Intron-exon structures. From molecular to population biology

Advances in Genome Biology

Volumn 5, Issue C, 1998, Pages 143-178

  Long, Manyuan ^a   de Souza, Sandro J ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0003491257     PISSN: 10675701     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1067-5701(98)80020-X     Document Type: Article

References (179)

1. Berget S.M., Moore C., and Sharp P.A. Spliced segments at the 5′ terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci. USA 74 (1977) 3171-3175
2. Chow L.T., Gelinas R.E., Broker T.R., and Roberts R.J. An amazing sequence arrangement at the 5′ ends of adenovirus 2 messenger RNA. Cell 12 (1977) 1-8
3. Mount S.M. A catalogue of splice junction sequences. Nucleic Acid Res. 10 (1982) 459-472
4. Dorit R.L., Schoenbach L., and Gilbert W. How big is the universe of exons?. Science 250 (1990) 1377-1382
5. Fichant G.A. Constraints acting on the exon positions of the splice site sequences and local amino acid composition of the protein. Hum. Mol. Genet. 1 (1992) 259-2647
6. Fedorov A., Suboch G., Bujakov M., and Fedorova L. Analysis of nonuniformaty in intron phase distribution. Nucleic Acids Res. 20 (1992) 2553-2557
7. Gilbert W. Why gene in pieces?. Nature 271 (1978) 501
8. Long M., de Souza S.J., and Gilbert W. Evolution of the intron/exon structure of eukaryotic genes. Curr. Opin. Genet. Dev. 5 (1995) 774-778
9. Moore M.J., Query C.C., and Sharp P.A. Splicing of precursors to mRNAs by the spliceosome. In: Gesteland R.F., and Atkins J.F. (Eds). The RNA world (1993), Cold Spring Harbor Laboratory, Cold Springer Harbor, NY 303-358
10. Sharp P.A. Split genes and RNA splicing. Cell 77 (1994) 805-815
11. Nilsen T.W. RNA-RNA interactions in the spliceosome: unraveling the ties that bind. Cell 78 (1994) 1-4
12. Moore M.J., and Sharp P.A. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 365 (1993) 294-295
13. Fabrizio P., and Abelson J. Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing. Science 250 (1990) 404-409
14. McPheeters D.S., and Abelson J. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71 (1992) 819-831
15. Legrain P., Seraphin B., and Rosbach M. Commitment of yeast pre-mRNA to the spliceosome pathway does not require U2snRNP. Mol. Cell. Biol. 8 (1988) 3755-3760
16. Zhaler A.M., Lone W.S., Stalk J.A., and Roth M.B. SR proteins: A conserved family of pre-mRNA splicing factors. Genes Dev. 6 (1992) 837-847
17. Stephens R.M., and Schneider T.D. Features of spliceosome evolution and function inferred from an anlysis of the information at human splice sites. J. Mol. Biol. 228 (1992) 1124-1136
18. Robberson B.L., Cote G.J., and Berget S.M. Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10 (1990) 84-94
19. Hall S.L., and Padgett R.A. Conserved sequences in a class of rate eukaryotic nuclear introns with non-consensus splice sites. J. Mol. Biol. 239 (1994) 357-365
20. Hall S.L., and Padgett R.A. Requirement for U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science 271 (1996) 1716-1718
21. Tam W.-Y., and Steitz J.A. A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class IAT-AC) intron in vitro. Cell 84 (1996) 801-811
22. Mount S.M. AT-AC introns: an attack on dogma. Science 271 (1996) 1690-1691
23. Kreivi J.-P., and Lamond A.I. RNA splicing: unexpected spliceosome diversity. Curr. Biol. 6 (1996) 802-805
24. Agabian N. Trans-splicing in nuclear pre-mRNAs. Cell 61 (1990) 1157-1160
25. Nilsen T.W. Trans-splicing in nematodes. Exp. Parasitol. 69 (1989) 413-416
26. Wissinger B., Schulster W., and Brennicke A. Trans-splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65 (1991) 473-482
27. Eul J., Graessmann M., and Graessmann A. Experimental evidence for RNA trans-splicing in mammalian cells. EMBO J. 14 (1995) 3226-3235
