Focus on mirnas evolution: A perspective from amphioxus

Briefings in Functional Genomics

Volumn 11, Issue 2, 2012, Pages 107-117

  Candiani, Simona ^a  

^a UNIVERSITY OF GENOA   (Italy)

Author keywords

Amphioxus; Evolution; Expression; Hox genes; MicroRNAs; MicroRNAs targets

Indexed keywords

MICRORNA;

AEDES AEGYPTI; ARTICLE; BRANCHIOSTOMA; CIONA INTESTINALIS; DEUTEROSTOMIA; DROSOPHILA MELANOGASTER; DROSOPHILA VIRILIS; EUKARYOTE EVOLUTION; FISH; GENE CLUSTER; GENE TARGETING; GENETIC LINKAGE; HALICLONA; HUMAN; IXODES SCAPULARIS; METAZOON; NONHUMAN; PETROMYZON; PRIMATE; PROTOSTOMIA; STRONGYLOCENTROTUS; TRIBOLIUM;

ANIMALS; CHORDATA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENETIC LINKAGE; HOMEODOMAIN PROTEINS; MICRORNAS;

BRANCHIOSTOMA LANCEOLATUM; METAZOA;

EID: 84859083406     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/els004     Document Type: Article

References (51)

1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97.
2. Baulcombe D. RNA silencing in plants. Nature 2004;431: 356-63.
3. Filipowicz W, Bhattacharyya SN, Sonenberg N, etal. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? NatRevGenet 2008;9:102-14.
4. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009;136:215-33.
5. Ambros V. The functions of animal microRNAs. Nature 2004;431:350-5.
6. He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004;5:522-31.
7. Pasquinelli AE, Hunter S, Bracht J. MicroRNAs: a developing story. Curr Opin Genet Dev 2005;15:200-5.
8. Nelson PT, Wang WX, Rajeev BW. MicroRNAs (miRNAs) in neurodegenerative diseases. Brain Pathol 2008;18:130-8.
9. Liu J, Zheng M, Tang YL, et al. MicroRNAs, an active and versatile group in cancers. IntJOral Sci 2011;3:165-75.
10. Sempere LF, Cole CN, McPeek MA, et al. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool (Mol Dev Evol) 2006;306B:575-88.
11. Prochnik SE, Rokhsar DS, Aboobaker AA. Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol 2007;217:73-7.
12. Peterson KJ, Dietrich MR, McPeek MA. MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion. Bioessays 2009;31: 736-47.
13. Wheeler BM, Heimberg AM, Moy VN, et al. The deep evolution of metazoan microRNAs. Evol Dev 2009; 11:50-68.
14. Grimson A, Srivastava M, Fahey B, et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008;455:1193-7.
15. Hertel J, Lindemeyer M, Missal K, et al. The expansion of the metazoan microRNA repertoire. BMCGenomics 2006; 7:25.
16. Bentwich I, Avniel A, Karov Y, et al. Identification of hundreds of conserved and non-conserved human microRNAs. Nat Genet 2005;37:766-70.
17. Campo-Paysaa F, Sémon M, Cameron RA, et al. microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev 2011;13:15-27.
18. Heimberg AM, Sempere LF, Moy VN, et al. MicroRNAs and the advent of vertebrate morphological complexity. ProcNatl Acad SciUSA 2008;105:2946-50.
19. Luo Y, Zhang S. Computational prediction of amphioxus microRNA genes and their targets. Gene 2009;428:41-6.
20. Dai Z, Chen Z, Ye H, etal. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol Dev 2009;11:41-9.
21. Chen X, Li Q, Wang J, et al. Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 2009;10:R78.
22. Hendrix D, Levine M, Shi W. miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol 2010;11: R39.
23. Delsuc F, Brinkmann H, Chourrout D, et al. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 2006;439:965-8.
24. Holland LZ, Gibson-Brown JJ. The Ciona intestinalis genome: when the constraints are off. Bioessays 2003;25: 529-32.
25. Shi W, Hendrix D, Levine M, Haley B. A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat StructMol Biol 2009;16:183-9.
26. Tyler DM, Okamura K, Chung WJ, et al. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. GenesDev 2008;22: 26-36.
27. Fu X, Adamski M, Thompson EM. Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Mol Biol Evol 2008;25:1067-80.
28. Altuvia Y, Landgraf P, Lithwick G, et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005;33:2697-706.
29. Tanzer A, Stadler PF. Molecular evolution of a microRNA cluster. JMol Biol 2004;339:327-35.
30. Tang GQ, Maxwell ES. Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via posttranscriptional regulation. GenomeRes 2008;18:104-12.
31. Xu S, Witmer PD, Lumayag S, et al. MicroRNA (miRNA) transcriptome of mouse retina and identification of a sensory organ-specific miRNA cluster. J Biol Chem 2007;282: 25053-66.
32. Nguyen HT, Frasch M. MicroRNAs in muscle differentiation: lessons from Drosophila and beyond. Curr Opin Genet Dev 2006;16:533-9.
33. Mishima Y, Abreu-Goodger C, Staton AA, et al. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev 2009;23: 619-32.
34. Chen JF, Mandel EM, Thomson JM, et al. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. NatGenet 2006;38:228-33.
35. Mansfield JH, Harfe BD, Nissen R, et al. MicroRNAresponsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet 2004;36:1079-83.
36. Yekta S, Tabin CJ, Bartel DP. MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nat Rev Genet 2008;9:789-96.
37. Stark A, Bushati N, Jan CH, et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev 2008;22:8-13.
38. Aboobaker A, Blaxter M. Hox gene evolution in nematodes: novelty conserved. Curr Opin Genet Dev 2003;13: 593-8.
39. Ikuta T, Yoshida N, Satoh N, et al. Ciona intestinalis Hox gene cluster: its dispersed structure and residual colinear expression in development. Proc Natl Acad Sci USA 2004;101: 15118-23.
40. Enright AJ, John B, Gaul U, et al. MicroRNA targets in Drosophila. Genome Biol 2003;5:R1.
41. Wienholds E, Plasterk RH. MicroRNA function in animal development. FEBS Lett 2005;579:5911-22.
42. Christodoulou F, Raible F, Tomer R, et al. Ancient animal microRNAs and the evolution of tissue identity. Nature 2010;463:1084-8.
43. Candiani S, Moronti L, De Pietri Tonelli D, etal. A study of neural-related microRNAs in the developing amphioxus. EvoDevo 2011;2:15.
44. Li Y, Wang F, Lee JA, et al. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev 2006;20:2793-805.
45. Lagos-Quintana M, Rauhut R, Yalcin A, et al. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002;12:735-9.
46. Sempere LF, Freemantle S, Pitha-Rowe I, et al. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 2004;5: R13.
47. Steinmetz PR, Kostyuchenko RP, Fischer A, et al. The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii. Evol Dev 2011;13:72-9.
48. Leucht C, Stigloher C, Wizenmann A, et al. MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary. NatNeurosci 2008;11:641-8.
49. Shkumatava A, Stark A, Sive H, et al. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev 2009;23:466-81.
50. Liu H, Kohane IS. Tissue and process specific microRNAmRNA co-expression in mammalian development and malignancy. PLoS One 2009;4:e5436.
51. Chen PY, Manninga H, Slanchev K, et al. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. GenesDev 2005;19:1288-93.