Journal Mobile Options
Table of Contents
Vol. 113, No. 1-4, 2006
Issue release date: March 2006
Cytogenet Genome Res 113:159–164 (2006)
(DOI:10.1159/000090828)

Lessons from comparative analysis of species-specific imprinted genes

Okamura K. · Ito T.
aDepartment of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto (Canada);

Individual Users: Register with Karger Login Information

Please create your User ID & Password





Contact Information











I have read the Karger Terms and Conditions and agree.

To view the fulltext, please log in

To view the pdf, please log in

Abstract

Genomic imprinting is generally believed to be conserved in all mammals except for egg-laying monotremes, suggesting that it is closely related to placental and fetal growth. As expected, the imprinting status of most imprinted genes is conserved between mouse and human, and some are imprinted even in marsupials. On the other hand, a small number of genes were reported to exhibit species-specific imprinting that is not necessarily accounted for by either the placenta or conflict hypotheses. Since mouse and human represent a single, phylogenetically restricted clade in the mammalian class, a much broader comparison including mammals diverged earlier than rodents is necessary to fully understand the species-specificity and variation in evolution of genomic imprinting. Indeed, comparative analysis of a species-specific imprinted gene Impact using a broader range of mammals led us to propose an alternative dosage control hypothesis for the evolution of genomic imprinting.



Copyright / Drug Dosage

Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

References

  1. Anniss AM, Apostolopoulos J, Dworkin S, Purton LE, Sparrow RL: An oxysterol-binding protein family identified in the mouse. DNA Cell Biol 21:571–580 (2002).
  2. Barlow DP: Methylation and imprinting: from host defense to gene regulation? Science 260:309–310 (1993).
  3. Barlow DP, Stoger R, Herrmann BG, Saito K, Schweifer N: The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 349:84–87 (1991).
  4. Bartolomei MS, Zemel S, Tilghman SM: Parental imprinting of the mouse H19 gene. Nature 351:153–155 (1991).
  5. Constancia M, Pickard B, Kelsey G, Reik W: Imprinting mechanisms. Genome Res 8:881–900 (1998).
  6. DeChiara TM, Robertson EJ, Efstratiadis A: Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64:849–859 (1991).
  7. Greally JM: Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci USA 99:327–332 (2002).
  8. Haig D: Genomic imprinting and kinship: how good is the evidence? Annu Rev Genet 38:553–585 (2004).
  9. Hagiwara Y, Hirai M, Nishiyama K, Kanazawa I, Ueda T, Sakaki Y, Ito T: Screening for imprinted genes by allelic message display: identification of a paternally expressed gene Impact on mouse chromosome 18. Proc Natl Acad Sci USA 94:9249–9254 (1997).
  10. Hatada I, Sugama T, Mukai T: A new imprinted gene cloned by a methylation-sensitive genome scanning method. Nucleic Acids Res 21:5577–5582 (1993).
  11. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, et al: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716 (2004).
  12. Hurst LD, McVean G, Moore T: Imprinted genes have few and small introns. Nat Genet 12:234–237 (1996).
  13. Huynh KD, Lee JT: X-chromosome inactivation: a hypothesis linking ontogeny and phylogeny. Nat Rev Genet 6:410–418 (2005).
  14. Jaworski CJ, Moreira E, Li A, Lee R, Rodriguez IR: A family of 12 human genes containing oxysterol-binding domains. Genomics 78:185–196 (2001).
  15. Kaneko-Ishino T, Kohda T, Ishino F: The regulation and biological significance of genomic imprinting in mammals. J Biochem 133:699–711 (2003).
  16. Kato Y, Sasaki H: Imprinting and looping: epigenetic marks control interactions between regulatory elements. BioEssays 27:1–4 (2005).
  17. Killian JK, Nolan CM, Stewart N, Munday BL, Andersen NA, Nicol S, Jirtle RL: Monotreme IGF2 expression and ancestral origin of genomic imprinting. J Exp Zool 291:205–212 (2001a).
  18. Killian JK, Nolan CM, Wylie AA, Li T, Vu TH, Hoffman AR, Jirtle RL: Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary. Hum Mol Genet 10:1721–1728 (2001b).
  19. Kim J, Bergmann A, Lucas S, Stone R, Stubbs L: Lineage-specific imprinting and evolution of the zinc-finger gene ZIM2. Genomics 84:47–58 (2004).
  20. Kubota H, Sakaki Y, Ito T: GI domain-mediated association of the eukaryotic initiation factor 2α kinase GCN2 with its activator GCN1 is required for general amino acid control in budding yeast. J Biol Chem 275:20243–20246 (2000).
  21. Lewis A, Redrup L: Genetic imprinting: conflict at the callipyge locus. Curr Biol 15:R291-R294 (2005).