28. Ullu E., and Tschudi C. Accurate modification of the tryanosome spliced leader cap structure in a homologous cell-free system. J. Biol. Chem. 270 (1995) 20365-20369
29. Hannon G.J., Maroney P.A., and Nilsen T.W. U small nuclear ribonucleoprotein requirements for nematode cis- and trans-splicing in vitro. J. Biol. Chem. 266 (1991) 22792-22795
30. McKeown M. Alternative mRNA splicing. Annu. Rev. Cell Biol. 8 (1992) 133-155
31. Hodges D., and Bernstein S.I. Genetic and biochemical analysis of alternative RNA splicing. Adv. Genet. 31 (1994) 207-228
32. Inoue K., and Shimura Y. Mechanisms of alternative RNA splicing. In: Go M., and Schimmel P. (Eds). Tracing Biological Evolution in Protein and Gene Structures (1995), Elsevier, Amsterdam 87-99
33. Cech T.R., and Bass B.L. Biological catalysis by RNA. Annu. Rev. Biochem. 55 (1986) 599-629
34. Cech T.R. Self-splicing of group I introns. Annu. Rev. Biochem. 59 (1990) 543-568
35. Burke J.M. Molecular genetics of group I introns: RNA structures and protein factors required for splicing-a review. Gene 73 (1988) 273-294
36. Lambowitz A.M., and Perlman P.S. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15 (1990) 440-444
37. Guo Q., and Lambowitz A.M. A tyrosil-tRNA synthetase binds specifically to the group I intron catalytic core. Genes Dev. 6 (1992) 1357-1372
38. Bell-Pedersen D., Quirk S., Clyman J., and Belfort M. Intron mobility in phage t4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications. Nucleic Acids Res. 18 (1990) 3763-3770
39. Loizos N., Tillier E.R.M., and Belfort M. Evolution of mobile group I introns: recognition of intron sequences by an intron-encoded endonuclease. Proc. Natl. Acad. Sci. USA 91 (1994) 11983-11987
40. Zimmerly S., Guo H., Eskes R., Yang J., Perlman P.S., and Lambowitz A.M. A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83 (1995) 529-538
41. Yang J., Zimmerly S., Perlman P.S., and Lambowitz A.M. Efficient integration of an intron RNA into double-stranded DNA by reverse splicing. Nature 381 (1996) 332-335
42. Hong L., and Hallick R.B. A group III intron is formed from domains of two individual group II introns. Genes Dev. 8 (1994) 1589-1599
43. Christopher D.A., and Hallick R.B. Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. Nucleic Acids Res. 17 (1989) 7591-7608
44. Drager R.G., and Hallick R.B. A complex twintron is excised as four individual introns. Nucleic. Acids Res. 21 (1993) 2389-2394
45. Hawkins J.D. A survey on intron and exon lengths. Nucleic Acids Res. 16 (1988) 9893-9898
46. Long M., Rosenberg C., and Gilbert W. Intron phase correlations and the evolution of the intron/exon structure of genes. Proc. Natl. Acad. Sci. USA 92 (1995) 12495-12499
47. Benian G.M., L'Hernaut S.W., and Morris M.E. Sequence of an unusually large protein implicaterd in regulation of myosin activity in C. elegans. Nature 342 (1989) 45-50
48. Uphold W.B., and Sandell L.J. Exon/intron organization of the chicken type II procollagen: intron size distribution suggests a minimum intron size. Proc. Natl. Acad. Sci. USA 83 (1986) 2325-2329
49. Mount S.M., Burks C., Hertz G., Stormo G.D., White O., and Fields C. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 20 (1992) 4255-4262
50. Fu X.-Y., Cilgan J., and Manley J.L. Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA. Mol. Cell. Biol. 8 (1988) 3582-3590
51. Russell C.B., Fraga D., and Henrichsen R.D. Extremetly short 20-33 nucleotide introns are the standard length in Paramecium tetraurelia. Nucleic Acids Res. 22 (1994) 1221-1225
52. Gilson P.R., and McFadden G.I. The miniaturized nuclear genome of a eukarytic endosymbiont contains genes that overlap, genes that are cotranscribed, and the smallest known spliceosomal introns. Proc. Natl. Acad. Sci. USA 93 (1996) 7737-7742
