MicroRNAs in the Hox network: An apparent link to posterior prevalence

Nature Reviews Genetics

Volumn 9, Issue 10, 2008, Pages 789-796

  Yekta, Soraya ^a,b   Tabin, Clifford J ^c   Bartel, David P ^a,b  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; DOMINANCE BEHAVIOR; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE LOCUS; GENE REPRESSION; GENE TARGETING; GENETIC SELECTION; HOX GENE; HUMAN; MOUSE; NONHUMAN; PLESIOMORPHY; PRIORITY JOURNAL;

ANIMALS; BODY PATTERNING; CHROMOSOME MAPPING; GENE REGULATORY NETWORKS; HOMEODOMAIN PROTEINS; HUMANS; LINKAGE (GENETICS); MICRORNAS; MODELS, BIOLOGICAL; TISSUE DISTRIBUTION;

BILATERIA; VERTEBRATA;

EID: 52149090746     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2400     Document Type: Article

References (59)

1. Duboule, D. The rise and fall of Hox gene clusters. Development 134, 2549-2560 (2007). This paper presents a synthesis of the current understanding of the structure, and the developmental and evolutionary significance, of the organization of the Hox clusters.
2. Krumlauf, R. Hox genes in vertebrate development. Cell 78, 191-201 (1994).
3. Nei, M. The new mutation theory of phenotypic evolution. Proc. Natl Acad. Sci. USA 104, 12235-12242 (2007).
4. Cameron, R. A. et al. Unusual gene order and organization of the sea urchin hox cluster. J. Exp. Zool. B Mol. Dev. Evol. 306, 45-58 (2006).
5. Spagnuolo, A. et al. Unusual number and genomic organization of Hox genes in the tunicate Ciona intestinalis. Gene 309, 71-79 (2003).
6. Seo, H. C. et al. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica. Nature 431, 67-71 (2004).
7. Shubin, N., Tabin, C. & Carroll, S. Fossils, genes and the evolution of animal limbs. Nature 388, 639-648 (1997).
8. Spitz, F. et al. Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev. 15, 2209-2214 (2001).
9. Chourrout, D. et al. Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature 442, 684-687 (2006).
10. Garcia-Fernandez, J. & Holland, P. W. Archetypal organization of the amphioxus Hox gene cluster. Nature 370, 563-566 (1994).
11. Powers, T. P. & Amemiya, C. T. Evidence for a Hox14 paralog group in vertebrates. Curr. Biol. 14, R183-R184 (2004).
12. Morata, G. Homeotic genes of Drosophila. Curr. Opin. Genet. Dev. 3, 606-614 (1993).
13. Duboule, D. The vertebrate limb: a model system to study the Hox/HOM gene network during development and evolution. Bioessays 14, 375-384 (1992).
14. Maconochie, M., Nonchev, S., Morrison, A. & Krumlauf, R. Paralogous Hox genes: function and regulation. Annu. Rev. Genet. 30, 529-556 (1996).
15. Chen, F. & Capecchi, M. R. Targeted mutations in hoxa-9 and hoxb-9 reveal synergistic interactions. Dev. Biol. 181, 186-196 (1997).
16. Krumlauf, R. Mouse Hox genetic functions. Curr. Opin. Genet. Dev. 3, 621-625 (1993).
17. Heard, E. & Bickmore, W. The ins and outs of gene regulation and chromosome territory organisation. Curr. Opin. Cell Biol. 19, 311-316 (2007).
18. Deschamps, J. Ancestral and recently recruited global control of the Hox genes in development. Curr. Opin. Genet. Dev. 17, 422-427 (2007).
19. Nelson, C. E. et al. Analysis of Hox gene expression in the chick limb bud. Development 122, 1449-1466 (1996).
20. Brend, T., Gilthorpe, J., Summerbell, D. & Rigby, P. W. Multiple levels of transcriptional and posttranscriptional regulation are required to define the domain of Hoxb4 expression. Development 130, 2717-2728 (2003).
21. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
22. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787-798 (2003).
23. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005). References 22 and 23 use comparative sequence analyses to develop seed-based target-prediction methods, uncover key features of mammalian miRNA-target recognition and reveal the widespread scope of targeting in vertebrates.
24. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005). This paper uses comparative sequence analyses and reporter assays to reveal widespread targeting and important features of target recognition in flies.
25. Krek, A. et al. Combinatorial microRNA target predictions. Nature Genet. 37, 495-500 (2005).
26. Yekta, S., Shih, I. H. & Bartel, D. P. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594-596 (2004).
