Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Li, Yang ^a,b   Li, Chaoqun ^c   Ding, Guohui ^d   Jin, Youxin ^a,b  

^a SHANGHAI UNIVERSITY   (China)

^b INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^c SHANGHAI PUBLIC HEALTH CLINICAL CENTER   (China)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; CONSERVATION GENETICS; DEVELOPMENTAL BIOLOGY; EUKARYOTE; FERTILITY; FLOWERING; GENE EXPRESSION; HERB; MATURATION; PHYLOGENY; RNA; SPATIOTEMPORAL ANALYSIS;

BRYOPHYTA; EUKARYOTA; GYMNOSPERMAE; LYCOPODIUM; MAGNOLIOPHYTA; SPERMATOPHYTA;

MICRORNA; PLANT RNA;

ARABIDOPSIS; ARTICLE; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; MUTATION; PLANT; UPREGULATION;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; MUTATION; NUCLEIC ACID CONFORMATION; PLANTS; RNA, PLANT; UP-REGULATION;

EID: 79955802124     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-122     Document Type: Article

References (76)

1. MicroRNAs: genomics, biogenesis, mechanism, and function. DP Bartel, Cell 2004 116 2 281 297 10.1016/S0092-8674(04)00045-5 14744438
2. Origin, biogenesis, and activity of plant microRNAs. O Voinnet, Cell 2009 136 4 669 687 10.1016/j.cell.2009.01.046 19239888
3. Criteria for annotation of plant MicroRNAs. BC Meyers MJ Axtell B Bartel DP Bartel D Baulcombe JL Bowman X Cao JC Carrington X Chen PJ Green S Griffiths-Jones SE Jacobsen AC Mallory RA Martienssen RS Poethig Y Qi H Vaucheret O Voinnet Y Watanabe D Weigel JK Zhu, Plant Cell 2008 20 12 3186 3190 10.1105/tpc.108.064311 19074682
4. MicroRNAS and their regulatory roles in plants. MW Jones-Rhoades DP Bartel B Bartel, Annu Rev Plant Biol 2006 57 19 53 10.1146/annurev.arplant.57. 032905.105218 16669754 (Pubitemid 44061017)
5. Sequence and expression differences underlie functional specialization of arabidopsis microRNAs miR159 and miR319. JF Palatnik H Wollmann C Schommer R Schwab J Boisbouvier R Rodriguez N Warthmann E Allen T Dezulian D Huson JC Carrington D Weigel, Dev Cell 2007 13 1 115 125 10.1016/j.devcel.2007.04.012 17609114 (Pubitemid 46972029)
6. Control of leaf morphogenesis by microRNAs. JF Palatnik E Allen X Wu C Schommer R Schwab JC Carrington D Weigel, Nature 2003 425 6955 257 263 10.1038/nature01958 12931144 (Pubitemid 37158395)
7. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. MW Jones-Rhoades DP Bartel, Mol Cell 2004 14 6 787 799 10.1016/j.molcel.2004.05.027 15200956 (Pubitemid 38780852)
8. The Arabidopsis GAMYB-like genes, MYB33 and MYB65, are microRNA-regulated genes that redundantly facilitate anther development. AA Millar F Gubler, Plant Cell 2005 17 3 705 721 10.1105/tpc.104.027920 15722475 (Pubitemid 43138215)
9. Antiquity of microRNAs and their targets in land plants. MJ Axtell DP Bartel, Plant Cell 2005 17 6 1658 1673 10.1105/tpc.105.032185 15849273
10. Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. RS Allen J Li MI Stahle A Dubroue F Gubler AA Millar, Proc Natl Acad Sci USA 2007 104 41 16371 16376 10.1073/pnas.0707653104 17916625 (Pubitemid 350099411)
11. ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. JL Reyes NH Chua, Plant J 2007 49 4 592 606 10.1111/j.1365-313X.2006.02980.x 17217461 (Pubitemid 46233079)
12. Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. N Ori AR Cohen A Etzioni A Brand O Yanai S Shleizer N Menda Z Amsellem I Efroni I Pekker JP Alvarez E Blum D Zamir Y Eshed, Nat Genet 2007 39 6 787 791 10.1038/ng2036 17486095 (Pubitemid 46848587)
13. Control of jasmonate biosynthesis and senescence by miR319 targets. C Schommer JF Palatnik P Aggarwal A Chetelat P Cubas EE Farmer U Nath D Weigel, PLoS Biol 2008 6 9 230 10.1371/journal.pbio.0060230 18816164
14. miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis. A Nag S King T Jack, Proc Natl Acad Sci USA 2009 106 52 22534 22539 10.1073/pnas.0908718106 20007771