    External Resources

  22. Morison IM, Reeve AE: A catalogue of imprinted genes and parent-of-origin effects in humans and animals. Hum Mol Genet 7:1599–1609 (1998).
  23. Murphy SK, Jirtle RL: Imprinting evolution and the price of silence. BioEssays 25:577–588 (2003).
  24. Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O’Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature 409:614–618 (2001).
  25. Nabetani A, Hatada I, Morisaki H, Oshimura M, Mukai T: Mouse U2af1-rs1 is a neomorphic imprinted gene. Mol Cell Biol 17:789–798 (1997).
  26. Neumann B, Kubicka P, Barlow DP: Characteristics of imprinted genes. Nat Genet 9:12–13 (1995).
  27. Oakey RJ, Matteson PG, Litwin S, Tilghman SM, Nussbaum RL: Nondisjunction rates and abnormal embryonic development in a mouse cross between heterozygotes carrying a (7, 18) Robertsonian translocation chromosome. Genetics 141:667–674 (1995).
  28. Oda T, Morikawa N, Saito Y, Masuho Y, Matsumoto S: Molecular cloning and characterization of a novel type of histamine receptor preferentially expressed in leukocytes. J Biol Chem 275:36781–36786 (2000).
  29. Okamura K, Hagiwara-Takeuchi Y, Li T, Vu TH, Hirai M, Hattori M, Sakaki Y, Hoffman AR, Ito T: Comparative genome analysis of the mouse imprinted gene Impact and its nonimprinted human homolog IMPACT: toward the structural basis for species-specific imprinting. Genome Res 10:1878–1889 (2000).
  30. Okamura K, Yamada Y, Sakaki Y, Ito T: An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighbors. DNA Res 11:381–390 (2004).
  31. Okamura K, Sakaki Y, Ito T: Comparative genomics approach toward critical determinants for the imprinting of an evolutionarily conserved gene Impact. Biochem Biophys Res Commun 329:824–830 (2005).
  32. O’Neill MJ, Ingram RS, Vrana PB, Tilghman SM: Allelic expression of IGF2 in marsupials and birds. Dev Genes Evol 210:18–20 (2000).
  33. Ono R, Kobayashi S, Wagatsuma H, Aisaka K, Kohda T, Kaneko-Ishino T, Ishino F: A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics 73:232–237 (2001).
  34. Pearsall RS, Shibata H, Brozowska A, Yoshino K, Okuda K, deJong PJ, Plass C, Chapman VM, Hayashizaki Y, Held WA: Absence of imprinting in U2AFBPL, a human homologue of the imprinted mouse gene U2afbp-rs. Biochem Biophys Res Commun 222:171–177 (1996).
  35. Pearsall RS, Plass C, Romano MA, Garrick MD, Shibata H, Hayashizaki Y, Held WA: A direct repeat sequence at the Rasgrf1 locus and imprinted expression. Genomics 55:194–201 (1999).
  36. Plass C, Shibata H, Kalcheva I, Mullins L, Kotelevtseva N, Mullins J, Kato R, Sasaki H, Hirotsune S, Okazaki Y, Held WA, Hayashizaki Y, Chapman VM: Identification of Grf1 on mouse chromosome 9 as an imprinted gene by RLGS-M. Nat Genet 14:106–109 (1996).
  37. Reik W, Lewis A: Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet 6:403–410 (2005).
  38. Reik W, Collick A, Norris ML, Barton SC, Surani MA: Genomic imprinting determines methylation of parental alleles in transgenic mice. Nature 328:248–251 (1987).
  39. Sakatani T, Kaneda A, Iacobuzio-Donahue CA, Carter MG, de Boom Witzel S, Okano H, Ko MS, Ohlsson R, Longo DL, Feinberg AP: Loss of imprinting of Igf2 alters intestinal maturation and tumorigenesis in mice. Science 307:1976–1978 (2005).
  40. Sandell LL, Guan XJ, Ingram R, Tilghman SM: Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta. Proc Natl Acad Sci USA 100:4622–4627 (2003).
  41. Schmidt JV, Matteson PG, Jones BK, Guan XJ, Tilghman SM: The Dlk1 and Gtl2 genes are linked and reciprocally imprinted. Genes Dev 14:1997–2002 (2000).
  42. Solter D: Differential imprinting and expression of maternal and paternal genomes. Annu Rev Genet 22:127–146 (1988).
  43. Sunahara S, Nakamura K, Nakao K, Gondo Y, Nagata Y, Katsuki M: The oocyte-specific methylated region of the U2afbp-rs/U2af1-rs1 gene is dispensable for its imprinted methylation. Biochem Biophys Res Commun 268:590–595 (2000).
  44. Suzuki S, Renfree MB, Pask AJ, Shaw G, Kobayashi S, Kohda T, Kaneko-Ishino T, Ishino F: Genomic imprinting of IGF2, p57KIP2 and PEG1/MEST in a marsupial, the tammar wallaby. Mech Dev 122:213–222 (2005).
  45. Walter J, Paulsen M: The potential role of gene duplications in the evolution of imprinting mechanisms. Hum Mol Genet 12:R215-R220 (2003).