53. Roberts R.G. Dystrophin, its gene, and the dystrophinopathies. Adv. Genet. 33 (1995) 177-231
54. Boyce F.M., Beggs A.H., Feener C., and Kunkel L.M. Dystrophin is transcribed in brain from a distant upstream promoter. Proc. Natl. Acad. Sci. USA 88 (1991) 1276-1280
55. Field C. Information content of Caenorhabditis elegans splice site sequence varies with intron length. Nucleic Acids Res. 18 (1992) 1509-1512
56. Hughes A.L., and Hughes M.K. Small genomes for better flyers. Nature 377 (1995) 391
57. Cohen I.R., Grassel S., Murdoch A.D., and Lozzo R.V. Structural characterization of the complete human perlecan gene and its promoter. Proc. Natl. Acad. Sci. USA 90 (1993) 10404-10408
58. Palmer J.D., and Logsdon J.M. The recent origins of introns. Curr. Opin. Genet. Dev. 1 (1991) 470-477
59. (in press). de Souza S.J., Long M., and Gilbert W. Introns and gene evolution. Genes Cells 1 (1996)
60. Brown N.P., Whittaker A.J., Newell W.R., Rawlings C.J., and Beck S. Identification and analysis of multigene families by comparison of exon fingerprints. J. Mol. Biol. 249 (1995) 342-359
61. Mattick J.S. Introns: evolution and function. Curr. Opin. Genet. Dev. 4 (1994) 823-831
62. Shaefer B., Wilde B., Massardo D.R., Manna F., Del Giudice L., and Wolf K. A mitochondrial group I intron in fission yeast encodes a maturase and is mobil in crosses. Curr. Genet. 25 (1994) 336-341
63. Shub D.A. The antiquity of group I introns. Curr. Opin. Genet. Dev. 1 (1991) 478-484
64. Kuhsel M.G., Strickland R., and Palmer J.D. An ancient group I intron shared by eubacteria and chloroplasts. Science 250 (1990) 1570-1573
65. Sharp P.A. On the origin of RNA splicing and introns. Cell 42 (1985) 397-400
66. Cech T. The generality of self-splicing RNA: relationship to nuclear mRNA splicing. Cell 44 (1986) 207-212
67. Saldanha R., Mohr G., Belfort M., and Lambowitz A.M. Group I and group II introns. FASEB J. 7 (1993) 15-24
68. Carignani G., Groudinsky O., Frezza D., Schiavon E., Bergantino E., and Slonimski P.P. An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35 (1983) 733-742
69. Goguel V., Delahodde A., and Jacq C. Connections between RNA splicing and DNA intron mobility in yeast mitochongria: RNA maturase and DNA endonuclease switching experiments. Mol. Cell. Biol. 12 (1992) 696-705
70. Matsuoka M., Matsubara M., Kakehi M., and Imanaka T. Homologous maturase-like protein are encoded within the group I introns in different mitochondrial genes specifying Yarrowa lipolytica cytochrome c oxidase subunit 3 and Saccharomyces cerevisiae apocytochrome b. Curr. Genet. 26 (1994) 377-381
71. Du J., Portetelle D., Harvengt L., Dumont M., and Wathelet B. Expression of intron-encoded maturase-like polypeptides in potato chloroplasts. Curr. Genet. 25 (1994) 158-163
72. Xiong Y., and Eickbush T.H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9 (1990) 3353-3362
73. Michel F., and Lang B.F. Mitochondrial class II introns encode proteins related to the reverse transcriptases of retrovirus. Nature 316 (1985) 641-643
74. Kennell J.C., Moran J.V., Perlman P.S., Butow R.A., and Lambowitz A.M. Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria. Cell 73 (1993) 133-146
75. Belfort M., and Perlman P.S. Mechanisms of intron mobility. J. Biol. Chem. 270 (1995) 30237-30240
76. Mueller M.W., Allmaier M., Eskes R., and Schweyen R. Transposition of group II intron all in yeast and invasion of mitochondrial genes at new locations. Nature 366 (1993) 174-176
77. Sellem C.H., Lecellier G., and Belcour L. Transposition of a group II intron. Nature 366 (1993) 176-178
