This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Luedi, P. P. Articles by Jirtle, R. L. Search for Related Content PubMed PubMed Citation Articles by Luedi, P. P. Articles by Jirtle, R. L. Social Bookmarking                   What's this?

Methods

Genome-wide prediction of imprinted murine genes

¹ Center for Bioinformatics and Computational Biology, Duke University, Durham, North Carolina 27708, USA ² Department of Computer Science, Duke University, Durham, North Carolina 27708, USA ³ Department of Radiation Oncology, University Program in Genetics and Genomics, Duke University Medical Center, Durham, North Carolina 27710, USA

Imprinted genes are epigenetically modified genes whose expression is determined according to their parent of origin. They are involved in embryonic development, and imprinting dysregulation is linked to cancer, obesity, diabetes, and behavioral disorders such as autism and bipolar disease. Herein, we train a statistical model based on DNA sequence characteristics that not only identifies potentially imprinted genes, but also predicts the parental allele from which they are expressed. Of 23,788 annotated autosomal mouse genes, our model identifies 600 (2.5%) to be potentially imprinted, 64% of which are predicted to exhibit maternal expression. These predictions allowed for the identification of putative candidate genes for complex conditions where parent-of-origin effects are involved, including Alzheimer disease, autism, bipolar disorder, diabetes, male sexual orientation, obesity, and schizophrenia. We observe that the number, type, and relative orientation of repeated elements flanking a gene are particularly important in predicting whether a gene is imprinted.

[Supplemental material is available online at www.genome.org.]

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3303505.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				P. B. Samollow The opossum genome: Insights and opportunities from an alternative mammal Genome Res., August 1, 2008; 18(8): 1199 - 1215. [Abstract] [Full Text] [PDF]

				J. M. Cheverud, R. Hager, C. Roseman, G. Fawcett, B. Wang, and J. B. Wolf Genomic imprinting effects on adult body composition in mice PNAS, March 18, 2008; 105(11): 4253 - 4258. [Abstract] [Full Text] [PDF]

				R. Hager, J. M. Cheverud, and J. B. Wolf Maternal Effects as the Cause of Parent-of-Origin Effects That Mimic Genomic Imprinting Genetics, March 1, 2008; 178(3): 1755 - 1762. [Abstract] [Full Text] [PDF]

				C. Bock and T. Lengauer Computational epigenetics Bioinformatics, January 1, 2008; 24(1): 1 - 10. [Abstract] [Full Text] [PDF]

				A. Miyashita, H. Arai, T. Asada, M. Imagawa, E. Matsubara, M. Shoji, S. Higuchi, K. Urakami, A. Kakita, H. Takahashi, et al. Genetic association of CTNNA3 with late-onset Alzheimer's disease in females Hum. Mol. Genet., December 1, 2007; 16(23): 2854 - 2869. [Abstract] [Full Text] [PDF]

				A. R. Dallosso, A. L. Hancock, S. Malik, A. Salpekar, L. King-Underwood, K. Pritchard-Jones, J. Peters, K. Moorwood, A. Ward, K. T.A. Malik, et al. Alternately spliced WT1 antisense transcripts interact with WT1 sense RNA and show epigenetic and splicing defects in cancer RNA, December 1, 2007; 13(12): 2287 - 2299. [Abstract] [Full Text] [PDF]

				P. P. Luedi, F. S. Dietrich, J. R. Weidman, J. M. Bosko, R. L. Jirtle, and A. J. Hartemink Computational and experimental identification of novel human imprinted genes Genome Res., December 1, 2007; 17(12): 1723 - 1730. [Abstract] [Full Text] [PDF]

				J. L. Glass, R. F. Thompson, B. Khulan, M. E. Figueroa, E. N. Olivier, E. J. Oakley, G. Van Zant, E. E. Bouhassira, A. Melnick, A. Golden, et al. CG dinucleotide clustering is a species-specific property of the genome Nucleic Acids Res., November 29, 2007; 35(20): 6798 - 6807. [Abstract] [Full Text] [PDF]

