Functional shifts in insect microRNA evolution

Genome Biology and Evolution

Volumn 2, Issue 1, 2010, Pages 686-696

  Marco, Antonio ^a   Hui, Jerome H L ^a   Ronshaugen, Matthew ^a   Griffiths Jones, Sam ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Arm switching; Deep sequencing; Embryonic development; miRNAs; Tribolium

Indexed keywords

MICRORNA;

ANIMAL; ARTICLE; DROSOPHILA MELANOGASTER; GENE LIBRARY; GENETICS; GENOME; INSECT; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; TRIBOLIUM;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE LIBRARY; GENOME; INSECTS; MICRORNAS; MOLECULAR SEQUENCE DATA; TRIBOLIUM;

ANIMALIA; DROSOPHILA MELANOGASTER; HEXAPODA; METAZOA; TRIBOLIUM CASTANEUM; VERTEBRATA;

EID: 77958474656     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq053     Document Type: Article

References (60)

1. Altschul SF, et al. 1997. Gapped BLASTand PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Altuvia Y, et al. 2005. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 33:2697-2706.
3. Aravin AA, et al. 2003. The small RNA profile during Drosophila melanogaster development. Dev Cell. 5:337-350.
4. Ashburner M, Golic KG, Hawley RS. 2004. Drosophila: a laboratory handbook. 2nd ed. New York: Cold Spring Harbor Laboratory Press.
5. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116:281-297.
6. Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell. 136:215-233.
7. Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 11:241-247.
8. Behura SK. 2007. Insect microRNAs: structure, function and evolution. Insect Biochem Mol Biol. 37:3-9.
9. Bell ML, Buvoli M, Leinwand LA. 2010. Uncoupling of expression of an intronic microRNA and its myosin host gene by exon skipping. Mol Cell Biol. 30:1937-1945.
10. Berezikov E, et al. 2010. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat Genet. 42:6-9.
11. Brown SJ, Denell RE, Beeman RW. 2003. Beetling around the genome. Genet Res. 82:155-161.
12. Cai Y, et al. 2010. Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics. doi:10.1007/s10142-010-0162-7
13. Chen K, Rajewsky N. 2007. The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet. 8:93-103.
14. Cheng L, Pastrana E, Tavazoie M, Doetsch F. 2009. miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci. 12:399-408.
15. Chiang HR, et al. 2010. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 24:992-1009.
16. Clark AM, et al. 2010. The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res. doi:10.1093/nar/gkq083.
17. Cloonan N, et al. 2009. RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data. Bioinformatics. 25:2615.
18. Davis GK, Patel NH. 2002. Short, long, and beyond: molecular and embryological approaches to insect segmentation. Annu Rev Entomol. 47:669-699.
19. de Wit E, Linsen S, Cuppen E, Berezikov E. 2009. Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res. 19:2064-2074.
20. Glazov EA, et al. 2008. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 18:957-964.
21. Griffiths-Jones S. 2005. RALEE-RNA ALignment editor in Emacs. Bioinformatics. 21:257-259.
22. Griffiths-Jones S, et al. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124.
23. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. 2008. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36: D154-D158.
24. Guerra-Assunção JA, Enright A. 2010. MapMi: automated mapping of microRNA loci. BMC Bioinformatics. 11:133.
25. Hofacker IL, et al. 1994. Fast folding and comparison of RNA secondary structures. Monatshefte Chemie/Chem Mon. 125:167-188.
26. Jagadeeswaran G, et al. 2010. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics. 11:52.
27. Kloosterman WP, Plasterk R H A. 2006. The diverse functions of micro-RNAs in animal development and disease. Dev Cell. 11:441-450.
28. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25.
29. Lee Y, et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature. 425:415-419.
30. Lee Y, Jeon K, Lee J, Kim S, Kim VN. 2002. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21:4663-4670.
31. Liu S, et al. 2010. MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori. BMC Genomics. 11:85.
32. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
33. Lu J, et al. 2008. The birth and death of microRNA genes in Drosophila. Nat Genet. 40:351-355.
34. Luo Q, et al. 2008. Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum. J Genet Genomics. 35:349-355.
35. Makeyev EV, Zhang J, Carrasco MA, Maniatis T. 2007. The MicroRNA miR-124 promotes neuronal differentiation by triggering brainspecific alternative pre-mRNA splicing. Mol Cell. 27:435-448.
36. Marques-Souza H, Aranda M, Tautz D. 2008. Delimiting the conserved features of hunchback function for the trunk organization of insects. Development. 135:881-888.
37. Nawrocki EP, Kolbe DL, Eddy SR. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics. 25:1335-1337.
38. Niwa R, Slack FJ. 2007. The evolution of animal microRNA function. Curr Opin Genet Dev. 17:145-150.
39. * species has substantial influence on microRNA and 3' UTR evolution. Nat Struct Mol Biol. 15:354-363.
40. Peel AD. 2009. Forward genetics in Tribolium castaneum: opening new avenues of research in arthropod biology. J Biol. 8:106.
41. Richards S, et al. 2008. The genome of the model beetle and pest Tribolium castaneum. Nature. 452:949-955.
42. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14:1902-1910.
43. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC. 2005. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev. 19:2947-2952.
44. Ruby JG, Jan CH, Bartel DP. 2007. Intronic microRNA precursors that bypass Drosha processing. Nature. 448:83-86.
45. Ruby JG, et al. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs. Genome Res. 17:1850-1864.
46. Saini HK, Enright AJ, Griffiths-Jones S. 2008. Annotation of mammalian primary microRNAs. BMC Genomics. 9:564.
47. Saini HK, Griffiths-Jones S, Enright AJ. 2007. Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci USA. 104:17719-17724.
48. Savard J, Tautz D, Lercher MJ. 2006. Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol Biol. 6:7.
49. Shippy TD, et al. 2008. Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters. Dev Genes Evol. 218:127-139.
50. Singh J, Nagaraju J. 2008. In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum). Insect Mol Biol. 17:427-436.
51. Sokal RR, Rohlf FJ. 1995. Biometry: the principles and practice of statistics in biological research. New York: WH Freeman and Company.
52. Stark A, et al. 2007. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17:1865-1879. (Pubitemid 351360009)
53. Tang G, Maxwell ES. 2008. Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res. 18:104-112.
54. Tautz D, Friedrich M, Schröder R. 1994. Insect embryogenesis-what is ancestral and what is derived? Development. 120 (Suppl): 193-199.
55. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
56. Tyler DM, et al. 2008. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22:26-36.
57. Wang L, Wang S, Li Y, Paradesi M S R, Brown SJ. 2007. BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res. 35: D476-D479.
58. Wheeler B, et al. 2009. The deep evolution of metazoan microRNAs. Evol Dev. 11:50-68.
59. Wiegmann BM, Kim J, Tratwein MD. 2009. Holometabola. In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press US. pp. 260-263.
60. Yekta S, Shih I, Bartel DP. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science. 304:594-596.