Ewolucja struktury genów

• Authors: Izabela Makałowska , Michał Kabza , Joanna Ciomborowska

Title variants

EN

Gene structure evolution

• Languages of publication: PL EN

Abstracts

EN

With the growing number of sequenced genomes comparative studies of lineage specific genomic features become both very rewarding and challenging. Large scale multiple genomes analyses allow to decipher many genomic features. They show that main differences between related species concern not as much the number of genes or the presence of species specific genes as the differences in the gene structure organization. Although much has been learned about gene structure evolution many problems remain unsolved. Alternative splicing is one of the main mechanisms leading to the proteome diversification. The raise of new splice variants is strictly connected with the exon and intron loss and gain. Main mechanisms of how the new exons originate are known, but question which of them, if any, plays the main role remains open. Another unsolved mystery is the intron origination. The dispute between "intro-early" and "intron-late" hypotheses supporters leads us to many interesting findings but the problem remains unsolved. One of the most fascinating discoveries in the genome studies is the role of so called 'junk DNA' in the evolution of human and other vertebrates. Repetitive elements and retrogenes are one of the most important elements in the gene structure evolution. They provide signals, motifs and coding sequences for new exons, splice sites or regulatory elements. Another phenomenon discovered in the process of whole genomes analyses is the common presence of overlapping genes and, at the same time, their low conservation level.

• Journal: Kosmos
• Year: 2009
• Volume: 58
• Issue: 1-2
• Pages: 5-16

Dates

published

2009

Contributors

author

Izabela Makałowska

• Pracownia Bioinformatyki, Wydział Biologii, Uniwersytet Adama Mickiewicza w Poznaniu, Umultowska 89, 61-614 Poznań, Polska

author

Michał Kabza

• Pracownia Bioinformatyki, Wydział Biologii, Uniwersytet Adama Mickiewicza w Poznaniu, Umultowska 89, 61-614 Poznań, Polska

author

Joanna Ciomborowska

• Pracownia Bioinformatyki, Wydział Biologii, Uniwersytet Adama Mickiewicza w Poznaniu, Umultowska 89, 61-614 Poznań, Polska

