Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture

BioEssays

Volumn 33, Issue 8, 2011, Pages 592-601

  Chavali, Sreenivas ^a   Morais, David A de Lima ^b   Gough, Julian ^b   Babu, M Madan ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Gene duplication; Introns; Protein domains; Tandem repeats; Transposable elements

Indexed keywords

UNTRANSLATED RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; EUKARYOTE; EUKARYOTE EVOLUTION; EXON; GENE DUPLICATION; GENE MUTATION; GENE ORDER; GENE STRUCTURE; GENETIC CONSERVATION; INTRON; MUTATION RATE; NONHUMAN; OIKOPLEURA DIOICA; OPERON; PHYLOGENY; RNA SPLICING; TURNOVER TIME;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE ORDER; INTRONS; MUTATION; PHYLOGENY; RNA SPLICING; RNA, UNTRANSLATED; SPLICEOSOMES; TANDEM REPEAT SEQUENCES; TRANSCRIPTION, GENETIC; UROCHORDATA;

EUKARYOTA; METAZOA; OIKOPLEURA DIOICA;

EID: 79960470935     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201100034     Document Type: Article

References (70)

1. Koonin EV. 2009. Evolution of genome architecture. Int J Biochem Cell Biol 41: 298-306.
2. Denoeud F, Henriet S, Mungpakdee S, Aury JM, et al. 2010. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330: 1381-5.
3. Bouquet JM, Spriet E, Troedsson C, Ottera H, et al. 2009. Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica J Plankton Res 31: 359-70.
4. Delsuc F, Brinkmann H, Chourrout D, Philippe H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-8.
5. Holland LZ. 2007. Developmental biology: A chordate with a difference. Nature 447: 153-5.
6. Canestro C, Postlethwait JH. 2007. Development of a chordate anterior-posterior axis without classical retinoic acid signaling. Dev Biol 305: 522-38.
7. Stach T, Winter J, Bouquet JM, Chourrout D, et al. 2008. Embryology of a planktonic tunicate reveals traces of sessility. Proc Natl Acad Sci USA 105: 7229-34.
8. Davila Lopez, Martinez M, Guerra JJ, Samuelsson T. 2010. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One 5: e10654.
9. Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, et al. 2007. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 17: 545-55.
10. Hurst LD, Pal C, Lercher MJ. 2004. The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310.
11. Lercher MJ, Urrutia AO, Hurst LD. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31: 180-3.
12. De S, Teichmann SA, Babu MM. 2009. The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res 19: 785-94.
13. De S, Babu MM. 2010. Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol 22: 326-33.
14. Seo HC, Edvardsen RB, Maeland AD, Bjordal M, et al. 2004. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica Nature 431: 67-71.
15. Keeling PJ, Slamovits CH. 2005. Causes and effects of nuclear genome reduction. Curr Opin Genet Dev 15: 601-8.
16. Williams BA, Slamovits CH, Patron NJ, Fast NM, et al. 2005. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc Natl Acad Sci USA 102: 10936-41.
17. Woolfe A, Goodson M, Goode DK, Snell P, et al. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
18. Sandelin A, Bailey P, Bruce S, Engstrom PG, et al. 2004. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 5: 99.
19. Blumenthal T, Gleason KS. 2003. Caenorhabditis elegans operons: Form and function. Nat Rev Genet 4: 112-20.
20. Blumenthal T. 2004. Operons in eukaryotes. Brief Funct Genomic Proteomic 3: 199-211.
21. Chothia C, Gough J, Vogel C, Teichmann SA. 2003. Evolution of the protein repertoire. Science 300: 1701-3.
22. Nakatani Y, Takeda H, Kohara Y, Morishita S. 2007. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17: 1254-65.
23. Huminiecki L, Heldin CH. 2010. 2R and remodeling of vertebrate signal transduction engine. BMC Biol 8: 146.
24. Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, et al. 2009. Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome Res 19: 1404-18.
25. Lespinet O, Wolf YI, Koonin EV, Aravind L. 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 12: 1048-59.
26. Henikoff S, Greene EA, Pietrokovski S, Bork P, et al. 1997. Gene families: The taxonomy of protein paralogs and chimeras. Science 278: 609-14.
27. Chothia C, Gough J. 2009. Genomic and structural aspects of protein evolution. Biochem J 419: 15-28.
28. Spada F, Steen H, Troedsson C, Kallesoe T, et al. 2001. Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica J Biol Chem 276: 20624-32.
29. Mattick JS. 2009. The genetic signatures of noncoding RNAs. PLoS Genet 5: e1000459.
30. Pauli A, Rinn JL, Schier AF. 2011. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12: 136-49.
31. Mattick JS, Amaral PP, Dinger ME, Mercer TR, et al. 2009. RNA regulation of epigenetic processes. BioEssays 31: 51-9.
