This Article Full Text Full Text (PDF) 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 Nikaido, I. Articles by Okazaki, Y. Search for Related Content PubMed PubMed Citation Articles by Nikaido, I. Articles by Okazaki, Y. Social Bookmarking                   What's this?

Letter

Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

¹Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan ²Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Yokohama, Kanagawa 230-0045, Japan ³Department of Molecular and Cell Genetics, School of Life Sciences, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan ⁴Department of BioScience, Tokyo University of Agriculture, Tokyo 156-8502, Japan ⁵JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK ⁶Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

Candidate imprinted transcriptional units in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays were used to detect differential expression dependent upon chromosomal parent of origin by comparing the mRNA levels in the total tissue of 9.5 dpc parthenogenote and androgenote mouse embryos. Of the FANTOM2 transcripts, 2114 were identified as candidates on the basis of the array data. Of these, 39 mapped to known imprinted regions of the mouse genome, 56 were considered as nonprotein-coding RNAs, and 159 were natural antisense transcripts. The imprinted expression of two transcripts located in the mouse chromosomal region syntenic to the human Prader-Willi syndrome region was confirmed experimentally. We further mapped all candidate imprinted transcripts to the mouse and human genome and were shown in correlation with the imprinting disease loci. These data provide a major resource for understanding the role of imprinting in mammalian inherited traits.

⁷ Shinji Kondo, Takahiro Arakawa, Piero Carninci, and Jun Kawai.

⁸ Corresponding author.
E-MAIL rgscerg{at}gsc.riken.go.jp; FAX 81-45-503-9216.

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

This article has been cited by other articles:

				T. R. Mercer, M. E. Dinger, S. M. Sunkin, M. F. Mehler, and J. S. Mattick Specific expression of long noncoding RNAs in the mouse brain PNAS, January 15, 2008; 105(2): 716 - 721. [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]

				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. S. Mattick A new paradigm for developmental biology J. Exp. Biol., May 1, 2007; 210(9): 1526 - 1547. [Abstract] [Full Text] [PDF]

				L. A. Kuehn, G. A. Rohrer, D. J. Nonneman, R. M. Thallman, and K. A. Leymaster Detection of single nucleotide polymorphisms associated with ultrasonic backfat depth in a segregating Meishan x White Composite population J Anim Sci, May 1, 2007; 85(5): 1111 - 1119. [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]

				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]

				M. R. Ginger, A. N. Shore, A. Contreras, M. Rijnkels, J. Miller, M. F. Gonzalez-Rimbau, and J. M. Rosen A noncoding RNA is a potential marker of cell fate during mammary gland development PNAS, April 11, 2006; 103(15): 5781 - 5786. [Abstract] [Full Text] [PDF]

				H. Kawaji, T. Kasukawa, S. Fukuda, S. Katayama, C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis Nucleic Acids Res., January 1, 2006; 34(suppl_1): D632 - D636. [Abstract] [Full Text] [PDF]

				RIKEN Genome Exploration Research Group and Genome, S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi, M. Nakamura, H. Nishida, C. C. Yap, M. Suzuki, et al. Antisense Transcription in the Mammalian Transcriptome Science, September 2, 2005; 309(5740): 1564 - 1566. [Abstract] [Full Text] [PDF]

				J. D. Choi, L. A. Underkoffler, A. J. Wood, J. N. Collins, P. T. Williams, J. A. Golden, E. F. Schuster Jr., K. M. Loomes, and R. J. Oakey A Novel Variant of Inpp5f Is Imprinted in Brain, and Its Expression Is Correlated with Differential Methylation of an Internal CpG Island Mol. Cell. Biol., July 1, 2005; 25(13): 5514 - 5522. [Abstract] [Full Text] [PDF]

				P. P. Luedi, A. J. Hartemink, and R. L. Jirtle Genome-wide prediction of imprinted murine genes Genome Res., June 1, 2005; 15(6): 875 - 884. [Abstract] [Full Text] [PDF]

				H. Kiyosawa, N. Mise, S. Iwase, Y. Hayashizaki, and K. Abe Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized Genome Res., April 1, 2005; 15(4): 463 - 474. [Abstract] [Full Text] [PDF]

				R. Quere, L. Manchon, M. Lejeune, O. Clement, F. Pierrat, B. Bonafoux, T. Commes, D. Piquemal, and J. Marti Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression Nucleic Acids Res., November 23, 2004; 32(20): e163 - e163. [Abstract] [Full Text] [PDF]

				C. B.M. Oudejans, J. Mulders, A. M.A. Lachmeijer, M. van Dijk, A. A.M. Konst, B. A. Westerman, I. J. van Wijk, P. A.J. Leegwater, H. D. Kato, T. Matsuda, et al. The parent-of-origin effect of 10q22 in pre-eclamptic females coincides with two regions clustered for genes with down-regulated expression in androgenetic placentas Mol. Hum. Reprod., August 1, 2004; 10(8): 589 - 598. [Abstract] [Full Text] [PDF]

				I. Nikaido, C. Saito, A. Wakamoto, Y. Tomaru, T. Arakawa, Y. Hayashizaki, and Y. Okazaki EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes Nucleic Acids Res., January 1, 2004; 32(90001): D548 - 551. [Abstract] [Full Text] [PDF]