				A. J. Wood, D. Bourc'his, T. H. Bestor, and R. J. Oakey Allele-specific demethylation at an imprinted mammalian promoter Nucleic Acids Res., November 29, 2007; 35(20): 7031 - 7039. [Abstract] [Full Text] [PDF]

				N. Ruf, S. Bahring, D. Galetzka, G. Pliushch, F. C. Luft, P. Nurnberg, T. Haaf, G. Kelsey, and U. Zechner Sequence-based bioinformatic prediction and QUASEP identify genomic imprinting of the KCNK9 potassium channel gene in mouse and human Hum. Mol. Genet., November 1, 2007; 16(21): 2591 - 2599. [Abstract] [Full Text] [PDF]

				J. Van Cleve and M. W. Feldman Sex-Specific Viability, Sex Linkage and Dominance in Genomic Imprinting Genetics, June 1, 2007; 176(2): 1101 - 1118. [Abstract] [Full Text] [PDF]

				L. Goh, S. K. Murphy, S. Muhkerjee, and T. S. Furey Genomic sweeping for hypermethylated genes Bioinformatics, February 1, 2007; 23(3): 281 - 288. [Abstract] [Full Text] [PDF]

				C. Seoighe, V. Nembaware, and K. Scheffler Maximum likelihood inference of imprinting and allele-specific expression from EST data Bioinformatics, December 15, 2006; 22(24): 3032 - 3039. [Abstract] [Full Text] [PDF]

				H.-S. Chang, M. D. Anway, S. S. Rekow, and M. K. Skinner Transgenerational Epigenetic Imprinting of the Male Germline by Endocrine Disruptor Exposure during Gonadal Sex Determination Endocrinology, December 1, 2006; 147(12): 5524 - 5541. [Abstract] [Full Text] [PDF]

				J L Seal, M C Gornick, N Gogtay, P Shaw, D K Greenstein, M Coffey, P A Gochman, T Stromberg, Z Chen, B Merriman, et al. Segmental uniparental isodisomy on 5q32-qter in a patient with childhood-onset schizophrenia J. Med. Genet., November 1, 2006; 43(11): 887 - 892. [Abstract] [Full Text] [PDF]

				H. G. Spencer and A. G. Clark A Chip off the Old Block: A Model for the Evolution of Genomic Imprinting via Selection for Parental Similarity Genetics, October 1, 2006; 174(2): 931 - 935. [Abstract] [Full Text] [PDF]

				R. Schulz, T. R. Menheniott, K. Woodfine, A. J. Wood, J. D. Choi, and R. J. Oakey Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies Nucleic Acids Res., July 19, 2006; 34(12): e88 - e88. [Abstract] [Full Text] [PDF]

				Y. Zhang, X. S. Liu, Q.-R. Liu, and L. Wei Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species Nucleic Acids Res., July 18, 2006; 34(12): 3465 - 3475. [Abstract] [Full Text] [PDF]

				K. M. Reilly, K. W. Broman, R. T. Bronson, S. Tsang, D. A. Loisel, E. S. Christy, Z. Sun, J. Diehl, D. J. Munroe, and R. G. Tuskan An Imprinted Locus Epistatically Influences Nstr1 and Nstr2 to Control Resistance to Nerve Sheath Tumors in a Neurofibromatosis Type 1 Mouse Model Cancer Res., January 1, 2006; 66(1): 62 - 68. [Abstract] [Full Text] [PDF]

				B. W. Sun, A. C. Yang, Y. Feng, Y. J. Sun, Y. f. Zhu, Y. Zhang, H. Jiang, C. L. Li, F. R. Gao, Z. H. Zhang, et al. Temporal and parental-specific expression of imprinted genes in a newly derived Chinese human embryonic stem cell line and embryoid bodies Hum. Mol. Genet., January 1, 2006; 15(1): 65 - 75. [Abstract] [Full Text] [PDF]