32. Fu X, Adamski M, Thompson EM. 2008. Altered miRNA repertoire in the simplified chordate, Oikopleura dioica Mol Biol Evol 25: 1067-80.
33. Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136: 629-41.
34. Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: Insights into functions. Nat Rev Genet 10: 155-9.
35. Martin W, Koonin EV. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature 440: 41-5.
36. Rodriguez-Trelles F, Tarrio R, Ayala FJ. 2006. Origins and evolution of spliceosomal introns. Annu Rev Genet 40: 47-76.
37. Roy SW, Gilbert W. 2006. The evolution of spliceosomal introns: Patterns, puzzles and progress. Nat Rev Genet 7: 211-21.
38. Mattick JS, Gagen MJ. 2001. The evolution of controlled multitasked gene networks: The role of introns and other noncoding RNAs in the development of complex organisms. Mol Biol Evol 18: 1611-30.
39. Le Hir H, Nott A, Moore MJ. 2003. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28: 215-20.
40. Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, et al. 2005. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii Science 310: 1325-6.
41. Carmel L, Rogozin IB, Wolf YI, Koonin EV. 2007. Patterns of intron gain and conservation in eukaryotic genes. BMC Evol Biol 7: 192.
42. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, et al. 2003. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13: 1512-7.
43. Mourier T, Jeffares DC. 2003. Eukaryotic intron loss. Science 300: 1393.
44. Lin K, Zhang DY. 2005. The excess of 5' introns in eukaryotic genomes. Nucleic Acids Res 33: 6522-7.
45. Seo HC, Kube M, Edvardsen RB, Jensen MF, et al. 2001. Miniature genome in the marine chordate Oikopleura dioica Science 294: 2506.
46. Edvardsen RB, Lerat E, Maeland AD, Flat M, et al. 2004. Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica J Mol Evol 59: 448-57.
47. Carmel L, Wolf YI, Rogozin IB, Koonin EV. 2007. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 17: 1034-44.
48. Simpson AG, MacQuarrie EK, Roger AJ. 2002. Eukaryotic evolution: Early origin of canonical introns. Nature 419: 270.
49. Keren H, Lev-Maor G, Ast G. 2010. Alternative splicing and evolution: Diversification, exon definition and function. Nat Rev Genet 11: 345-55.
50. Artamonova II, Gelfand MS. 2007. Comparative genomics and evolution of alternative splicing: The pessimists' science. Chem Rev 107: 3407-30.
51. Niu DK, Hou WR, Li SW. 2005. mRNA-mediated intron losses: Evidence from extraordinarily large exons. Mol Biol Evol 22: 1475-81.
52. Orgel LE, Crick FH. 1980. Selfish DNA: The ultimate parasite. Nature 284: 604-7.
53. Gemayel R, Vinces MD, Legendre M, Verstrepen KJ. 2010. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44: 445-77.
54. Vergnaud G, Denoeud F. 2000. Minisatellites: Mutability and genome architecture. Genome Res 10: 899-907.
55. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, et al. 2007. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-82.
56. Slotkin RK, Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-85.
57. Saito K, Siomi MC. 2010. Small RNA-mediated quiescence of transposable elements in animals. Dev Cell 19: 687-97.
58. Jacquier A. 2009. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10: 833-44.
59. Channon K, Bromley EH, Woolfson DN. 2008. Synthetic biology through biomolecular design and engineering. Curr Opin Struct Biol 18: 491-8.
60. Khalil AS, Collins JJ. 2010. Synthetic biology: Applications come of age. Nat Rev Genet 11: 367-79.
61. Agapakis CM, Silver PA. 2009. Synthetic biology: Exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst 5: 704-13.
62. Carr PA, Church GM. 2009. Genome engineering. Nat Biotechnol 27: 1151-62.
63. Lu TK, Khalil AS, Collins JJ. 2009. Next-generation synthetic gene networks. Nat Biotechnol 27: 1139-50.
64. An W, Chin JW. 2009. Synthesis of orthogonal transcription-translation networks. Proc Natl Acad Sci USA 106: 8477-82.
65. Leisner M, Bleris L, Lohmueller J, Xie Z, et al. 2010. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol 5: 666-70.
66. Chalancon G, Babu MM. 2010. Nanobiotechnology: Scaling up synthetic gene circuits. Nat Nanotechnol 5: 631-3.
67. Chin JW. 2006. Modular approaches to expanding the functions of living matter. Nat Chem Biol 2: 304-11.
68. de Lima Morais DA, Fang H, Rackham OJ, Wilson D, et al. 2011. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res 39: D427-34.
69. Jorda J, Kajava AV. 2009. T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm. Bioinformatics 25: 2632-8.
70. Smith DJ, Konarska MM, Query CC. 2009. Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast. Mol Cell 34: 333-43.