27. Mansfield, J. H. et al. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genet. 36, 1079-1083 (2004).
28. Hornstein, E. et al. The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development. Nature 438, 671-674 (2005).
29. Ma, L., Teruya-Feldstein, J. & Weinberg, R. A. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449, 682-688 (2007).
30. Woltering, J. M. & Durston, A. J. miR-10 represses HoxB1a and HoxB3a in zebrafish. PLoS ONE 3, e1396 (2008).
31. Bender, W. MicroRNAs in the Drosophila Bithorax complex. Genes Dev. 22, 14-19 (2008).
32. Ronshaugen, M., Biemar, F., Piel, J., Levine, M. & Lai, E. C. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev. 19, 2947-2952 (2005).
33. Ruby, J. G. et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850-1864 (2007).
34. Tyler, D. M. et al. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22, 26-36 (2008).
35. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105 (2007).
36. Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature 438, 685-689 (2005).
37. Farh, K. K. et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817-1821 (2005).
38. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773 (2005).
39. Giraldez, A. J. et al. Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75-79 (2006).
40. Wienholds, E. et al. MicroRNA expression in zebrafish embryonic development. Science 309, 310-311 (2005).
41. Kloosterman, W. P., Wienholds, E., de Bruijn, E., Kauppinen, S. & Plasterk, R. H. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nature Methods 3, 27-29 (2006).
42. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853-858 (2001).
43. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862 (2001).
44. Palakodeti, D., Smielewska, M. & Graveley, B. R. MicroRNAs from the planarian Schmidtea mediterranea, a model system for stem cell biology. RNA 12, 1640-1649 (2006).
45. Sempere, L. F., Cole, C. N., McPeek, M. A. & Peterson, K. J. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. B Mol. Dev. Evol. 306, 575-588 (2006).
46. Stark, A. et al. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17, 1865-1879 (2007).
47. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A. & Tuschl, T. New microRNAs from mouse and human. RNA 9, 175-179 (2003).
48. Stark, A. et al. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22, 8-13 (2008).
49. Duboule, D. & Morata, G. Colinearity and functional hierarchy among genes of the homeotic complexes. Trends Genet. 10, 358-364 (1994). This paper develops the concept of posterior prevalence between genes of the Hox clusters.
50. + gene product in ensuring the selective expression of segment-specific homeotic genes in Drosophila. J. Embryol. Exp. Morphol. 76, 297-331 (1983). This paper is the original source for the concept of hierarchical activity among Hox genes, which was deduced from classical genetics experiments in flies.
51. Gibson, G. & Gehring, W. Head and thoracic transformations caused by ectopic expression of Antennapedia during Drosophila development. Development 102, 657-675 (1988).
52. Lufkin, T. et al. Homeotic transformation of the occipital bones of the skull by ectopic expression of a homeobox gene. Nature 359, 835-841 (1992).
53. Pollock, R. A., Sreenath, T., Ngo, L. & Bieberich, C. J. Gain of function mutations for paralogous Hox genes: implications for the evolution of Hox gene function. Proc. Natl Acad. Sci. USA 92, 4492-4496 (1995).
54. Burglin, T. R. & Ruvkun, G. The Caenorhabditis elegans homeobox gene cluster. Curr. Opin. Genet. Dev. 3, 615-620 (1993).
55. Martindale, M. Q. The evolution of metazoan axial properties. Nature Rev. Genet. 6, 917-927 (2005).
56. Davis, G. K. & Patel, N. H. The origin and evolution of segmentation. Trends Cell Biol. 9, M68-M72 (1999).
57. Waskiewicz, A. J., Rikhof, H. A. & Moens, C. B. Eliminating zebrafish pbx proteins reveals a hindbrain ground state. Dev. Cell 3, 723-733 (2002).
58. Williams, M. E., Lehoczky, J. A. & Innis, J. W. A group 13 homeodomain is neither necessary nor sufficient for posterior prevalence in the mouse limb. Dev. Biol. 297, 493-507 (2006).
59. Bartel, D. P. & Chen, C. Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Rev. Genet. 5, 396-400 (2004).