs Cell 136 2009 669 687
4. R.A. Mosher, M.G. Lewsey, and P.V. Shivaprasad RNA silencing in plants: flash report! Silence 1 2010 13
5. B. Zhang, X. Pan, G.P. Cobb, and T.A. Anderson Plant microRNA: a small regulatory molecule with big impact Dev. Biol. 289 2006 3 16
6. W. Filipowicz, L. Jaskiewicz, F.A. Kolb, and R.S. Pillai Post-transcriptional gene silencing by siRNAs and miRNAs Curr. Opin. Struct. Biol. 15 2005 331 341
7. R.C. Lee, R.L. Feinbaum, and V. Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 1993 843 854
8. B. Li, Y. Qin, H. Duan, W. Yin, and X. Xia Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica J. Exp. Bot. 62 2011 3765 3779
9. C. Wang, J. Han, C. Liu, K.N. Kibet, E. Kayesh, L. Shangguan, X. Li, and J. Fang Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics BMC Genomics 13 2012 122
10. Y. Ren, L. Chen, Y. Zhang, X. Kang, Z. Zhang, and Y. Wang Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress Funct. Integr. Genomics 12 2012 327 339
11. S. Lu, Y.H. Sun, H. Amerson, and V.L. Chiang MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development Plant J. 51 2007 1077 1098
12. I.A. Yakovlev, C.G. Fossdal, and O. Johnsen MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce New Phytol. 187 2010 1154 1169
13. B. Li, W. Yin, and X. Xia Identification of microRNAs and their targets from Populus euphratica Biochem. Biophys. Res. Commun. 388 2009 272 277
14. M.J. Axtell, J.A. Snyder, and D.P. Bartel Common functions for diverse small RNAs of land plants Plant Cell 19 2007 1750 1769
15. Z.J. Wang, J.Q. Huang, Y.J. Huang, Z. Li, and B.S. Zheng Discovery and profiling of novel and conserved microRNAs during flower development in Carya cathayensis via deep sequencing Planta 236 2012 613 621
16. L.C. Wan, F. Wang, X. Guo, S. Lu, Z. Qiu, Y. Zhao, H. Zhang, and J. Lin Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing BMC Plant Biol. 12 2012 146
17. C. Song, C. Wang, C. Zhang, N.K. Korir, H. Yu, Z. Ma, and J. Fang Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata) BMC Genomics 11 2010 431
18. G.Q. Fan, Z.Q. Yang, Y.C. Cao, and X.Q. Zhai Induction of Autotetraploid of Paulownia tomentosa Plant Physiol. Commun. 43 2007 109 111
19. X.S. Zhang, X.Q. Zhai, G.Q. Fan, M.J. Deng, and Z.L. Zhao Observation on microstructure of leaves and stress tolerance analysis of different tetraploid paulownia J. Henan Agric. Univ. 46 2012 646 650
20. X.Q. Zhai, X.S. Zhang, Z.L. Zhao, M.J. Deng, and G.Q. Fan Study on wood physical properties of tetraploid Paulownia fortunei J. Henan Agric. Univ. 46 2012 651 654
21. S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, and A. Bateman Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res. 33 2005 D121 D124
22. I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster Fast folding and comparison of RNA secondary structures Monatsh. Chem. 125 1994 167 188
23. B.C. Meyers, M.J. Axtell, B. Bartel, D.P. Bartel, D. Baulcombe, J.L. Bowman, X. Cao, J.C. Carrington, X. Chen, P.J. Green, S. Griffiths-Jones, S.E. Jacobsen, A.C. Mallory, R.A. Martienssen, R.S. Poethig, Y. Qi, H. Vaucheret, O. Voinnet, Y. Watanabe, D. Weigel, and J.K. Zhu Criteria for annotation of plant microRNAs Plant Cell 20 2008 3186 3190
24. C. Addo-Quaye, T.W. Eshoo, D.P. Bartel, and M.J. Axtell Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome Curr. Biol. 18 2008 758 762
25. M.A. German, M. Pillay, D.H. Jeong, A. Hetawal, S. Luo, P. Janardhanan, V. Kannan, L.A. Rymarquis, K. Nobuta, R. German, E. De Paoli, C. Lu, G. Schroth, B.C. Meyers, and P.J. Green Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends Nat. Biotechnol. 26 2008 941 946
26. A. Conesa, S. Gotz, J.M. Garcia-Gomez, J. Terol, M. Talon, and M. Robles Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Bioinformatics 21 2005 3674 3676
27. C. Chen, D.A. Ridzon, A.J. Broomer, Z. Zhou, D.H. Lee, J.T. Nguyen, M. Barbisin, N.L. Xu, V.R. Mahuvakar, M.R. Andersen, K.Q. Lao, K.J. Livak, and K.J. Guegler Real-time quantification of microRNAs by stem-loop RT-PCR Nucleic Acids Res. 33 2005 e179
28. M. Capra, P.G. Nuciforo, S. Confalonieri, M. Quarto, M. Bianchi, M. Nebuloni, R. Boldorini, F. Pallotti, G. Viale, M.L. Gishizky, G.F. Draetta, and P.P. Di Fiore Frequent alterations in the expression of serine/threonine kinases in human cancers Cancer Res. 66 2006 8147 8154
29. Y. Liao, H.-F. Zou, W. Wei, Y.-J. Hao, A.-G. Tian, J. Huang, Y.-F. Liu, J.-S. Zhang, and S.-Y. Chen Soybean GmbZIP44, GmbZIP62 and GmbZIP78 genes function as negative regulator of ABA signaling and confer salt and freezing tolerance in transgenic Arabidopsis Planta 228 2008 225 240
30. C.A. Pise-Masison, J. Dittmer, K.E. Clemens, and J.N. Brady Physical and functional interaction between the human T-cell lymphotropic virus type 1 Tax1 protein and the CCAAT binding protein NF-Y Mol. Cell. Biol. 17 1997 1236 1243
31. M.W. Jones-Rhoades, D.P. Bartel, and B. Bartel MicroRNAs and their regulatory roles in plants Annu. Rev. Plant Biol. 57 2006 19 53
32. R. Sunkar, and J.K. Zhu Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis Plant Cell 16 2004 2001 2019
33. E.T. Kipreos, and M. Pagano The F-box protein family Genome Biol. 1 2000 R3002
34. R. Sunkar, A. Kapoor, and J.-K. Zhu Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance Plant Cell 18 2006 2051 2065
35. X. Jia, W.X. Wang, L. Ren, Q.J. Chen, V. Mendu, B. Willcut, R. Dinkins, X. Tang, and G. Tang Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana Plant Mol. Biol. 71 2009 51 59
36. R. Munns, and R.A. James Screening methods for salinity tolerance: a case study with tetraploid wheat Plant Soil 253 2003 201 218
37. R. Geddy, and G.G. Brown Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection BMC Genomics 8 2007 130