MicroRNAs and the advent of vertebrate morphological complexity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 8, 2008, Pages 2946-2950

  Heimberg, Alysha M ^a   Sempere, Lorenzo F ^b   Moy, Vanessa N ^a   Donoghue, Philip C J ^c   Peterson, Kevin J ^a  

^a Dartmouth College   (United States)

^b DARTMOUTH MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Chordate; Genome duplication; Lamprey; Macroevolution; Shark

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

ANALYSIS; ANIMAL TISSUE; ARTICLE; CHORDATA; CLINICAL ARTICLE; GENE; GENE DUPLICATION; GENETIC VARIABILITY; GENOMICS; HISTORY; HUMAN; LAMPREY; MOLECULAR EVOLUTION; MORPHOLOGICAL TRAIT; MOUSE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; VERTEBRATE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; HISTOLOGY; MOLECULAR GENETICS; NORTHERN BLOTTING; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALIA; ASCIDIACEA; BRANCHIOSTOMA LANCEOLATUM; CHONDRICHTHYES; PETROMYZONTIDAE; VERTEBRATA;

ANIMALS; BASE SEQUENCE; BLOTTING, NORTHERN; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; MICRORNAS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHENOTYPE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VERTEBRATES;

EID: 42949146575     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712259105     Document Type: Article

References (44)

1. Valentine JW, Collins AG, Meyer CP (1994) Morphological complexity increase in metazoans. Paleobiology 20:131-142.
2. Aburomia R, Khaner O, Sidow A (2003) Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail. J Struct Funct Genomics 3:45-52.
3. Ohno S (1970) Evolution by Gene Duplication (Springer, Heidelberg).
4. Holland PWH, Garcia-Fernàndez J, Williams, Nic A, Sidow A (1994) in The Evolution of Developmental Regulatory Mechanisms, eds Akam M, Holland P, Ingham P, Wray G (The Company of Biologists Limited, Cambridge, UK), pp 125-133.
5. Sidow A (1996) Genome duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715-722.
6. Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. Plos Biol 3:e314.
7. Stadler PF, etal. (2004) Evidence for independent Hox gene duplications in the hagfish lineage: A PCR-based gene inventory of Eptatretus stoutii. Mol Phylogenet Evol 32:686-694.
8. Spring J (2002) Genome duplications strikes back. Nat Genet 31:128-129.
9. Stellwag EJ (2004) Are genome evolution, organism complexity, and species diversity linked? Integrat Comp Biol 44:358-365.
10. Donoghue PCJ, Purnell MA (2005) Genome duplication, extinction, and vertebrate evolution. Trends Ecol Evol 20:312-319.
11. Putnam NH, et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:86-94.
12. Valentine JW (2000) Two genomic paths to the evolution of complexity in bodyplans. Paleobiology 26:513-519.
13. Vogel C, Chothia C (2006) Protein family expansions and biological complexity. PLoS Comput Biol 2:e48.
14. Frith MC, Pheasant M, Mattick JS (2005) The amazing complexity of the human transcriptome. Eur J Hum Genet 13:894-897.
15. Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA, eukaryotic complexity. BioEssays 29:288-299.
16. Lee C-T, Risom T, Strauss WM (2007) Evolutionary conservation of microRNA regulatory circuits: An examination of microRNA gene complexity and conserved microRNA target interactions DNA Cell Biol 26:209-218.
17. Sempere LF, Cole CN, McPeek MA, Peterson KJ (2006) The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J Exp Zool 306:575-588.
18. Huang Y, Gu X (2007) A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs. BMC Genomics 8:66.
19. Hertel J, et al. (2006) The expansion of the metazoan microRNA repertoire. BMC Genomics 7:25.
20. Ruby JG, et al. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17:1850-1864.
21. Stark A, et al. (2007) Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res 17:1865-1879.
22. Sempere LF, Martinez P, Cole C, Baguñà J, Peterson KJ (2007) Phylogenetic distribution of microRNAs supports the basal position of acoel flatworms and the polyphyly of Platyhelminthes. Evol Dev 9:409-415.
23. Delsuc F, Brinkman H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439:965-968.
24. Prochnik SE, Rokhsar D, Aboobaker AA (2007) Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol 217:73-77.
25. Venkatesh B, et al. (2007) Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5:e101.
26. Peterson KJ, Cotton JA, Gehling JG, Pisani D (2007) The Ediacaran emergence of bilaterians: Congruence between the genetic and geologic fossil records. Philos Trans R Soc London Ser B, in press.
27. Chen J-Y, Huang D-Y, Peng Q-Q, Chi H-M, Feng M (2003) The first tunicate from the Early Cambrian of South China. Proc Natl Acad Sci USA 100:8314-8318.
28. Donoghue PCJ, Forey PL, Aldridge RJ (2000) Conodont affinity and chordate phylogeny. Biol Rev 75:191-251.
29. Müller KJ, Hinz-Schallreuter I (1998) Internal structure of Cambrian conodonts. J Paleontol 72:91-112.
30. Sokal RR, Rohlf FJ (1994) Biometry (Freeman, New York).
31. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8:93-103.
32. Kohn M, et al. (2006) Reconstruction of a 450-My-old ancestral vertebrate protokaryotype. Trends Genet 22:203-210.
33. Tanzer A, Amemiya CT, Kim C-B, Stadler PF (2005) Evolution of microRNAs located within Hox gene clusters. J Exp Zool 304:1-10.
34. Fried C, Prohaska SJ, Stadler PF (2003) Independent Hox-cluster duplications in lamprey. J Exp Zool 299:18-25.
35. Wienholds E, et al. (2005) MicroRNA expression in zebrafish embryonic development. Science 309:310-311.
36. Plasterk RHA (2006) MicroRNAs in animal development. Cell 124:877-881.
37. Wienholds E, Plasterk RHA (2005) MicroRNA function in animal development. FEBS Lett 579:5911-5922.
38. Meyer A, Van de Peer Y (2005) From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD). BioEssays 27:937-945.
39. Kloosterman WP, et al. (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res 34:2558-2569.
40. Lynch M (2007) The Origins of Genome Architecture (Sinauer, Sunderland, MA).
41. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006) miRBase: MicroRNA sequences, targets, and gene nomenclature. Nucleic Acids Res 34:D140-D144.
42. Zuker M (1999) Mfold web server for nucleic acid folding and hybridization predictions. Nucleic Acids Res 31:3406-3415.
43. Ambros V, et al. (2003) A uniform system for microRNA annotation. RNA 9:277-279.
44. Benton MJ, Donoghue PCJ (2007) Paleontological evidence to date the tree of life. Mol Biol Evol 24:26-53.