Browse > Article
http://dx.doi.org/10.5713/ajas.2009.80485

Comparative Analysis of Repetitive Elements of Imprinting Genes Reveals Eleven Candidate Imprinting Genes in Cattle  

Kim, HyoYoung (Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology Seoul National University)
Kim, Heebal (Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology Seoul National University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.22, no.6, 2009 , pp. 893-899 More about this Journal
Abstract
Few studies have reported the existence of imprinted genes in cattle compared to the human and mouse. Genomic imprinting is expressed in monoallelic form and it depends on a single parent-specific form of the allele. Comparative analysis of mammals other than the human is a valuable tool for explaining the genomic basis of imprinted genes. In this study, we investigated 34 common imprinted genes in the human and mouse as well as 35 known non-imprinted genes in the human. We found short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and long terminal repeats (LTRs) in imprinted (human and mouse) and control (cattle) genes. Pair-wise comparisons for the three species were conducted using SINEs, LINEs, and LTRs. We also calculated 95% confidence intervals of frequencies of repetitive sequences for the three species. As a result, most genes had a similar interval between species. We found 11 genes with conserved SINEs, LINEs, and LTRs in the human, mouse, and cattle. In conclusion, eleven genes (CALCR, Grb10, HTR2A, KCNK9, Kcnq1, MEST, OSBPL5, PPP1R9A, Sgce, SLC22A18, and UBE3A) were identified as candidate imprinted genes in cattle.
Keywords
Cattle; Correlation Coefficient; Imprinting Gene; Repetitive Elements;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
Times Cited By Web Of Science : 0  (Related Records In Web of Science)
Times Cited By SCOPUS : 0
연도 인용수 순위
1 Lee, Yun-Mi, Ji-Hong Lee and Jong-Joo Kim. 2007. Evaluatino of reciprocal cross design on detection and characterization of non-mendelian QTL in $F_{2}$ outbred populations: I. parent-of origin effect. Asian-Aust. J. Anim. Sci. 20:1805-1811
2 Luedi, Philippe P., Fred S. Dietrich, Jennifer R. Weidman, Jason M. Bosko, Randy L. Jirtle and Alexander J. Hartemink. 2007. Computational and experimental identification of novel human imprinted genes. Genome Res. 17:1723-1730   DOI   ScienceOn
3 Pei, L., Ofer Wiser, Anthony Slavin, David Mu, Scott Powers, Lily Yeh Jan and Timothy Hoey. 2003. Oncogenic potential of TASK3 (Kcnk9) depends on $K^{+}$ channel function. PNAS. 100:7803-7807   DOI   ScienceOn
4 Suzuki, S., Ryuichi Ono, Takanori Narita, Andrew J. Pask, Geoffery Shaw, Changshan Wang, Taksshi Kohda, Amber E. Alsop, Jennifer A. Marshall Graves, Yuji Kohara, Fumitoshi Ishino, Marilyn B. Renfree and Tomoko Kaneko-Ishino. 2007. Reteotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genetics. 3:e55   DOI   PUBMED   ScienceOn
5 Watson, James D., Tania A.Baker, Stephen P. Bell, Alexander Gann, Michael Levine and Richard Losick. 2007. Molecular biology of the gene. Benjamin Cummings, San Francisco, pp. 140-141
6 Xiayi, K., Simon N. Thomas, David O. Robinson and Andrew Collins. 2002. The distinguishing sequence characteristics of mouse imprinted genes. Mamm. Genome. 13:639-645   DOI   ScienceOn
