Introns First

Biological Theory

Volumn 7, Issue 3, 2013, Pages 196-203

  Forsdyke, Donald R ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

Conventional phenotype; Exons; Genome phenotype; Introns; RNA world; Stem loops

Indexed keywords

EID: 84894997773     PISSN: 15555542     EISSN: 15555550     Source Type: Journal    
DOI: 10.1007/s13752-013-0090-6     Document Type: Article

References (54)

1. Battail G (2007) Information theory and error-correcting codes in genetics and biological evolution. In: Barbieri M (ed) Introduction to biosemiotics: the new biological synthesis. Springer, Dordrecht, pp 299–345 DOI: 10.1007/1-4020-4814-9_13
2. Bechtel JM, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A (2008) Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC Genom 9:284. doi:10.1186/1471-2164-9-284 DOI: 10.1186/1471-2164-9-284
3. Butler S (1926) The Shrewsbury edition of the works of Samuel Butler. Vol. 20. Jones HF, Bartholomew AT (eds), Jonathan Cape, London
4. Chargaff E (1951) Structure and function of nucleic acids as cell constituents. Fed Proc 10:654–659
5. Cock AG, Forsdyke DR (2008) Treasure your exceptions: the science and life of William Bateson. Springer, New York, pp 339–377 DOI: 10.1007/978-0-387-75688-2
6. Crick F (1971) General model for chromosomes of higher organisms. Nature 234:25–27 DOI: 10.1038/234025a0
7. Crick F (1979) Split genes and RNA splicing. Science 204:264–271 DOI: 10.1126/science.373120
8. D’Onofrio G, Mouchiroud D, Aïssani B, Gauter C, Bernardi G (1991) Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol 32:504–510 DOI: 10.1007/BF02102652
9. Darnell JE (1978) Implications of RNA–RNA splicing in evolution of eukaryotic cells. Science 202:1257–1260 DOI: 10.1126/science.364651
10. Dawson WK, Yamamoto K (1999) Mean free energy topology for nucleotide sequences of varying composition on secondary structure calculations. J Theor Biol 201:113–140 DOI: 10.1006/jtbi.1999.1018
11. Doolittle WF (1978) Genes in pieces: were they ever together? Nature 272:581–582 DOI: 10.1038/272581a0
12. Doolittle RF (1985) The genealogy of some recently evolved vertebrate proteins. Trends Biochem Sci 10:233–237 DOI: 10.1016/0968-0004(85)90140-9
13. Faria LCB, Rocha ASL, Kleinschmidt JH, Silva-Filho MC, Bim E, Herai RH, Yamagishi MEB, Palazzo R (2012) Is a genome a codeword of an error-correcting code? PLoS ONE 7(5):e36644. doi:10.1371/journal.pone.0036644 DOI: 10.1371/journal.pone.0036644
14. Forsdyke DR (1981) Are introns in-series error detecting sequences? J Theor Biol 93:861–866 DOI: 10.1016/0022-5193(81)90344-1
15. Forsdyke DR (1995a) A stem-loop “kissing” model for the initiation of recombination and the origin of introns. Mol Biol Evol 12:949–958
16. 2 genes: an application of FORS-D analysis. Mol Biol Evol 12:1157–1165
17. Forsdyke DR (1995c) Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J Mol Evol 41:573–581
18. Forsdyke DR (1996) Different biological species “broadcast” their DNAs at different (G + C)% “wavelengths.” J Theor Biol 178:405–417 DOI: 10.1006/jtbi.1996.0038
19. Forsdyke DR (2007a) Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. J Theor Biol 248:745–753 DOI: 10.1016/j.jtbi.2007.07.008
20. Forsdyke DR (2007b) Molecular sex: the importance of base composition rather than homology when nucleic acids hybridize. J Theor Biol 249:325–330 DOI: 10.1016/j.jtbi.2007.07.023
21. Forsdyke DR (2011a) The interrupted gene. In: Krebs JE, Goldstein ES, Kilpatrick ST (eds) Lewin’s genes X. Jones and Bartlett, Boston, pp. 79–97, 172–175
22. Forsdyke DR (2011b) Evolutionary bioinformatics, 2nd edn. Springer, New York, pp 249–266 DOI: 10.1007/978-1-4419-7771-7
23. Forsdyke DR (2011c) The selfish gene revisited: reconciliation of Williams–Dawkins and conventional definitions. Biol Theor 5:246–255 DOI: 10.1162/BIOT_a_00054
24. Forsdyke DR, Bell SJ (2004) Purine-loading, stem-loops, and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations. App Bioinf 3:3–8
25. Gilbert W (1978) Why genes in pieces? Science 271:501
26. Gilbert W (1981) DNA sequencing and gene structure. Science 214:1305–1312 DOI: 10.1126/science.7313687
27. Gould SJ (1993) Fulfilling the spandrels of world and mind. In: Selzer J (ed) Understanding scientific prose. University of Wisconsin Press, Madison, pp 310–336
28. Hamming RW (1980) Coding and information theory. Prentice-Hall, Englewood Cliffs