78. Schmidt W.R., Schweyen R.J., Wilf K., and Mueller M.W. Transposable group II introns in fission and budding yeast. Site-specific genomic instabilities and formation of group II IVS plD-NAs. J. Mol. Biol. 243 (1994) 157-166
79. Levra-Juillet E., Boulet A., Seraphin B., Simon M., and Faye G. Mitochondrial introns all and/or al2 are needed for the in vivo deletion of intervening sequences. Mol. Gen. Genet. 217 (1989) 168-171
80. Benyajati C., Spoerel N., Haymerle H., and Ashburner M. The messenger RNA for alcohol dehydrogenase in Drosophila melanogaster differs in its 5′ end in different developmental stages. Cell 33 (1983) 125-133
81. Monaco L., Vicini E., and Conti M. Structure of two rat genes coding for closely related rolipramsensitive cAMP phophodiesterase: multiple mRNA variants originate from alternative splicing and multiple start sites. J. Biol. Chem. 269 (1994) 347-357
82. Irniger S., Egli C.M., Kuenzler M., and Braus G.H. The yeast actin intron contains a cryptic promoter that can be switched on by preventing transcriptional interference. Nucleic Acids Res. 20 (1992) 4733-4739
83. Meyer K.B., Sharpe M.J., Surani M.A., and Neuberger M.S. The importance of the 3′-enhancer region in immunoglobulin kappa gene expression. Nucleic Acids Res. 18 (1990) 5609-5615
84. Jonsson J.J., Converse A., and Mclvor R.S. An enhancer in the first intron of the human purine nucleoside phosphorylase-encoding gene. Gene 140 (1994) 187-193
85. Brooks A.R., and Levy W.B. Hepatocyte nuclear factor 1 and C/EBP are essential for the activity of the human apolipoprotein B gene second-intron enhancer. Mol. Cell. Biol. 12 (1992) 1134-1148
86. Xie Y., Favot P., Dunn T.L., Cassady A.I., and Hume D.A. Expression of mRNA encoding the macrophage colony-stimulating factor receptor (c-fms) is controlled by a constitutive promoter and tissue-specific transcription elongation. Mol. Cell. Biol. 13 (1993) 3191-3201
87. Lavett D.K. Secondary structure and intron-promoter homology in globin-switching. Am. J. Hum. Genet. 36 (1984) 338-345
88. Lavett D.K. A model for transcriptional regulation based upon homology between introns and promoter regions and secondary structure in the promoter regions: the human globins. J. Theor. Biol. 107 (1984) 1-36
89. Henikoff S., Keene M.A., Fechtel K., and Fristrom J.W. Gene within a gene: nested Drosophila genes encoded proteins on opposite DNA strands. Cell 44 (1986) 33-42
90. Chalfie M., Eddy S., Hengartner M.O., Hodgkin J., Kohara Y., Plasterk H.A., Waterson R.H., and White J.G. Genome maps VI Caenorhabditis elegans. Science 270 (1995) 415-430
91. Maxwell E.S., and Fournier M.J.A. The small nuclear RNAs. Annu. Rev. Biochem. 35 (1995) 899-934
92. Sollner-Webb B. Novel intron-encoded small nucleolar RNAs. Cell 75 (1993) 403-405
93. Nicoloso M., Ferrer C.M., Michot B., Azum M.C., and Bachellerie J.P. U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin gene in mammals. Mol. Cell. Biol. 14 (1994) 5766-5776
94. Tycowski K.T., Shu M.-D., and Steitz J.A. A mammalian gene with introns instead of exons generating stable RNA products. Nature 379 (1996) 464-466
95. Li W.-H., and Graur D. Fundamentals of molecular Evolution (1991), Sinauer Associates, Sunderland, MA 67-98
96. Ohno S. Evolution by Gene Duplication (1970), Springer-Verlag, Berlin
97. Sudhof T.C., Russell D.W., Goldstein J.I., Brown M.S., Sanchez-Pescador R., and Bell G.I. Cassette of eight exons shared by genes for LDL receptor and EGF precursor. Science 228 (1985) 893-895
98. Patthy L. Evolution of the proteases of blood coagulation and fibrinosis by assembly from modules. Cell 41 (1985) 657-663
99. Long M., and Langley C.H. Natural selection and origin of jingwei: a chimeric processed functional gene. Science 260 (1993) 91-95
