Evolution of plant microRNA gene families

Cell Research

Volumn 17, Issue 3, 2007, Pages 212-218

  Li, Aili ^a   Mao, Long ^a,b  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b NORTHERN ILLINOIS UNIVERSITY   (United States)

Author keywords

MicroRNAs; Post transcriptional regulation; Segmental duplication; Tandem duplication

Indexed keywords

MICRORNA;

ANIMAL; ARTICLE; GENE; GENE DUPLICATION; GENETIC VARIABILITY; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PLANT; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PLANTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

ANIMALIA;

EID: 33947309774     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/sj.cr.7310113     Document Type: Article

References (47)

1. Bartel B, Bartel DP. MicroRNAs: at the root of plant development? Plant Physiol 2003; 132:709-717.
2. Hertel J, Lindemeyer M, Missal K, et al. The expansion of the metazoan microRNA repertoire. BMC Genomics 2006; 7:25.
3. Floyd SK, Bowman JL. Gene regulation: ancient microRNA target sequences in plants. Nature 2004; 428:485-486.
4. Mallory AC, Vaucheret H. Functions of microRNAs and related small RNAs in plants. Nat Genet 2006; 38:S31-S36.
5. Palatnik JF, Allen E, Wu X, et al. Control of leaf morphogenesis by microRNAs. Nature 2003; 425:257-263.
6. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004; 303:2022-2025.
7. Jones-Rhoades MW, Bartel DP. Computational identification of plant MicroRNAs and their targets, including a stress-induced miRNA. Mol Cell 2004; 14:787-799.
8. Wang JW, Wang LJ, Mao YB, et al. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 2005; 17:2204-2216.
9. Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999; 286:950-952.
10. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75:843-854.
11. Pasquinelli AE, McCoy A, Jimenez E, et al. Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol Dev 2003; 5:372-378.
12. Pasquinelli AE, Reinhart BJ, Slack F, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000; 408:86-89.
13. Tanzer A, Stadler PF. Molecular evolution of a microRNA cluster. J Mol Biol 2004; 339:327-335.
14. Tanzer A, Stadler PF. Evolution of MicroRNAs. In microRNA protocols, methods in molecular biology. Edited by: Yig SY. Totowa. NJ: Humana Press Inc., 2006, in press.
15. Lagos-Quintana M, Rauhut R, Yalcin A, et al. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002; 12:735-739.
16. Kim J, Krichevsky A, Grad Y, et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA 2004; 101:360-365.
17. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and fonction. Cell 2004; 116:281-297.
18. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucl Acids Res 2006; 34:D140-D144
19. Papp I, Mette MF, Aufsatz W, et al. Evidence for nuclear processing of plant MicroRNA and short interfering RNA precursors. Plant Physiol 2003; 132:1382-1390.
20. Kasschau KD, Xie Z, Allen E, et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev Cell 2003; 4:205-217.
21. Llave C, Xie Z, Kasschau KD, Carrington JC. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002; 297:2053-2056.
22. Aukerman MJ, Sakai H. Correction: Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2004; 16:555.
23. Volpe TA, Kidner C, Hall IM, et al. Regulation of heterochromatic silencing and histone 113 lysine-9 methylation by RNAi. Science 2002; 297:1833-1837.
24. 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 Ambidopsis. Genes Dev 2004; 18:2368-2379.
25. Vazquez F, Vaucheret H, Rajagopalan R, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 2004; 16:69-79.
26. Allen E, Xie Z, Gustafson AM, Carrington JC. MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 2005; 121:207-221.
27. Tanzer A, Amemiya CT, Kim CB, Stadler PF. Evolution of MicroRNAs located within Hox gene clusters. J Exp Zool: Mol Dev Evol 2005; 304B:75-85.
28. Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res 2006; 16:510-519.
29. Guddeti S, Zhang dC, Li AL, et al. Molecular evolution of the rice miR395 gene family. Cell Res 2005; 15:631-638.
30. Bompfünewerer AF, Flamm C, Fried C, et al. Evolutionary patterns of non-coding RNAs. Theor Biosci 2005; 123:301-369.
31. Bartel DP, Chen CZ. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 2004; 5:396-400.
32. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005; 120:15-20.
33. Jones-Rhoades MW, Bartel DP, Bartel DP. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 2006; 57:19-53.
34. Chen PY, Manninga H, Slanchev K, et al. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 2005; 19:1288-1.293.
35. Giraldez AJ, Cinalli RM, Glasner ME, et al. MicroRNAs regulate brain morphogenesis in zebrafish. Science 2005; 308:833-838.
36. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. Vertebrate microRNA genes. Science 2003; 299:1540.
37. Lim LP, Lau NC, Weinstein EG, et al. The microRNAs of Caenorhabditis elegans. Genes Dev 2003; 17:991-1008.
38. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J 2006; 46:243-259.
39. Lee Y, Jeon K, Lee JT, Kim S, Kim VN. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002; 21:4663-4670.
40. Allen E, Xie Z, Gustafson AM, et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 2004; 36:1245-1246.
41. O'Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005; 435:839-843.
42. Town CD, Cheung F, Maiti R, et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006: tpc. 106.041665.
43. AGI. Analysis of the genome sequence of the flowering plant Arabisopsis thaliana. Nature 2000; 408:796-815.
44. Prince VE, Pickett FB. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 2002; 3:827-837.
45. Cannon S, Mitra A, Baumgarten A, Young N, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 2004; 4:1.0.
46. Lu S, Sun YH, Shi R, et al. Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 2005; 17:2186-2203.
47. Force A, Lynch M, Pickett FB, et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999; 151:1531-1545.