The molecular elements that underlie developmental evolution

Nature Reviews Genetics

Volumn 6, Issue 9, 2005, Pages 709-715

  Alonso, Claudio R ^a   Wilkins, Adam S ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b BioEssays Editorial Office Cambridge   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSCRIPTION FACTOR; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; CONSENSUS DEVELOPMENT; ENHANCER REGION; GENE FUNCTION; GENE MUTATION; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSCRIPTION REGULATION; UNTRANSLATED REGION; ARTICLE; BIOLOGICAL MODEL; EMBRYO DEVELOPMENT; EVOLUTION; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MUTATION; REGULATORY SEQUENCE;

ALTERNATIVE SPLICING; EMBRYONIC DEVELOPMENT; EPIGENESIS, GENETIC; EVOLUTION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MODELS, GENETIC; MUTATION; REGULATORY ELEMENTS, TRANSCRIPTIONAL; RNA, MESSENGER; VARIATION (GENETICS);

EID: 23944472640     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1676     Document Type: Review

References (55)

1. King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107-116 (1975).
2. Britten, R. J. & Davidson, E. H. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q. Rev. Biol. 46, 111-138 (1971).
3. Mann, R. S. & Carroll, S. B. Molecular mechanisms of selector gene function and evolution. Curr. Opin. Genet. Dev. 12, 592-600 (2002).
4. Simpson, P. Evolution of development in closely related species of flies and worms. Nature Rev. Genet. 3, 907-917 (2002).
5. Levine, M. & Tjian, R. Transcription regulation and animal diversity. Nature 424, 147-151 (2003).
6. Wray, G. A. Transcriptional regulation and the evolution of development. Int. J. Dev. Biol. 47, 675-684 (2003).
7. Davidson, E. H. Genomic regulatory systems (Academic Press, San Diego, California, 2001).
8. Carroll, S. B. Homeotic genes and the evolution of arthropods and chordates. Nature 376, 479-485 (1995).
9. Akam, M. Hox genes, homeosis and the evolution of segment identity: no need for hopeless monsters. Int. J. Dev. Biol. 42, 445-451 (1998).
10. Stern, D. L. Evolutionary developmental biology and the problem of variation. Evolution 54, 1079-1091 (2000).
11. Ludwig, M. Z., Patel, N. H. & Kreitman, M. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125, 949-958 (1998).
12. Wray, G. A. et al. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20, 1377-1419 (2003).
13. Rockman, M. V. & Wray, G. A. Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol. 19, 1991-2004 (2002).
14. Crick, F. H. On protein synthesis. Symp. Soc. Exp. Biol. 12, 138-163 (1958).
15. Simeone, A. et al. A vertebrate gene related to orthodenticle contains a homeodomain of the bicoid class and demarcates anterior neuroectoderm in the gastrulating mouse embryo. EMBO J. 12, 2735-2747 (1993).
16. Simeone, A. Otx1 and Otx2 in the development and evolution of the mammalian brain. EMBO J. 17, 6790-6798 (1998).
17. Boyl, P. P. et al. Forebrain and midbrain development requires epiblast-restricted Otx2 translational control mediated by its 3′ UTR. Development 128, 2989-3000 (2001).
18. Acampora, D. et al. Otx genes in evolution: are they involved in instructing the vertebrate brain morphology? J. Anat. 199, 53-62 (2001).
19. Kuersten, S. & Goodwin, E. B. The power of the 3′ UTR: translational control and development. Nature Rev. Genet. 4, 626-637 (2003).
20. Palacios, I. M. & St Johnston, D. Getting the message across: the intracellular localization of mRNAs in higher eukaryotes. Annu. Rev. Cell Dev. Biol. 17, 569-614 (2001).
21. Zaidi, S. H. & Malter, J. S. Nucleolin and heterogeneous nuclear ribonucleoprotein C proteins specifically interact with the 3′- untranslated region of amyloid protein precursor mRNA. J. Biol. Chem. 270, 17292-17298 (1995).
22. Maniatis, T. & Tasic, B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418, 236-243 (2002).
23. Black, D. L. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103, 367-370 (2000).
24. Graveley, B. R. Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 17, 100-107 (2001).
