Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians

Nature Genetics

Volumn 40, Issue 8, 2008, Pages 971-976

  Smits, Guillaume ^a   Mungall, Andrew J ^b   Griffiths Jones, Sam ^c   Smith, Paul ^a   Beury, Delphine ^a   Matthews, Lucy ^b   Rogers, Jane ^b   Pask, Andrew J ^d   Shaw, Geoff ^d   VandeBerg, John L ^e   McCarrey, John R ^f   Renfree, Marilyn B ^d   Reik, Wolf ^a   Dunham, Ian ^b,g  

^a BABRAHAM INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d UNIVERSITY OF MELBOURNE   (Australia)

^e SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^f UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

^g EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA H19; SOMATOMEDIN BINDING PROTEIN 2;

ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE LOCUS; GENE SILENCING; GENOME IMPRINTING; HUMAN; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE;

ANIMALS; BASE SEQUENCE; DNA METHYLATION; EVOLUTION, MOLECULAR; FEMALE; GENOMIC IMPRINTING; HUMANS; INSULIN-LIKE GROWTH FACTOR II; MACROPODIDAE; MALE; MICE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT;

EUTHERIA; MAMMALIA; METATHERIA; THERIA;

EID: 48249141249     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.168     Document Type: Article

References (50)

1. Wilkins, J.F. & Haig, D. What good is genomic imprinting: the function of parent-specific gene expression. Nat. Rev. Genet. 4, 359-368 (2003).
2. Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21-32 (2001).
3. O'Neill, M.J., Ingram, R.S., Vrana, P.B. & Tilghman, S.M. Allelic expression of IGF2 in marsupials and birds. Dev. Genes Evol. 210, 18-20 (2000).
4. Killian, J.K. et al. M6P/IGF2R imprinting evolution in mammals. Mol. Cell 5, 707-716 (2000).
5. Weidman, J.R., Dolinoy, D.C., Maloney, K.A., Cheng, J.F. & Jirtle, R.L. Imprinting of opossum Igf2r in the absence of differential methylation and air. Epigenetics 1, 49-54 (2006).
6. Killian, J.K. et al. Monotreme IGF2 expression and ancestral origin of genomic imprinting. J. Exp. Zool. 291, 205-212 (2001).
7. Weidman, J.R., Murphy, S.K., Nolan, C.M., Dietrich, F.S. & Jirtle, R.L. Phylogenetic footprint analysis of IGF2 in extant mammals. Genome Res. 14, 1726-1732 (2004).
8. Suzuki, S. et al. Genomic imprinting of IGF2, p57(KIP2) and PEG1/MEST in a marsupial, the tammar wallaby. Mech. Dev. 122, 213-222 (2005).
9. Suzuki, S. et al. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet. 3, e55 (2007).
10. Rapkins, R.W. et al. Recent assembly of an imprinted domain from non-imprinted components. PLoS Genet. 2, e182 (2006).
11. Ager, E. et al. Insulin is imprinted in the placenta of the marsupial, Macropus eugenii. Dev. Biol. 309, 317-328 (2007).
12. Reik, W. & Lewis, A. Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat. Rev. Genet. 6, 403-410 (2005).
13. Gabory, A., Ripoche, M.A., Yoshimizu, T. & Dandolo, L. The H19 gene: regulation and function of a non-coding RNA. Cytogenet. Genome Res. 113, 188-193 (2006).
14. Hao, Y., Crenshaw, T., Moulton, T., Newcomb, E. & Tycko, B. Tumour-suppressor activity of H19 RNA. Nature 365, 764-767 (1993).
15. Matouk, I.J. et al. The H19 non-coding RNA is essential for human tumor growth. PLoS ONE 2, e845 (2007).
16. Mineno, J. et al. The expression profile of microRNAs in mouse embryos. Nucleic Acids Res. 34, 1765-1771 (2006).
17. Cai, X. & Cullen, B.R. The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13, 313-316 (2007).
18. Murrell, A., Heeson, S. & Reik, W. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36, 889-893 (2004).
19. Kurukuti, S. et al. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc. Natl. Acad. Sci. USA 103, 10684-10689 (2006).
20. Bartolomei, M.S., Webber, A.L., Brunkow, M.E. & Tilghman, S.M. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev. 7, 1663-1673 (1993).
