Intron Loss and Gain

Abstract

Introns, the nonprotein coding regions of genes that are interspersed between protein‐coding exons are present in all eukaryotes' genomes. The variation in intron abundance in eukaryotic genomes signifies that intron loss and intron gain have occurred at varying degrees during the evolution of eukaryotes. Intron gain or loss events have been rare in human and other mammalian genomes, but intron loss in other eukaryotes is starting to be understood in terms of the biology of genomes.

Keywords: introns; evolution; genome; eukaryotes

Figure 1.

Schematic illustration of the suggested mechanisms for intron gain and loss discussed in the article. Intron loss shown in light grey box, all other boxes concern intron gain. DNA is shown as grey bars. Reverse transcribed extra‐chromosomal DNA is labelled ‘cDNA’, all other DNA sequences are genomic. White bars denote RNA. Introns are shown as black lines regardless whether they are DNA or RNA. See text for detailed description of intron gain and loss mechanisms.

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References

Archibald JM, O'Kelly CJ and Doolittle WF (2002) The chaperonin genes of jakobid and jakobid‐like flagellates: implications for eukaryotic evolution. Molecular Biology and Evolution 19: 422–431.

Carmel L, Rogozin IB, Wolf YI and Koonin EV (2007a) Evolutionarily conserved genes preferentially accumulate introns. Genome Research 17(7): 1045–1050.

Carmel L, Wolf YI, Rogozin IB and Koonin EV (2007b) Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Research 17(7): 1034–1044.

Coghlan A and Wolfe KH (2004) Origins of recently gained introns in Caenorhabditis. Proceedings of the National Academy of Sciences of the USA 101: 11362–11367.

Coulombe‐Huntington J and Majewski J (2007) Characterization of intron loss events in mammals. Genome Research 17: 23–32.

Hankeln T, Friedl H, Ebersberger I, Martin J and Schmidt ER (1997) A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. Gene 205: 151–160.

Iwamoto M, Maekawa M, Saito A, Higo H and Higo K (1998) Evolutionary relationship of plant catalase genes inferred from exon–intron structures: isozyme divergence after the separation of monocots and dicots. Theoretical and Applied Genetics 97: 9–19.

Jeffares DC, Penkett CJ and Bähler J (unpublished data). Selection against introns in genes with rapidly changing expression levels.

Modrek B and Lee CJ (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genetics 34(2): 177–180.

Pozzoli U, Menozzi G, Comi GP et al. (2007) Intron size in mammals: complexity comes to terms with economy. Trends in Genetics 23(1): 20–24.

Raible F, Tessmar‐Raible K, Osoegawa K et al. (2005) Vertebrate‐type intron‐rich genes in the marine annelid Platynereis dumerilii. Science 310: 1325–1326.

Roy SW, Fedorov A and Gilbert W (2003) Large‐scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proceedings of the National Academy of Sciences of the USA 100(12): 7158–7162.

Roy SW and Gilbert W (2005) Rates of intron loss and gain: implications for early eukaryotic evolution. Proceedings of the National Academy of Sciences of the USA 102: 5773–5778.

Roy SW and Penny D (2006) Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. Molecular Biology and Evolution 23: 2259–2262.

Roy SW and Penny D (2007) Patterns of intron loss and gain in plants: intron loss‐dominated evolution and genome‐wide comparison of O. sativa and A. thaliana. Molecular Biology and Evolution 24: 171–181.

The Encode Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146): 799–816.

Wolf YI, Kondrashov FA and Koonin EV (2001) Footprints of primordial introns on the eukaryotic genome: still no clear traces. Trends in Genetics 17: 499–501.

Zhuo D, Madden R, Elela SA and Chabot B (2007) Modern origin of numerous alternatively spliced human introns from tandem arrays. Proceedings of the National Academy of Sciences of the USA 104: 882–886.

Further Reading

Collins L and Penny D (2005) Complex spliceosomal organization ancestral to extant eukaryotes. Molecular Biology and Evolution 22: 1053–1066.

Jeffares DC, Mourier T and Penny D (2006) The biology of intron gain and loss. Trends in Genetics 22: 16–22.

Koonin EV (2006) The origin of introns and their role in eukaryogenesis: a compromise solution to the introns‐early versus introns‐late debate? Biology Direct 1: 22.

Lynch M (2002) Intron evolution as a population‐genetic process. Proceedings of the National Academy of Sciences of the USA 99: 6118–6123.

Mourier T and Jeffares DC (2003) Eukaryotic intron loss. Science 300: 1393.

Poole AM, Jeffares DC and Penny D (1998) The path from the RNA world. Journal of Molecular Evolution 46: 1–17.

Rodríguez‐Trelles F, Tarrío R and Ayala FJ (2006) Origins and evolution of spliceosomal introns. Annual Review of Genetics 40: 47–76.

Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG and Koonin EV (2003) Remarkable interkingdom conservation of intron positions and massive, lineage‐specific intron loss and gain in eukaryotic evolution. Current Biology 13: 1512–1517.

Roy SW and Gilbert W (2005) Complex early genes. Proceedings of the National Academy of Sciences of the USA 102: 1986–1991.

Roy SW and Gilbert W (2006) The evolution of spliceosomal introns: patterns, puzzles and progress. Nature Reviews Genetics 7: 211–221.

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How to Cite close
Mourier, Tobias, and Jeffares, Daniel C(Dec 2007) Intron Loss and Gain. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020785]