25. Garcia-Blanco, M. A., Baraniak, A. P. & Lasda, E. L. Alternative splicing in disease and therapy. Nature Biotechnol. 22, 535-546 (2004).
26. Mine, M. et al. Splicing error in E1α pyruvate dehydrogenase mRNA caused by novel intronic mutation responsible for lactic acidosis and mental retardation. J. Biol. Chem. 278, 11768-11772 (2003).
27. Hutton, M. et al. Association of missense and 5′-splice-site mutations in tau with the inherited dementia FTDP-17. Nature 393, 702-705 (1998).
28. Varani, L. et al. Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17. Proc. Natl Acad. Sci. USA 96, 8229-8234 (1999).
29. Jiang, Z., Cote, J., Kwon, J. M., Goate, A. M. & Wu, J. Y. Aberrant splicing of tau pre-mRNA caused by intronic mutations associated with the inherited dementia frontotemporal dementia with parkinsonism linked to chromosome 17. Mol. Cell. Biol. 20, 4036-4048 (2000).
30. Schutt, C. & Nothiger, R. Structure, function and evolution of sex-determining systems in Dipteran insects. Development. 127, 667-677 (2000).
31. Soller, M. & White, K. ELAV inhibits 3′-end processing to promote neural splicing of ewg pre-mRNA. Genes Dev. 17, 2526-2538 (2003).
32. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. & Cohen, S. M. bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25-36 (2003).
33. 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).
34. Hsieh, J. J., Cheng, E. H. & Korsmeyer, S. J. Taspase1: a threonine aspartase required for cleavage of MLL and proper HOX gene expression. Cell 115, 293-303 (2003).
35. Chambeyron, S. & Bickmore, W. A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 18, 1119-1130 (2004).
36. Schadt, E. E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297-302 (2003).
37. Wittkopp, P. J., Haerum, B. K. & Clark, A. G. Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88 (2004).
38. Yvert, G. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nature Genet. 35, 57-64 (2003).
39. Krawczak, M., Reiss, J. & Cooper, D. N. The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Hum. Genet. 90, 41-54 (1992).
40. Caceres, J. F. & Kornblihtt, A. R. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18, 186-193 (2002).
41. Pagani, F. & Baralle, F. E. Genomic variants in exons and introns: identifying the splicing spoilers. Nature Rev. Genet. 5, 389-396 (2004).
42. Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961).
43. Denny, P. C. & Tyler, A. Activation of protein biosynthesis in non-nucleate fragments of sea urchin eggs. Biochem. Biophys. Res. Commun. 14, 245-249 (1964).
44. Gross, P. R. & Cousineau, G. H. Effects of actinomycin D on macromolecule synthesis and early development in sea urchin eggs. Biochem. Biophys. Res. Commun. 10, 321-326 (1963).
45. Gross, P. R. & Cousineau, G. H. Macromolecule synthesis and the influence of actinomycin on early development. Exp. Cell Res. 33, 368-395 (1964).
46. Brachet, J. & Denis, H. Effects of actinomycin D on morphogenesis. Nature 198, 205-206 (1963).
47. Rifkin, S. A., Kim, J. & White, K. P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genet. 33, 138-144 (2003).
48. Khaitovich, P. et al. Regional patterns of gene expression in human and chimpanzee brains. Genome Res. 14, 1462-1473 (2004).
49. Prasad, J., Colwill, K., Pawson, T. & Manley, J. L. The protein kinase Clk/Sty directly modulates SR protein activity: both hyper- and hypophosphorylation inhibit splicing. Mol. Cell. Biol. 19, 6991-7000 (1999).
50. Kadonaga, J. T. The DPE, a core promoter element for transcription by RNA polymerase II. Exp. Mol. Med. 34, 259-264 (2002).
51. Misra, S. et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3, RESEARCH0083 (2002).
52. Fairbrother, W. G., Yeh, R. F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013 (2002).
53. Fairbrother, W. G. et al. RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res. 32, W187-W190 (2004).
54. Brem, R. B., Yvert, G., Clinton, R. & Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755 (2002).
55. Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743-747 (2004).