Abstract
The Xist gene belongs to the class of long noncoding regulatory RNA genes which play a key role in the process of inactivation of one of the X chromosomes in females of placental mammals. Based on inter-specific comparative sequence analysis performed using a set of bioinformatic programs and approaches, the exon-intron gene structure was first described in two species, elephant and armadillo, belonging to the most primitive placental mammal groups, Afrotheria and Xenarthra. Using multiple sequence alignment of the species representing all main groups of placental mammals (12 species), consensus sequence of the ancestral gene was reconstructed. In the gene structure four evolutionary conserved regions with the identity level of 90% and the sizes of more than 100 bp were identified. Substantial contribution of transposable elements to the gene origin, as well as mosaic evolution of certain elements of the Xist locus was demonstrated. It is likely that the ancestral gene consisted of ten exons and was formed before the radiation of placental mammals, in the period from 140 to 105 Myr ago.
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References
Elisaphenko, E.A., Kolesnikov, N.N., Shevchenko, A.I., et al., A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements, PLoS One, 2008, vol. 3, no. 6, p. e2521.
Gordon, D., Viewing and Editing Assembled Sequences Using Consed, Curr. Protoc. Bioinform., 2003, vol. 11, unit 11.2.
Benson, G., Tandem Repeats Finder: A Program to Analyze DNA Sequences, Nucleic Acids Res., 1999, vol. 27, no. 2, pp. 573–80.
Elisaphenko, E.A., Kolesnikov, N.N., Shevchenko, A.I., and Zakiyan, S.M., Reconstruction of the Ancestral XIST Gene and It’s Evolution in Mammals, Inform. Vestn. VOGiS, 2008, vol. 12, pp. 186–196.
Nesterova, T.B., Slobodyanyuk, S.Y., Elisaphenko, E.A., et al., Characterization of the Genomic Xist Locus in Rodents Reveals Conservation of Overall Gene Structure and Tandem Repeats but Rapid Evolution of Unique Sequence, Genome Res., 2001, vol. 11, no. 5, pp. 833–49.
Wutz, A., Rasmussen, T.P., and Jaenisch, R., Chromosomal Silencing and Localization Are Mediated by Different Domains of Xist RNA, Nat. Genet., 2002, vol. 30, no. 2, pp. 167–74.
Zhao, J., Sun, B.K., Erwin, J.A., et al., Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome, Science, 2008, vol. 322, no. 5902, pp. 750–756.
Dindot, S.V., Kent, K.C., Evers, B., et al., Conservation of Genomic Imprinting at the XIST, IGF2, and GTL2 Loci in the Bovine, Mamm. Genome, 2004, vol. 15, no. 12, pp. 966–974.
Loots, G.G. and Ovcharenko, I., ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 2007, vol. 23, no. 1, pp. 122–124.
Siepel, A., Bejerano, G., Pedersen, J.S., et al., Evolutionary Conserved Elements in Vertebrate, Insect, Worm, and Yeast Genomes, Genome Res., 2005, vol. 15, pp. 1034–1050.
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Original Russian Text © N.N. Kolesnikov, E.A. Elisaphenko, 2010, published in Genetika, 2010, Vol. 46, No. 10, pp. 1379–1385.
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Kolesnikov, N.N., Elisaphenko, E.A. Exon-intron structure of the Xist gene in elephant, armadillo, and the ancestor of placental mammals. Russ J Genet 46, 1217–1222 (2010). https://doi.org/10.1134/S1022795410100194
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DOI: https://doi.org/10.1134/S1022795410100194