    External Resources

  46. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al: Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562 (2002).
  47. Weidman JR, Murphy SK, Nolan CM, Dietrich FS, Jirtle RL: Phylogenetic footprint analysis of IGF2 in extant mammals. Genome Res 14:1726–1732 (2004).
  48. Wilkins JF, Haig D: Parental modifiers, antisense transcripts and loss of imprinting. Proc R Soc Lond B Biol Sci 269:1841–1846 (2002).
  49. Wutz A, Theussl HC, Dausman J, Jaenisch R, Barlow DP, Wagner EF: Non-imprinted Igf2r expression decreases growth and rescues the Tme mutation in mice. Development 128:1881–1887 (2001).
  50. Yamada Y, Hagiwara Y, Shiokawa K, Sakaki Y, Ito T: Spatiotemporal, allelic, and enforced expression of Ximpact, the Xenopus homolog of mouse imprinted gene Impact. Biochem Biophys Res Commun 256:162–169 (1999).
  51. Yokomine T, Kuroiwa A, Tanaka K, Tsudzuki M, Matsuda Y, Sasaki H: Sequence polymorphisms, allelic expression status and chromosome locations of the chicken IGF2 and MPR1 genes. Cytogenet Cell Genet 93:109–113 (2001).
  52. Yokomine T, Shirohzu H, Purbowasito W, Toyoda A, Iwama H, Ikeo K, Hori T, Mizuno S, Tsudzuki M, Matsuda Y, Hattori M, Sakaki Y, Sasaki H: Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2-Igf2-H19 region. Genome Res 15:154–165 (2005).
  53. Yoon BJ, Herman H, Sikora A, Smith LT, Plass C, Soloway PD: Regulation of DNA methylation of Rasgrf1. Nat Genet 30:92–96 (2002).


Pay-per-View Options
Direct payment This item at the regular price: USD 38.00
Payment from account With a Karger Pay-per-View account (down payment USD 150) you profit from a special rate for this and other single items.
This item at the discounted price: USD 26.50