100. Patthy L. Modular exchange principles in proteins. Curr. Opin. Struct. Biol. 1 (1991) 351-361
101. Patthy L. Introns and exons. Curr. Opin. Struct. Biol. 4 (1994) 383-392
102. Doolittle R.F. The multiplicity of domains in proteins. Annu. Rev. Biochem. 64 (1995) 287-314
103. Dorit R.L., and Gilbert W. The limited universe of exons. Curr. Opin. Struct. Biol. 1 (1991) 973-977
104. Long M., de Souza S.J., Rosenberg C., and Gilbert W. Exon shuffling and the origin of the mitochondrial targetting function in plant cytochrome c1 precursor. Proc. Natl. Acad. Sci. USA 93 (1996) 7727-7731
105. Nugent J.M., and Palmer J.D. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66 (1991) 374-381
106. Gantt J.S., Baldauf S.L., Calie P.J., Weeden N.F., and Palmer J.D. Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 10 (1991) 3073-3078
107. Hurst L.D., and McVean G.T. Molecular evolution: a difficult phase for introns-early. Curr. Biol. 6 (1996) 533-536
108. Cerff R. The chimeric nature of nuclear genomes and the antiquity of introns as demonstrated in the GAPDH gene system. In: Go M., and Schimmel P. (Eds). Tracing Biological Evolution in Protein and Gene Structures (1995), Elsevier, Amsterdam 205-227
109. Takahashi Y., Urushiyama S., Tani T., and Ohshima Y. An mRNA-type intron is present in the Rhodotorula hasegawae U2 small nuclear RNA gene. Mol. Cell. Biol. 5 (1991) 1022-1231
110. Tani T., and Ohshima Y. mRNA-type introns in U6 small nuclear RNA genes: implications for the catakysis in pre-mRNA splicing. Genes Dev. 5 (1991) 1022-1031
111. Tani T., and Ohshima Y. The gene for the U6 small nuclear RNA in fission yeast has an intron. Nature 337 (1989) 87-90
112. Muller K., and Schmitt R. Histone genes of Volvox carteri: DNA sequence and organization of two H3-H4 gene loci. Nucleic Acids Res. 16 (1988) 4121-4136
113. Jellie A.M., Tate W.P., and Trotman C.N.A. Evolutionary history of introns in a multidomain globin gene. J. Mol. Evol. 42 (1996) 641-647
114. Feller W. An Introduction to Probability Theory and Its Applications Vol. 1 (1950), John Wiley & Sons, New York 303-341
115. Gilbert W. The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol. 52 (1987) 901
116. Seidel H.M., Pomplianp D.L., and Knowles J.R. Exons as microgenes?. Science 257 (1992) 1489-1490
117. Senapathy P., Bertolaet B.L., Seidel H.M., and Knowles J.R. Introns and the origin of protein-coding genes. Science 268 (1995) 1366-13647
118. Senapathy P. Origin of eukaryotic introns: a hypothesis, based on codon distribution statistics in genes, and its implications. Proc. Natl. Acad. Sci. USA 83 (1986) 2133-2137
119. Senapathy P. Possible evolution of splicing-junction signals in eukaryotic genes from stop codons. Proc. Natl. Acad. Sci. USA 85 (1988) 1129-1133
120. Forsdyke D.R. Conservation of stem-loop potential in introns of snake venom phospholipase A2 genes: an application of FORS-D analysis. Mol. Biol. Evol. 12 (1995) 1157-1165
121. Forsdyke D.R. A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol. Biol. Evol. 12 (1995) 949-958
122. Doolittle W.F. Gene-in-pieces: were they ever together?. Nature 272 (1978) 581-582
123. Darnell Jr. J.E. Implications of RNA-RNA splicing in evolution of eukaryotic cells. Science 202 (1978) 1257-1261
124. Blake C.C.F. Do genes-in-pieces imply protein in pieces?. Nature 273 (1978) 267
125. Go M. Correlations of DNA exonic regions with protein structural units in haemoglobin. Nature 291 (1981) 90-93
126. Bertolaet B.L., and Knowles J.R. Complementation of fragments of triosephosphate isomerase defined by exon boundaries. Biochemistry 34 (1995) 5736-5743
127. Shiba K. Dissection of an enzyme into two fragments at intron-exon boundaries. In: Go M., and Schimmel P. (Eds). Tracing Biological Evolution in Protein and Gene Structures (1995), Elsevier, Amsterdam 11-22