7 Zaitoun, Ismail and Hasan Khatib. 2006 Assessment of genomics imprinting of SLC38A4, NNAT, NAPIL5, and H19 in cattle. BMC Genetics, 7:49   DOI   PUBMED   ScienceOn
8 Zaitoun, I. and H. Khatib. 2008. Comparative genomic imprinting and expression analysis of six cattle genes. J. Anim. Sci. 86:25-32   DOI   ScienceOn
9 Allen, E., Steve Horvath, Frances Tong, Peter Kraft, Elizabeth Spiteri, Arthur D. Riggs and York Marahrens. 2003. High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. PNAS. 100:9940-9945   DOI   ScienceOn
10 Bland, J. Martin and Douglas G. Altman. 1986. Statistical methods for assessing agreement between two methods of clinical measurement. Lancet. i:307:310   DOI   ScienceOn
11 Cheng, H. C., F. W. Zhang, C. Y. Deng, C. D. Jiang, Y. Z. Xiong, F. E. Li and M. G. Lei. 2007. ASCL2 gene expression analysis and its association with carcass traits in pigs. Asian-Aust. J. Anim. Sci. 20:1485-1489
12 Downer, J. 2002. Epigenetics and imprinted genes. http://www.hopkinsmedicine.org/press/2002/November/epigen etics.htm
13 Onyango, P., Webb Miller, Jessica Lehoczky, Cheuk T. Leung, Bruce Birren, Sarah Wheelan, Ken Dewar and Andrew P. Feinberg. 2000. Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain. Genome Res. 10:1697-1710   DOI   ScienceOn
14 Khatib, H., Ismail Zaitoun and Eui-Soo Kim. 2007. Comparative analysis of sequence characteristics of imprinted genes in human, mouse, and cattle. Mamm Genome. 18:538-547   DOI   ScienceOn
15 Pandey, A., Hangjun Duan, Pier Paolo Di Fiore and Vishva M. Dixit. 1995. The ret receptor protein tyrosine kinase associates with the SH2-containing adapter protein Grb10. J. Biological Chem. 270:21461-21463   DOI   ScienceOn
16 Miyoshi, N., Yoshimi Kuroiwa, Takashi Kohda, Hiroshi Shitara, Hiromichi Yonekawa, Tohru Kawabe, Hideaki Hasegawa, Sheilla C. Barton, M. Azim Surani, Tomoko Kaneko-Ishino and Fumitoshi Ishino. 1998. Identification of the Meg1/Grb10 imprinted gene on mouse proximal chromosome 11, a candidate for the Silver-Russell syndrome gene. Proc. Natl. Acad. Sci. 95:1102-1107   DOI   ScienceOn
17 Nakabayashi, K., S. Makino, S. Minagawa, A. C. Smith, J. S. Bamforth, P. Stanier, M. Preece, L. Parker-Katiraee, T. Paton, M. Oshimura, P. Mill, Y. Yoshikawa, C. C. Hui, D. Monk, G. E. Moore and S. W. Scherer. 2004. Genomic imprinting of PPP1R9A encoding neurabin l in skeletal muscle and extraembryonic tissues. J. Med. Genet. 41:601-608   DOI   ScienceOn
18 Pearsall, R. Scott, C. Plass, M. A. Romano, M. D. Garrick, H. Shibata, Y. Hayashizaki and W. A. Held. 1998. A direct repeat sequence at the Rasgrf1 locus and imprinted expression. Genomics. 55:194-201   DOI   ScienceOn
19 Tycko, B. and Ian M. Morison. 2002. Physiological functions of imprinted genes. J. Cellular Physiol. 192:245-258   DOI   ScienceOn
20 Lee, H. K., S. S. Lee, T. H. Kim, G. J. Jeon, H. W. Jung, Y. S. Shin, J. Y. Han, B. H. Choi and I. C. Cheong. 2003. Detection of imprinted quantitative trait loci (QTL) for growth traits in pigs. Asian-Aust. J. Anim. Sci. 16:1087-1092
