Research Article | Open Access
Valia Shoja, T. M. Murali, Liqing Zhang, "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse", International Journal of Genomics, vol. 2007, Article ID 060964, 8 pages, 2007. https://doi.org/10.1155/2007/60964
Expression Divergence of Tandemly Arrayed Genes in Human and Mouse
Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship between gene orientation and expression similarity. We also found that downstream TAG members do not show significantly narrower expression breadth than upstream members, contrary to what we predict based on TAG expression divergence hypothesis that we propose. Finally, we show that both chromosomal proximity and expression correlation in TAGs do not differ significantly from their neighboring non-TAG gene pairs, suggesting that tandem duplication is unlikely to be the cause for the higher-than-random expression association between neighboring genes on a chromosome in human and mouse.
- A. Force, M. Lynch, F. B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait, “Preservation of duplicate genes by complementary, degenerative mutations,” Genetics, vol. 151, no. 4, pp. 1531–1545, 1999.
- X. He and J. Zhang, “Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution,” Genetics, vol. 169, no. 2, pp. 1157–1164, 2005.
- L. Huminiecki and K. H. Wolfe, “Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse,” Genome Research, vol. 14, no. 10a, pp. 1870–1879, 2004.
- A. van Hoof, “Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication,” Genetics, vol. 171, no. 4, pp. 1455–1461, 2005.
- W. Wang, H. Yu, and M. Long, “Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species,” Nature Genetics, vol. 36, no. 5, pp. 523–527, 2004.
- X. Gu, Z. Zhang, and W. Huang, “Rapid evolution of expression and regulatory divergences after yeast gene duplication,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 3, pp. 707–712, 2005.
- Z. Gu, D. Nicolae, H. H.-S. Lu, and W.-H. Li, “Rapid divergence in expression between duplicate genes inferred from microarray data,” Trends in Genetics, vol. 18, no. 12, pp. 609–613, 2002.
- K. D. Makova and W.-H. Li, “Divergence in the spatial pattern of gene expression between human duplicate genes,” Genome Research, vol. 13, no. 7, pp. 1638–1645, 2003.
- C. Rizzon, L. Ponger, and B. S. Gaut, “Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice,” PLoS Computational Biology, vol. 2, no. 9, p. e115, 2006.
- V. Shoja and L. Zhang, “A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat,” Molecular Biology and Evolution, vol. 23, no. 11, pp. 2134–2141, 2006.
- J. Yu, J. Wang, W. Lin et al., “The genomes of Oryza sativa: a history of duplications,” PLoS Biology, vol. 3, no. 2, p. e38, 2005.
- L. Zhang and B. S. Gaut, “Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?” Genome Research, vol. 13, no. 12, pp. 2533–2540, 2003.
- B. A. Cohen, R. D. Mitra, J. D. Hughes, and G. M. Church, “A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression,” Nature Genetics, vol. 26, no. 2, pp. 183–186, 2000.
- M. J. Lercher, T. Blumenthal, and L. D. Hurst, “Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes,” Genome Research, vol. 13, no. 2, pp. 238–243, 2003.
- P. T. Spellman and G. M. Rubin, “Evidence for large domains of similarly expressed genes in the Drosophila genome,” Journal of Biology, vol. 1, no. 1, pp. 5.1–5.8, 2002.
- E. J. B. Williams and D. J. Bowles, “Coexpression of neighboring genes in the genome of Arabidopsis thaliana,” Genome Research, vol. 14, no. 6, pp. 1060–1067, 2004.
- A. I. Su, T. Wiltshire, S. Batalov et al., “A gene atlas of the mouse and human protein-encoding transcriptomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 16, pp. 6062–6067, 2004.
- E. Hubbell, W.-M. Liu, and R. Mei, “Robust estimators for expression analysis,” Bioinformatics, vol. 18, no. 12, pp. 1585–1592, 2002.
- A. I. Su, M. P. Cooke, K. A. Ching et al., “Large-scale analysis of the human and mouse transcriptomes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 7, pp. 4465–4470, 2002.
- I. Yanai, D. Graur, and R. Ophir, “Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control,” OMICS, vol. 8, no. 1, pp. 15–24, 2004.
- B.-Y. Liao and J. Zhang, “Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution,” Molecular Biology and Evolution, vol. 23, no. 6, pp. 1119–1128, 2006.
- P. Rice, I. Longden, and A. Bleasby, “EMBOSS: the European molecular biology open software suite,” Trends in Genetics, vol. 16, no. 6, pp. 276–277, 2000.
- Z. Yang, “PAML: a program package for phylogenetic analysis by maximum likelihood,” Computer Applications in the Biosciences, vol. 13, no. 5, pp. 555–556, 1997.
- A. Wagner, “Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 12, pp. 6579–6584, 2000.
- V. Katju and M. Lynch, “The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome,” Genetics, vol. 165, no. 4, pp. 1793–1803, 2003.
- V. Katju and M. Lynch, “On the formation of novel genes by duplication in the Caenorhabditis elegans genome,” Molecular Biology and Evolution, vol. 23, no. 5, pp. 1056–1067, 2006.
- M. Long, “Evolution of novel genes,” Current Opinion in Genetics & Development, vol. 11, no. 6, pp. 673–680, 2001.
- M. J. Lercher, A. O. Urrutia, and L. D. Hurst, “Clustering of housekeeping genes provides a unified model of gene order in the human genome,” Nature Genetics, vol. 31, no. 2, pp. 180–183, 2002.
- N. Chen and L. D. Stein, “Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans,” Genome Research, vol. 16, no. 5, pp. 606–617, 2006.
Copyright © 2007 Valia Shoja et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.