128. Hawley R.S., and Arbel T. Yeast genetics and the fall of the classical view of meiosis. Cell 72 (1993) 301-303
129. Tomizawa J. Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38 (1984) 861-870
130. Kleckner N., and Weiner B.M. Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic and premeiotic cells. Cold Spring Harb. Symp. Quant. Biol. 58 (1993) 553-565
131. Dibb N.J. Proto-splice site model of intron origin. J. Theor. Biol. 151 (1991) 405-416
132. Rogers J. How were introns inserted into nuclear genes?. Trends Genet. 5 (1989) 213
133. Patthy L. Exons-original building blocks of proteins?. BioEssays 13 (1991) 187-192
134. Cavalier-Smith T. Selfish DNA and the origin of introns. Nature 315 (1985) 283-284
135. Cavalier-Smith T. Intron phylogeny: a new hypothesis. Trends Genet. 7 (1991) 145-148
136. Stoltzfus A., Spencer D.F., Zuker M., Logsdon Jr. J.M., and Doolittle W.F. Testing the exon theory of genes: the evidence from protein structure. Science 265 (1994) 202-207
137. Wessler S.R. The splicing of maize transposable elements from pre-mRNA-a mini-review. Gene 82 (1989) 127-133
138. Menssen A., Hohmann S., Martin W., et al. The En/Spm transposable element of Zea mays contains splice sites at the termini generating a novel intron from a dSpm element in the A2 gene. EMBO J. 9 (1990) 3051-3057
139. Fridell R.A., Pret A.M., and Searles L.L. A retrotransposon 412 insertion within an exon of the Drosophila melanogaster vermilion gene is spliced from the precursor RNA. Genes Dev. 4 (1990) 559-566
140. Rogers J.H. The role of introns in evolution. FEBS Lett. 268 (1990) 339-343
141. Charlesworth B., and Langley C.H. The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23 (1989) 251-287
142. Cameron J.R., Loh E.Y., and Davis R.W. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell 16 (1979) 739-751
143. Hartl D.L., Medhora M., Green L., and dykhuizen D.E. The evolution of DNA sequences in Escherichia coli. Philos. Trans. R. Soc. Lond. Biol. 312 (1986) 191-204
144. Palmer J.D. Comparative organization of chloroplast genomes. Annu. Rev. Genet. 19 (1985) 325-354
145. Tonegawa S., Maxam A.M., Tizard R., Bernard O., and Gilbert W. Sequence of a mouse germ-line gene for a variable region of an immunoglobulin light chain. Proc. Natl. Acad. Sci. USA 74 (1978) 1485-1489
146. Crick F. Split genes and RNA splicing. Science 204 (1979) 264-271
147. Dibb N.J., and Newman A.J. Evidence that introns arose at proto-splice site. EMBO J. 8 (1989) 2015-2022
148. Marchionni M., and Gilbert W. The triosephosphate isomerase gene from maize: Introns antedate the plant-animal divergence. Cell 46 (1986) 133-141
149. Shah D.M., Hightower R.C., and Meagher R.B. Genes encoding actin in higher plants: intron positions are highly conserved but the coding sequences are not. J. Mol. Appl. Genet. 2 (1983) 111-126
150. Nawrath C., Schell J., and Koncz C. Homologous domains of the largest subunit of eucaryotic RNA polymerase II are conserved in plants. Mol. Gen. Genet. 223 (1990) 5-75
151. Pardo J.M., and Serrano R. Structure of a plasma membrane H+-ATPase gene from the plant Arabidopsis thaliana. J. Biol. Chem. 264 (1989) 8557-8562
152. Wing S.S., and Bonville D. The 14-kDa ubiquitin conjugating enzyme: structure of the rat gene and regulation of mRNA levels upon fasting and by insulin. Am. J. Physiol. 267 (1994) E39-E48
153. Kersanach R., Brinkmann H., Liaud M.-F., Zhang D.-X., Martin W., and Cerff R. Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature 367 (1994) 387-389
154. Setoyama C., Joh T., Tsuzuk T., and Shimada K. Structural organization of the mouse cytosolic malate dehydrogenase gene: comparison with that of the mouse mitochondrial malate dehydrogenase gene. J. Mol. Biol. 202 (1988) 355-364