21. Ferguson-Smith, A.C., Sasaki, H., Cattanach, B.M. & Surani, M.A. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature 362, 751-755 (1993).
22. Reese, K.J., Lin, S., Verona, R.I., Schultz, R.M. & Bartolomei, M.S. Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genet. 3, e137 (2007).
23. Mikkelsen, T.S. et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177 (2007).
24. Brannan, C.I., Dees, E.C., Ingram, R.S. & Tilghman, S.M. The product of the H19 gene may function as an RNA. Mol. Cell. Biol. 10, 28-36 (1990).
25. Bininda-Emonds, O.R. et al. The delayed rise of present-day mammals. Nature 446, 507-512 (2007).
26. Kim, T.H. et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231-1245 (2007).
27. Butler, C.M., Shaw, G., Clark, J. & Renfree, M.B. The functional development of Leydig cells in a marsupial. J. Anat. 212, 55-66 (2008).
28. Ishihara, K., Oshimura, M. & Nakao, M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol. Cell 23, 733-742 (2006).
29. Odom, D.T. et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 39, 730-732 (2007).
30. Saini, H.K., Griffiths-Jones, S. & Enright, A.J. Genomic analysis of human microRNA transcripts. Proc. Natl. Acad. Sci. USA 104, 17719-17724 (2007).
31. Edwards, C.A. et al. The evolution of the DLK1-DIO3 imprinted domain in mammals. PLoS Biol. 6, e135 (2008).
32. Duret, L., Chureau, C., Samain, S., Weissenbach, J. & Avner, P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 312, 1653-1655 (2006).
33. Schmid, J., Andersen, N.A., Speakman, J.R. & Nicol, S.C. Field energetics of free-living, lactating and non-lactating echidnas (Tachyglossus aculeatus). Comp. Biochem. Physiol. A Mol. Integr. Physiol. 136, 903-909 (2003).
34. Kaneda, M. et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900-903 (2004).
35. Bourc'his, D. & Bestor, T.H. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96-99 (2004).
36. Webster, K.E. et al. Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc. Natl. Acad. Sci. USA 102, 4068-4073 (2005).
37. Yokomine, T., Hata, K., Tsudzuki, M. & Sasaki, H. Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet. Genome Res. 113, 75-80 (2006).
38. Schoenherr, C.J., Levorse, J.M. & Tilghman, S.M. CTCF maintains differential methylation at the Igf2/H19 locus. Nat. Genet. 33, 66-69 (2003).
39. Pant, V. et al. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes Dev. 17, 586-590 (2003).
40. Fedoriw, A.M., Stein, P., Svoboda, P., Schultz, R.M. & Bartolomei, M.S. Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 303, 238-240 (2004).
41. Jelinic, P., Stehle, J.C. & Shaw, P. The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. PLoS Biol. 4, e355 (2006).
42. Kato, Y. et al. Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum. Mol. Genet. 16, 2272-2280 (2007).
43. La Salle, S. et al. Loss of spermatogonia and wide-spread DNA methylation defects in newborn male mice deficient in DNMT3L. BMC Dev. Biol. 7, 104 (2007).
44. Wood, A.J. et al. A screen for retrotransposed imprinted genes reveals an association between X chromosome homology and maternal germ-line methylation. PLoS Genet. 3, e20 (2007).
45. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
46. Ovcharenko, I., Loots, G.G., Hardison, R.C., Miller, W. & Stubbs, L. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14, 472-477 (2004).
47. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. & Enright, A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34, D140-D144 (2006).
48. Eddy, S.R. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3, 18 (2002).
49. Griffiths-Jones, S. RALEE-RNA alignment editor in Emacs. Bioinformatics 21, 257-259 (2005).
50. Ro, S., Park, C., Jin, J., Sanders, K.M. & Yan, W. A PCR-based method for detection and quantification of small RNAs. Biochem. Biophys. Res. Commun. 351, 756-763 (2006).