29. Kleckner N, Weiner BM (1993) Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic and premeiotic cells. Cold Spring Harb Symp Quant Biol 58:553–565 DOI: 10.1101/SQB.1993.058.01.062
30. Le S-Y, Maizel JV (1989) A method for assessing the statistical significance of RNA folding. J Theor Biol 138:495–510 DOI: 10.1016/S0022-5193(89)80047-5
31. Liebovitch LS, Tao Y, Todorov AT, Levine L (1996) Is there an error-correcting code in the base sequence of DNA? Biophys J 71:1539–1544 DOI: 10.1016/S0006-3495(96)79356-6
32. Matsuo K, Clay O, Kunzler P, Georgiev O, Urbanek P, Schaffner W (1994) Short introns interrupting the Oct-2 POU domain may prevent recombination between POU family genes without interfering with potential POU domain ‘shuffling’ in evolution. Biol Chem Hoppe-Seyler 375:675–683 DOI: 10.1515/bchm3.1994.375.10.675
33. Morange M (1998) A history of molecular biology. Harvard University Press, Cambridge, MA
34. Morgan TH (1911) Random segregation versus coupling in Mendelian inheritance. Science 34:384 DOI: 10.1126/science.34.873.384
35. Orgel LE, Crick FHC, Sapienza C (1980) Selfish DNA. Nature 288:645–646 DOI: 10.1038/288645a0
36. Penny D, Hoeppner MP, Poole AM, Jeffares DC (2009) An overview of the intron-first theory. J Mol Evol 69:527–540 DOI: 10.1007/s00239-009-9279-5
37. Pfeifer K, Tilghman SM (1994) Allele-specific gene expression in mammals: the curious case of imprinted RNAs. Genes Devel 8:1867–1874 DOI: 10.1101/gad.8.16.1867
38. Prabhu VV (1993) Symmetry observations in long nucleotide sequences. Nucleic Acids Res 21:2797–2800 DOI: 10.1093/nar/21.12.2797
39. Reanney DC (1978) Noncoding sequences in adaptive genetics. In: Fox CF, Todaro GJ, Stevens JG (eds) Persistent viruses. Proceedings of the 1978 ICN-UCLA symposium on molecular and cellular biology held in Keystone, Colorado. Academic Press, New York, pp 311–330
40. Reanney DC (1979) RNA splicing and polynucleotide evolution. Nature 277:598–600 DOI: 10.1038/277598b0
41. Reanney DC (1984) RNA splicing as an error-screening mechanism. J Theor Biol 110:315–321 DOI: 10.1016/S0022-5193(84)80177-0
42. Reese V (2002) Mutation repair: a proposed mechanism that would enable complex genomes to better resist mutational entropy, and which suggests a novel function for meiosis. The human behavior and evolution society 14th annual meeting, Rutgers University. Abstracts of presentations to session on “New Developments in Biology,” p 40
43. Robertson M (1977) Immunoglobulin genes and the immune response. Nature 269:648–650 DOI: 10.1038/269648a0
44. Rogozin IB, Carmel L, Csuros M, Koonin EV (2012) Origin and evolution of spliceosomal introns. Biol Direct 7:11. doi:10.1186/1745-6150-7-11 DOI: 10.1186/1745-6150-7-11
45. Rudner R, Karkas JD, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands. III. Direct analysis. Proc Natl Acad Sci USA 60:921–922 DOI: 10.1073/pnas.60.3.921
46. Tiemeier DC, Tilghman SM, Polsky FI, Seidman JG, Leder A, Edgell MH, Leder P (1978) A comparison of two cloned mouse β-globin genes and their surrounding and intervening sequences. Cell 14:237–245 DOI: 10.1016/0092-8674(78)90110-1
47. Tomizawa J (1984) Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38:861–870 DOI: 10.1016/0092-8674(84)90281-2
48. Vinogradov AE (2001) Within-intron correlation with base composition of adjacent exons in different genomes. Gene 276:143–151 DOI: 10.1016/S0378-1119(01)00638-2
49. Wilkinson DM, Ruxton GD (2012) Understanding selection for long necks in different taxa. Biol Rev 87:616–630 DOI: 10.1111/j.1469-185X.2011.00212.x
50. Witkowski JA (1988) The discovery of ‘split’ genes: a scientific revolution. Trends Biochem Sci 13:110–113 DOI: 10.1016/0968-0004(88)90052-7
51. Yang S, Yuan Y, Wang L, Li J, Wang W, Liu H, Chen J-Q, Hurst LD, Tian D (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci USA 109:20992–20997 DOI: 10.1073/pnas.1211827110
52. Zhang C, Xu S, Wei J-F, Forsdyke DR (2008a) Microsatellites that violate Chargaff’s second parity rule have base order-dependent asymmetries in the folding energies of complementary DNA strands and may not drive speciation. J Theor Biol 254:168–177 DOI: 10.1016/j.jtbi.2008.05.013
53. Zhang C, Li W-H, Krainer AR, Zhang MQ (2008b) RNA landscape of evolution for optimal exons and intron discrimination. Proc Natl Acad Sci USA 105:5797–5802 DOI: 10.1073/pnas.0801692105
54. Zuker M (1990) Prediction of optimal and suboptimal secondary structure for RNA. Meth Enzymol 183:281–306 DOI: 10.1016/0076-6879(90)83019-6