References

• Alekseyenko A. V., kim N., Lee C. J., 2007. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 13, 661-670.
• Babenko V. N., Rogozin I. B., Mekhedov S. L., Koonin E. V., 2004. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res. 32, 3724-3733.
• Baertsch R., Diekhans M., Kent W. J., Haussler D., Brosius J., 2008. Retrocopy contributions to the evolution of the human genome. BMC Genomics 9, 466.
• Balakirev E. S., Ayala F. J., 2003. Pseudogenes: are they 'junk' or functional DNA? Annu. Rev. Genet. 37, 123-151.
• Barrell B. G., Air G. M., Hutchison C. A., 3rd, 1976. Overlapping genes in bacteriophage phiX174. Nature 264, 34-41.
• Betran E., Long M., 2003. Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 164, 977-988.
• Betran E., Wang W., Jin L., Long M., 2002. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol. Biol. Evol. 19, 654-663.
• Black D. L., 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291-336.
• Borsani O., Zhu J., Verslues P. E., Sunkar R., Zhu J. K., 2005. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279-1291.
• Brosius J., 1991. Retroposons--seeds of evolution. Science 251, 753.
• Brosius J., Gould S. J., 1992. On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. Proc. Natl. Acad. Sci. USA 89, 10706-10710.
• Burki F., Kaessmann H., 2004. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat. Genet. 36, 1061-1063.
• Carmel L., Wolf Y. I., Rogozin I. B., Koonin E. V., 2007. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res. 17, 1034-1044.
• Cavalier-Smith T., 1985. Selfish DNA and the origin of introns. Nature 315, 283-284.
• Consortium. I. C. G. S., 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716.
• Consortium T. C. S. A. A., 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87.
• Coulombe-Huntington J., Majewski J., 2007. Characterization of intron loss events in mammals. Genome Res. 17, 23-32.
• Dahary D., Elroy-Stein O., Sorek R., 2005. Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res. 15, 364-368.
• Dan I., Watanabe N. M., Kajikawa E., Ishida T., Pandey A., Kusumi A., 2002. Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Res. 30, 2906-2910.
• Eichinger L., Pachebat J. A., Glockner G., Rajandream M. A., Sucgang R. i współaut., 2005. The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43-57.
• Fedorov A., Merican A. F., Gilbert W., 2002. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl. Acad. Sci. USA 99, 16128-16133.
• Fedorov A., Roy S., Fedorova L., Gilbert W., 2003. Mystery of intron gain. Genome Res. 13, 2236-2241.
• Ferlini A., Galie N., Merlini L., Sewry C., Branzi A., Muntoni F., 1998. A novel Alu-like element rearranged in the dystrophin gene causes a splicing mutation in a family with X-linked dilated cardiomyopathy. Am. J. Hum. Genet. 63, 436-446.
• Galagan J. E., Calvo S. E., Cuomo C., Ma L. J., Wortman J. R., Batzoglou S. i współaut., 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438, 1105-1115.
• Gerber A., O'connell M. A., Keller W., 1997. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA 3, 453-463.
• Gibbs R. A., Rogers J., Katze M. G., Bumgarner R., Weinstock G. M., Mardis E. R. i współaut., 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234.
• Gilbert W., 1978. Why genes in pieces? Nature 271, 501.
• Gilbert W., 1987. The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol. 52, 901-905.
• Gotea V., Makalowski W., 2006. Do transposable elements really contribute to proteomes? Trends Genet. 22, 260-267.
• Graveley B. R., 2001. Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 17, 100-107.
• Hastings M. L., Milcarek C., Martincic K., Peterson M. L., Munroe S. H., 1997. Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels. Nucleic Acids Res. 25, 4296-4300.
• Hughes A. L., 1999. Adaptive evolution of Genes and Genomes. Oxford University press, New York, Oxford.
• Iwabe N., Miyata T., 2001. Overlapping genes in parasitic protist Giardia lamblia. Gene 280, 163-167.
• Keese P. K., Gibbs A., 1992. Origins of genes: 'big bang' or continuous creation? Proc. Natl. Acad. Sci. USA 89, 9489-9493.
• Kimelman D., Kirschner M. W., 1989. An antisense mRNA directs the covalent modification of the transcript encoding fibroblast growth factor in Xenopus oocytes. Cell 59, 687-696.
• Kiyosawa H., Yamanaka I., Osato N., Kondo S., Hayashizaki Y., 2003. Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13, 1324-1334.
• Kondrashov F. A., Koonin E. V., 2001. Origin of alternative splicing by tandem exon duplication. Hum. Mol. Genet. 10, 2661-2669.
• Kondrashov F. A., Koonin E. V., 2003. Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends Genet. 19, 115-119.
• Koonin E. V., 2006. The origin of introns and their role in eukaryogenesis: a cpmpromise solution to the introns-early versus introns-late debate? Biology Direct 1, 22.
• Lander E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J. i współaut., 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
• Lehner B., Williams G., Campbell R. D., Sanderson C. M., 2002. Antisense transcripts in the human genome. Trends Genet. 18, 63-65.
• Lev-Maor G., Sorek R., Shomron N., Ast G., 2003. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 300, 1288-1291.
• Loftus B. J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D. i współaut., 2005. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307, 1321-1324.
• Logsdon J. M., Jr., 1998. The recent origins of spliceosomal introns revisited. Curr. Opin. Genet. Dev. 8, 637-648.
• Long M., Langley C. H., 1993. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260, 91-95.
• Long M., Betran E., Thornton K., Wang W., 2003. The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4, 865-875.
• Lorenc A., Makalowski W., 2003. Transposable elements and vertebrate protein diversity. Genetica 118, 183-191.
• Makalowska I., 2008. Comparative analysis of an unusual gene arrangement in the human chromosome 1. Gene 423, 172-179.
• Makalowska I., Lin C. F., Hernandez K., 2007. Birth and death of gene overlaps in vertebrates. BMC Evol. Biol. 7, 193.
• Makalowski W., 2000. Genomic scrap yard: how genomes utilize all that junk. Gene 259, 61-67.
• Makalowski W., Toda Y., 2007. Modulation of host genes by mammalian transposable elements. Genome Dyn. 3, 163-174.
• Makalowski W., Mitchell G. A., Labuda D., 1994. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10, 188-193.