15. Common functions for diverse small RNAs of land plants. MJ Axtell JA Snyder DP Bartel, Plant Cell 2007 19 6 1750 1769 10.1105/tpc.107.051706 17601824 (Pubitemid 47218838)
16. Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Y Li W Li YX Jin, Acta Biochim Biophys Sin (Shanghai) 2005 37 2 75 87 10.1093/abbs/37.2.75 (Pubitemid 40685518)
17. A loop-to-base processing mechanism underlies the biogenesis of plant microRNAs miR319 and miR159. NG Bologna JL Mateos EG Bresso JF Palatnik, EMBO J 2009 28 23 3646 3656 10.1038/emboj.2009.292 19816405
18. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. C Addo-Quaye JA Snyder YB Park YF Li R Sunkar MJ Axtell, RNA 2009 15 12 2112 2121 10.1261/rna.1774909 19850910
19. miRBase: microRNA sequences, targets and gene nomenclature. S Griffiths-Jones RJ Grocock S van Dongen A Bateman AJ Enright, Nucleic Acids Res 2006 34 Database 140 144
20. In silico identification of conserved microRNAs in large number of diverse plant species. R Sunkar G Jagadeeswaran, Bmc Plant Biology 2008 8
21. Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae. N Warthmann S Das C Lanz D Weigel, Mol Biol Evol 2008 25 5 892 902 10.1093/molbev/msn029 18296705
22. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839 (Pubitemid 37038874)
23. Evolution of Arabidopsis microRNA families through duplication events. C Maher L Stein D Ware, Genome Res 2006 16 4 510 519 10.1101/gr.4680506 16520461
24. MicroRNAs in plants. BJ Reinhart EG Weinstein MW Rhoades B Bartel DP Bartel, Genes Dev 2002 16 13 1616 1626 10.1101/gad.1004402 12101121 (Pubitemid 34743323)
25. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. MA German M Pillay DH Jeong A Hetawal S Luo P Janardhanan V Kannan LA Rymarquis K Nobuta R German E De Paoli C Lu G Schroth BC Meyers PJ Green, Nat Biotechnol 2008 26 8 941 946 10.1038/nbt1417 18542052
26. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Z Ma C Coruh MJ Axtell, Plant Cell 2010 22 4 1090 1103 10.1105/tpc.110.073882 20407023
27. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. N Fahlgren S Jogdeo KD Kasschau CM Sullivan EJ Chapman S Laubinger LM Smith M Dasenko SA Givan D Weigel JC Carrington, Plant Cell 2010 22 4 1074 1089 10.1105/tpc.110.073999 20407027
28. Endogenous, tissue-specific short interfering RNAs silence the chalcone synthase gene family in glycine max seed coats. JH Tuteja G Zabala K Varala M Hudson LO Vodkin, Plant Cell 2009 21 10 3063 3077 10.1105/tpc.109.069856 19820189
29. Comparative Sequencing of Plant Small RNAs. http://smallrna.udel.edu/ index.php
30. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. C Addo-Quaye TW Eshoo DP Bartel MJ Axtell, Curr Biol 2008 18 10 758 762 10.1016/j.cub.2008.04.042 18472421
31. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. JA Chekanova BD Gregory SV Reverdatto H Chen R Kumar T Hooker J Yazaki P Li N Skiba Q Peng J Alonso V Brukhin U Grossniklaus JR Ecker DA Belostotsky, Cell 2007 131 7 1340 1353 10.1016/j.cell.2007.10.056 18160042 (Pubitemid 350297418)
32. Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica). T Li H Li YX Zhang JY Liu, Nucleic Acids Res 2011 39 7 2821 2833 10.1093/nar/gkq1047 21113019
33. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. X Wang AA Elling X Li N Li Z Peng G He H Sun Y Qi XS Liu XW Deng, Plant Cell 2009 21 4 1053 1069 10.1105/tpc.109.065714 19376930
34. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. SH Cho C Addo-Quaye C Coruh MA Arif Z Ma W Frank MJ Axtell, PLoS Genet 2008 4 12 1000314 10.1371/journal.pgen.1000314 19096705
35. Cloning and characterization of micro-RNAs from moss. T Arazi M Talmor-Neiman R Stav M Riese P Huijser DC Baulcombe, Plant J 2005 43 6 837 848 10.1111/j.1365-313X.2005.02499.x 16146523
36. Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. I Fattash B Voss R Reski WR Hess W Frank, BMC Plant Biol 2007 7 13 10.1186/1471-2229-7-13 17359535