155. Obaru K., Tsuzuki T., Setoyama C., and Shimada K. Structural organization of the mouse aspertate aminotransferase isozyme genes: introns antedate the divergence of cytosolic and mitochondrial isozyme genes. J. Mol. Biol. 200 (1988) 13-22
156. Green P., Lipman D., Hillier L., Waterson R., States D., and Claverie J.-M. Ancient conserved regions in new gene sequences and the protein database. Science 259 (1993) 1711-1717
157. Logsdon Jr. J.M., Tyshenko M.G., Dixon C., Jafari J.D., Walker V.K., and Palmer J.D. Seven newly discovered intron position in the triose-phosphate isomerase gene: evidence for the introns-late theory. Proc. Natl. Acad. Sci. USA 92 (1995) 8507-8511
158. Kwiatowski J., Krawczyk M., Kornacki M., Bailey K., and Ayala F.J. Evidence against the exon theory of genes derived from the triose-phosphate isomerase gene. Proc. Natl. Acad. Sci. USA 92 (1995) 8503-8506
159. Fink G.R. Pseudogenes in yeast?. Cell 49 (1987) 5-6
160. Nyberg A.M., and Cronhjort M.B. Intron evolution: a statistical comparison of two models. J. Theor. Biol. 157 (1992) 175-190
161. Giroux M.J., Clancy M., Baier J., Ingham L., McCarty D., and Hannah L.C. De novo synthesis of an intron by the maize transposable element dissociation. Proc. Natl. Acad. Sci. USA 91 (1994) 12150-12154
162. Hall D.H., Liu Y., and Shub D.A. Exon shuffling by recombination between self-splicing introns of bacteriophage T4. Nature 340 (1989) 574-576
163. Shub D.A. The antiquity of group I introns. Curr. Opin. Genet. Dev. 1 (1991) 478-484
164. Bryk M., and Belfort M. Spontaneous shuffling of domains between introns of phage T4. Nature 346 (1990) 394-396
165. Mikheeva S., and Jarrell K. Use of engineered ribozymes to catalyze chimeric gene assembly. Proc. Natl. Acad. Sci. USA 93 (1996) 7486-7490
166. Haldane J.B.S. The Causes of Evolution (1932), Longmans, New York
167. Caffarelli E., Arese M., Santoro B., Fragapane P., and Bozzoni I. In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol. Cell. Biol. 14 (1994) 2966-2974
168. Ohno S. Evolution by Gene Duplication (1970), Springer-Verlag, Berlin
169. Ohta T. On the evolution of multigene families. Theor. Popul. Biol. 23 (1983) 216-240
170. Ohta T. Simulating evolution by gene duplication. Genetics 115 (1987) 207-213
171. Ohta T. The role of gene duplication in evolution. Genome 31 (1989) 187-192
172. in press. deSouza S.J., Long M., and Gilbert W. Introns and Gene Evolution. From Genes to Cells Vol. 1 (1996)
173. Haldane J.B.S. A Mathematical Theory of Natural Selection. VIII. Stable Metapopulation. Proc. Cambridge Philos. Soc. 27 (1931) 137-142
174. Wright S. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proc. Sixth Int. Cong. Genet. 1 (1932) 356-366
175. Stephan W., and Kirby D.A. RNA folding in Drosophila shows a distance effect for compensatory fitness interaction. Genetics 135 (1993) 97-103
176. Kirby D.A., Muse S.V., and Stephan W. Maintenance of pre-mRNA secondary structure by epistatic selection. Proc. Natl. Acad. Sci. USA 92 (1995) 9047-9051
177. de Souza S.J., Long M., Scheonbach L., and Gilbert W. Intron position correlate with module boundaries in ancient proteins. Proc. Natl. Acad. Sci. USA 93 (1996) 14632-14636
178. Desseyn J.L., Guyonnet Duperat V., Porchet N., Aubert J.P., and Laine A. Human mucin gene muc5B: The large, 10.7-kb-large central exon encodes various alternate subdomains resulting in a super-repeat-Structural evidence for a 11p15.5 gene family. J. Biol. Chem. 272 (1997) 3168-3178
179. van den Hoff M.J.B., Jonker A., Beintema J.J., and Lamers W.H. Evolutionary relationships of the carbamoylphosphate synthetase. J. Mol. Evol. 41 (1995) 813-832