• Marques A. C., Dupanloup I., Vinckenbosch N., Reymond A., Kaessmann H., 2005. Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3, e357.
• Mighell A. J., Smith N. R., Robinson P. A., Markham A. F., 2000. Vertebrate pseudogenes. FEBS Lett. 468, 109-114.
• Mikkelsen T. S., Wakefield M. J., Aken B., Amemiya C. T., Chang J. L., Duke S. i współaut. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177.
• Mironov A. A., Fickett J. W., Gelfand M. S., 1999. Frequent alternative splicing of human genes. Genome Res. 9, 1288-1293.
• Mitchell G. A., Labuda D., Fontaine G., Saudubray J. M., Bonnefont J. P., Lyonnet S., Brody L. C., Steel G., Obie C., Valle D., 1991. Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Proc. Natl. Acad. Sci. USA 88, 815-819.
• Modrek B., Lee C. J., 2003. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat. Genet. 34, 177-180.
• Modrek B., Resch a., Grasso c., Lee C., 2001. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 29, 2850-2859.
• Numata K., Okada Y., Saito R., Kiyosawa H., Kanai A., Tomita M., 2007. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene 392, 134-141.
• Ohno S., 1970. Evolution by Gene Duplication. Springer, Berlin, Alemania.
• Pan Q., Bakowski M. A., Morris Q., Zhang W., Frey B. J., Hughes T. R., Blencowe B. J., 2005. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet. 21, 73-77.
• Penny D., Poole A., 1999. The nature of the last universal common ancestor. Curr. Opin. Genet. Dev. 9, 672-677.
• Prescott E. M., Proudfoot N. J., 2002. Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. USA 99, 8796-8801.
• Qiu W. G., Schisler N., Stoltzfus A., 2004. The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol. Biol. Evol. 21, 1252-1263.
• Rastogi S., Liberles D. A., 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol. Biol. 5, 28.
• Rogozin I. B., Lyons-weiler J., Koonin E. V., 2000. Intron sliding in conserved gene families. Trends Genet. 16, 430-432.
• Rogozin I. B., Wolf Y. I., Sorokin A. V., Mirkin B. G., Koonin E. V., 2003. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol. 13, 1512-1517.
• Roy S. W., Gilbert W., 2005a. Rates of intron loss and gain: implications for early eukaryotic evolution. Proc. Natl. Acad. Sci. USA 102, 5773-5778.
• Roy S. W., Gilbert W., 2005b. The pattern of intron loss. Proc. Natl. Acad. Sci. USA 102, 713-718.
• Roy S. W., Penny D., 2007a. On the incidence of intron loss and gain in paralogous gene families. Mol. Biol. Evol. 24, 1579-1581.
• Roy S. W., Penny D., 2007b. Widespread intron loss suggests retrotransposon activity in ancient apicomplexans. Mol. Biol. Evol. 24, 1926-1933.
• Roy S. W., Penny D., 2007c. A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol. Biol. Evol. 24, 1447-1457.
• Roy S. W., Fedorov A., Gilbert W., 2003. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc. Natl. Acad. Sci. USA 100, 7158-7162.
• Sakai H., Koyanagi K. O., Imanishi T., Itoh T., Gojobori T., 2007. Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Gene 389, 196-203.
• Sanna C. R., Li W. H., Zhang L., 2008. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 169.
• Sela N., Mersch B., Gal-mark N., Lev-maor G., Hotz-wagenblatt A., Ast G., 2007. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol. 8, R127.
• Shendure J., Church G. M., 2002. Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol. 3, RESEARCH0044.
• Shintani S., O'huigin C., Toyosawa S., Michalova V., Klein J., 1999. Origin of gene overlap: the case of TCP1 and ACAT2. Genetics 152, 743-754.
• Solda G., Suyama M., Pelucchi P., Boi S., Guffanti A., Rizzi E., Bork P., Tenchini M. L., Ciccarelli F. D., 2008. Non-random retention of protein-coding overlapping genes in Metazoa. BMC Genomics 9, 174.
• Sorek R., 2007. The birth of new exons: mechanisms and evolutionary consequences. RNA 13, 1603-1608.
• Sorek R., Ast G., Graur D., 2002. Alu-containing exons are alternatively spliced. Genome Res 12, 1060-1067.
• Spencer C. A., Gietz R. D., Hodgetts R. B., 1986. Overlapping transcription units in the dopa decarboxylase region of Drosophila. Nature 322, 279-281.
• Stoltzfus A., Logsdon J. M., JR., Palmer J. D., Doolittle W. F., 1997. Intron 'sliding' and the diversity of intron positions. Proc. Natl. Acad. Sci. USA 94, 10739-10744.
• Veeramachaneni V., Makalowski W., Galdzicki M., Sood R., Makalowska I., 2004. Mammalian overlapping genes: the comparative perspective. Genome Res. 14, 280-286.
• Vinckenbosch N., Dupanloup I., Kaessmann H., 2006. Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl. Acad. Sci. USA 103, 3220-3225.
• Wang W., Brunet F. G., Nevo E., Long M., 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99, 4448-4453.
• Wang W., Zheng H., Yang S., Yu H., Li J., Jiang H., Su J., Yang L., Zhang J., Mcdermott J., Samudrala R., Wang J., Yang H., Yu J., Kristiansen K., Wong G. K., Wang J., 2005. Origin and evolution of new exons in rodents. Genome Res. 15, 1258-1264.
• Wang H., Chua N. H., Wang X. J., 2006a. Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biol. 7, R92.
• Wang W., Zheng H., Fan C., Li J., Shi J., Cai Z., Zhang G., Liu D., Zhang J., Vang, S., Lu Z., Wong G. K., Long M., Wang J., 2006b. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18, 1791-1802.
• Warren W. C., Hillier L. W., Marshall Graves J. A., Birney E., Ponting C. P. i współaut., 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453, 175-183.
• Waterston R. H., Lindblad-toh K., Birney E., Rogers J., Abril J. F. i współaut. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562.
• Williams T., Fried M., 1986. A mouse locus at which transcription from both DNA strands produces mRNAs complementary at their 3' ends. Nature 322, 275-279.
• Yelin R., Dahary D., Sorek R., Levanon E. Y., Goldstein O., Shoshan A., Diber A., Biton S., Tamir Y., Khosravi R., Nemzer S., Pinner E., Walach S., Bernstein J., Savitsky K., Rotman G., 2003. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21, 379-386.
• Yeo G. W., Van Nostrand E., Holste D., Poggio T., Burge C. B., 2005. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102, 2850-2855.
• Zhang, X. H., Chasin L. A., 2006. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc. Natl. Acad. Sci. USA 103, 13427-13432.
• Zheng D., Gerstein M. B., 2007. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet. 23, 219-224.
• Zhou Q., Wang W., 2008. On the origin and evolution of new genes--a genomic and experimental perspective. J. Genet. Genomics 35, 639-648.