37. Genetic and functional diversification of small RNA pathways in plants. Z Xie LK Johansen AM Gustafson KD Kasschau AD Lellis D Zilberman SE Jacobsen JC Carrington, PLoS Biol 2004 2 5 104 10.1371/journal.pbio.0020104 15024409
38. Genome-wide profiling and analysis of Arabidopsis siRNAs. KD Kasschau N Fahlgren EJ Chapman CM Sullivan JS Cumbie SA Givan JC Carrington, PLoS Biol 2007 5 3 57 10.1371/journal.pbio.0050057 17298187
39. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. N Fahlgren MD Howell KD Kasschau EJ Chapman CM Sullivan JS Cumbie SA Givan TF Law SR Grant JL Dangl JC Carrington, PLoS One 2007 2 2 219 10.1371/journal.pone.0000219 17299599
40. Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs. V Gasciolli AC Mallory DP Bartel H Vaucheret, Curr Biol 2005 15 16 1494 1500 10.1016/j.cub.2005.07.024 16040244 (Pubitemid 41187489)
41. Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. K Nobuta C Lu R Shrivastava M Pillay E De Paoli M Accerbi M Arteaga-Vazquez L Sidorenko DH Jeong Y Yen PJ Green VL Chandler BC Meyers, Proc Natl Acad Sci USA 2008 105 39 14958 14963 10.1073/pnas.0808066105 18815367
42. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. QH Zhu A Spriggs L Matthew L Fan G Kennedy F Gubler C Helliwell, Genome Res 2008 18 9 1456 1465 10.1101/gr.075572.107 18687877
43. Characterization of unique small RNA populations from rice grain. SE Heisel Y Zhang E Allen L Guo TL Reynolds X Yang D Kovalic JK Roberts, PLoS One 2008 3 8 2871 10.1371/journal.pone.0002871 18716673
44. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. T Zhao G Li S Mi S Li GJ Hannon XJ Wang Y Qi, Genes Dev 2007 21 10 1190 1203 10.1101/gad.1543507 17470535
45. The expansion of the metazoan microRNA repertoire. J Hertel M Lindemeyer K Missal C Fried A Tanzer C Flamm IL Hofacker PF Stadler, BMC Genomics 2006 7 25 10.1186/1471-2164-7-25 16480513
46. The evolution of animal microRNA function. R Niwa FJ Slack, Curr Opin Genet Dev 2007 17 2 145 150 10.1016/j.gde.2007.02.004 17317150 (Pubitemid 46566505)
47. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. R Rajagopalan H Vaucheret J Trejo DP Bartel, Genes Dev 2006 20 24 3407 3425 10.1101/gad.1476406 17182867 (Pubitemid 44969159)
48. The birth and death of microRNA genes in Drosophila. J Lu Y Shen Q Wu S Kumar B He S Shi RW Carthew SM Wang CI Wu, Nat Genet 2008 40 3 351 355 10.1038/ng.73 18278047 (Pubitemid 351311763)
49. Many roads to maturity: microRNA biogenesis pathways and their regulation. J Winter S Jung S Keller RI Gregory S Diederichs, Nature Cell Biology 2009 11 3 228 234 10.1038/ncb0309-228 19255566
50. Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. T Katoh Y Sakaguchi K Miyauchi T Suzuki S Kashiwabara T Baba, Genes Dev 2009 23 4 433 438 10.1101/gad.1761509 19240131
51. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. H Vaucheret AC Mallory DP Bartel, Mol Cell 2006 22 1 129 136 10.1016/j.molcel.2006.03.011 16600876
52. Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. S Laubinger T Sachsenberg G Zeller W Busch JU Lohmann G Ratsch D Weigel, Proc Natl Acad Sci USA 2008 105 25 8795 8800 10.1073/pnas.0802493105 18550839 (Pubitemid 351987759)
53. A link between RNA metabolism and silencing affecting Arabidopsis development. BD Gregory RC O'Malley R Lister MA Urich J Tonti-Filippini H Chen AH Millar JR Ecker, Dev Cell 2008 14 6 854 866 10.1016/j.devcel.2008.04.005 18486559
54. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. AL Eamens NA Smith SJ Curtin MB Wang PM Waterhouse, RNA 2009 15 12 2219 2235 10.1261/rna.1646909 19861421
55. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. V Ramachandran X Chen, Science 2008 321 5895 1490 1492 10.1126/science.1163728 18787168