21 Quist, J. F., C. L. Barr, R. Schachar, W. Roberts, M. Malone, R. Tannock, V. S. Basile, J. Beitchman and J. L. Kennedy. 2000. Evidence for the serotonin HTR2A receptor gene as a susceptibility factor in attention deficit hyperactivity disorder (ADHD). Molecular Psychiatry. 5:537-541   DOI   ScienceOn
22 Weidman, Jennifer R., Susan K. Murphy, Catherine M. Nolan, Fred S. Dietrich and Randy L. Jirtle. 2004. Phylogenetic footprint analysis of IGF2 in extant mammals. Genome Res. 14:1726-1732   DOI   ScienceOn
23 Greally, John M. 2002. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. PNAS. 99:327-332   DOI   ScienceOn
24 Ke, X., Simon N. Thomas, David O. Robinson and Andrew Collins. 2002. The distinguishing sequence characteristics of mouse imprinted genes. Mamm Genome. 13:639-645   DOI   ScienceOn
25 McKillup, Steve. 2006. Statistics Explained. Cambridge University Press, UK, pp. 77-243
26 Thomas, J. W., J. W. Touchman, R. W. Blakesley, G. G. Bouffard, S. M. Beckstorm-Sternberg, E. H. Margulies, M. Blanchette, A. C. Siepel, P. J. Thomas, J. C. McDowell, B. Maskeri, N. F. Hansen, M. S. Schwartz, R. J. Weber, W. J. Kent, D. Karolchik, T. C. Bruen, R. Bevan, D. J. Cutler, S. Schwartz, L. Elnitski, J. R. Idol, A. B. Prasad, S. Q. Lee-Lin, V. V. B. Maduro, T. J. Summers, M. E. Portnoy, N. L. Dietrich, N. Akhter, K. Ayele, X. Guan, B. Benjamin, K. Cariaga, C. P. Brinkley, S. Y. Brooks, S. Granite, X. Guan, J. Gupta, P. Haghighi, S. L. Ho, M. C. Huang, E. Karlins, P. L. Laric, R. Legaspi, M. J. Lim, Q. L. Maduro, C. A. Masiello, S. D. Mastrian, J. C. McCloskey, R. Pearson, S. Stantripop, E. E. Tiongson, J. T. Tran, C. Tsurgeon, J. L. Vogt, M. A. Walker, K. D. Wetherby, L. S. Wiggins, A. C. Young, L. H. Zhang, K. Osoegawa, B. Zhu, B. Zhao, C. L. Shu, P. J. De Jong, C. E. Lawrence, A. F. Smit, A. Chakravarti, D. Haussler, P. Green, W. Miller and E. D. Green. 2003. Comparative analyses of multi-species sequences from targeted genomic regions. Nature. 424   DOI   ScienceOn
27 Reik, W. and Jorn Walter. 2001. Genomic imprinting: parental influence on the genome. Nat. Rev. Gnet. 2:21-32   DOI   ScienceOn
28 Walter, J., B. Hutter, T. Khare and M. Paulsen. 2006. Repetitive elements in imprinted genes. Cytogenet Genome Res. 113:109-115   DOI   ScienceOn
29 Jirtle, Randy L. 2006. Geneimprint. http://www.geneimprint.com/site/genes-by-species.Mus+musculus
30 Takafusa H., Kohda, Takashi, Kaneko-Ishino, Tomoko, Ishino and Fumitoshi. 2003. Imprinting regulation of the murine Meg1/Grb10 and human GRB10 genes; roles of brain-specific promoters and mouse-specific CTCF-binding sites. Nucleic Acids Research. 31:1398-1406   DOI   ScienceOn
31 Schaffner, Stephen F. 2004. The X chromosome in population genetics. Nature Reviews. 5.   DOI   PUBMED   ScienceOn
32 Stroop, Steven D., Deborah L. Thompson, Rolf E. Kuestner and Emma E. Moore. 1993. A recombinant human calcitonin receptor functions as an extracellular calcium sensor. J. Biological Chem. 268:19927-19930   PUBMED
33 Crawley, Michael J. 2005. Statistics an introduction using R. Imperial College London, UK, pp. 45-99
34 Hoshiya, H., M. Meguro, A. Kashiwagi, C. Okita and M. Oshimura. 2003. Calcr, a brain-specific imprinted mouse calcitonin receptor gene in the imprinted cluster of the proximal region of chromosome 6. J. Human Genetics. 48:208-211   DOI   ScienceOn