56. Specialization and evolution of endogenous small RNA pathways. EJ Chapman JC Carrington, Nat Rev Genet 2007 8 11 884 896 10.1038/nrg2179 17943195 (Pubitemid 47609087)
57. Roles of plant small RNAs in biotic stress responses. V Ruiz-Ferrer O Voinnet, Annu Rev Plant Biol 2009 60 485 510 10.1146/annurev.arplant.043008. 092111 19519217
58. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. C Lu K Kulkarni FF Souret R MuthuValliappan SS Tej RS Poethig IR Henderson SE Jacobsen W Wang PJ Green BC Meyers, Genome Res 2006 16 10 1276 1288 10.1101/gr.5530106 16954541 (Pubitemid 44506961)
59. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. Y Jia DR Lisch K Ohtsu MJ Scanlon D Nettleton PS Schnable, PLoS Genet 2009 5 11 1000737 10.1371/journal.pgen.1000737 19936292
60. Transcriptional control of gene expression by microRNAs. B Khraiwesh MA Arif GI Seumel S Ossowski D Weigel R Reski W Frank, Cell 2010 140 1 111 122 10.1016/j.cell.2009.12.023 20085706
61. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Y Qi X He XJ Wang O Kohany J Jurka GJ Hannon, Nature 2006 443 7114 1008 1012 10.1038/nature05198 16998468 (Pubitemid 44646179)
62. Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice. S Lacombe H Nagasaki C Santi D Duval B Piegu M Bangratz JC Breitler E Guiderdoni C Brugidou J Hirsch X Cao C Brice O Panaud WM Karlowski Y Sato M Echeverria, BMC Plant Biol 2008 8 123 10.1186/1471-2229-8-123 19055717
63. Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proc Natl Acad Sci USA 1988 85 8 2444 2448 10.1073/pnas.85.8.2444 3162770
64. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712
65. Fast Folding and Comparison of Rna Secondary Structures. IL Hofacker W Fontana PF Stadler LS Bonhoeffer M Tacker P Schuster, Monatshefte Fur Chemie 1994 125 2 167 188 10.1007/BF00818163
66. miRBase: microRNA sequences, targets and gene nomenclature. S Griffiths-Jones RJ Grocock S van Dongen A Bateman AJ Enright, Nucleic Acids Research 2006 34 140 D144 10.1093/nar/gkj112 16381832
67. WWW-query: an on-line retrieval system for biological sequence banks. G Perriere M Gouy, Biochimie 1996 78 5 364 369 10.1016/0300-9084(96)84768-7 8905155 (Pubitemid 26394644)
68. T-Coffee: A novel method for fast and accurate multiple sequence alignment. C Notredame DG Higgins J Heringa, J Mol Biol 2000 302 1 205 217 10.1006/jmbi.2000.4042 10964570
69. 4SALE - a tool for synchronous RNA sequence and secondary structure alignment and editing. PN Seibel T Muller T Dandekar J Schultz M Wolf, BMC Bioinformatics 2006 7 498 10.1186/1471-2105-7-498 17101042
70. ConStruct: Improved construction of RNA consensus structures. A Wilm K Linnenbrink G Steger, BMC Bioinformatics 2008 9 219 10.1186/1471-2105-9-219 18442401
71. RNAalifold: improved consensus structure prediction for RNA alignments. SH Bernhart IL Hofacker S Will AR Gruber PF Stadler, BMC Bioinformatics 2008 9 474 10.1186/1471-2105-9-474 19014431
72. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. IL Hofacker M Fekete C Flamm MA Huynen S Rauscher PE Stolorz PF Stadler, Nucleic Acids Res 1998 26 16 3825 3836 10.1093/nar/26.16.3825 9685502 (Pubitemid 28367992)
73. Semiautomated improvement of RNA alignments. ES Andersen A Lind-Thomsen B Knudsen SE Kristensen JH Havgaard E Torarinsson N Larsen C Zwieb P Sestoft J Kjems J Gorodkin, RNA 2007 13 11 1850 1859 10.1261/rna.215407 17804647 (Pubitemid 350005210)
74. Displaying the information contents of structural RNA alignments: the structure logos. J Gorodkin LJ Heyer S Brunak GD Stormo, Computer Applications in the Biosciences 1997 13 6 583 586 9475985 (Pubitemid 28039651)
75. Dendroscope: An interactive viewer for large phylogenetic trees. DH Huson DC Richter C Rausch T Dezulian M Franz R Rupp, BMC Bioinformatics 2007 8 460 10.1186/1471-2105-8-460 18034891
76. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)