Comparative genomic sequencing identifies novel tissue-specific enhancers and sequence elements for methylation-sensitive factors implicated in Igf2/H19 imprinting

Genome Research

Volumn 10, Issue 5, 2000, Pages 664-671

  Ishihara, Ko ^a,b,c   Hatano, Naoya ^c,f   Furuumi, Hiroyasu ^a,c   Kato, Reiko ^a,c,g   Iwaki, Toru ^c   Miura, Kiyonori ^d,h   Jinno, Yoshihiro ^d,e   Sasaki, Hiroyuki ^a,b,c  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d NAGASAKI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^e UNIVERSITY OF THE RYUKYUS SCHOOL OF MEDICINE   (Japan)

^f Ministry of International Trade and Industry   (Japan)

^g KITASATO UNIVERSITY   (Japan)

^h HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEAR FACTOR;

ANIMAL CELL; COMPARATIVE STUDY; COMPLEX FORMATION; CONTROLLED STUDY; ECTODERM; ENHANCER REGION; EVOLUTION; GENE SEQUENCE; GENE TARGETING; GENOME IMPRINTING; HUMAN; HUMAN CELL; LETTER; MESODERM; METHYLATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REGULATOR GENE; REPORTER GENE; TISSUE SPECIFICITY; TRANSGENIC MOUSE;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA METHYLATION; ENDODERM; ENHANCER ELEMENTS (GENETICS); EVOLUTION, MOLECULAR; GENOMIC IMPRINTING; HUMANS; INSULIN-LIKE GROWTH FACTOR II; MICE; MICE, TRANSGENIC; MOLECULAR SEQUENCE DATA; MUSCLE PROTEINS; ORGAN SPECIFICITY; RATS; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, DNA;

ANIMALIA; MUS MUSCULUS; RODENTIA;

EID: 0034127018     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.5.664     Document Type: Letter

References (28)

1. Ainscough, J.F.-X., T. Koide, M. Tada, S.C. Barton, and M.A. Surani. 1997. Imprinting of Igf2 and H19 from a 130 kb YAC transgene. Development 124: 3621-3632.
2. Bartolomei, M.S. and S.M. Tilghman. 1992. Parental imprinting of mouse chromosome 7. Semin. Dev. Biol. 3: 107-117.
3. Bell, A.C., A.G. West, and G. Felsenfeld. 1999. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98: 387-396.
4. Brannan, C.I., E.C. Dees, R.S. Ingram, and S.M. Tilghman. 1990. The product of the H19 gene may function as an RNA. Mol. Cell. Biol. 10: 28-36.
5. Brenton, J.D., R.A. Drewell, S. Viville, K.J. Hilton, S.C. Barton, J.F.-X. Ainscough, and M.A. Surani. 1999. A silencer element identified in Drosophila is required for imprinting of H19 reporter transgenes in mice. Proc. Natl. Acad. Sci. USA 96: 9242-9247.
6. Elson, D.A. and M.S. Bartolomei. 1997. A 5′ differentially methylated sequence and the 3′-flanking region are necessary for H19 transgene imprinting. Mol. Cell. Biol. 17: 309-317.
7. Frevel, M.A.E., S.J. Sowerby, G.B. Petersen, and A.E. Reeve. 1999a. Methylation sequencing analysis refines the region of H19 epimutation in Wilms Tumor. J. Biol. Chem. 247: 29331-29340.
8. Frevel, M.A.E., J.J. Hornberg, and A.E. Reeve. 1999b. A potential imprint control element: Identification of a conserved 42-bp sequence upstream H19. Trends Genet. 15: 216-218.
9. Hark, A.T. and S.M. Tilghman. 1998. Chromatin conformation of the H19 epigenetic mark. Hum. Mol. Genet. 7: 1979-1985.
10. Hatano, N., P. Eversole-Cire, A.C. Ferguson-Smith, P.A. Jones, M.A. Surani, and H. Sasaki. 1998. Enhancer-dependent, locus-wide regulation of the imprinted mouse insulin-like growth factor II gene. J. Biochem. 123: 984-991.
11. Ishihara, K., R. Kato, H. Furuumi, M. Zubair, and H. Sasaki. 1998. Sequence of a 42-kb mouse region containing the imprinted H19 locus: Identification of a novel muscle-specific transcription unit showing biallelic expression. Mamm. Genome 9: 775-777.
12. Jinno, Y., K. Sengoku, M. Nakao, K. Tamate, T. Miyamoto, T. Matsuzaka, J.S. Sutcliffe, T. Anan, N. Takuma, K. Nishiwaki, Y. Ikeda, T. Ishimaru, M. Ishikawa, and N. Niikawa. 1996. Mouse/human sequence divergence in a region with a paternal-specific methylation imprint at the human H19 locus. Hum. Mol. Genet. 5: 1155-1161.
13. Kato, R., H. Shirohzu, T. Yokomine, S. Mizuno, T. Mukai, and H. Sasaki. 1999. Sequence-ready 1-Mb YAC, BAC and cosmid contigs covering the distal imprinted region of mouse chromosome 7. DNA Res. 6: 401-405.
14. Khosla, S., A. Aitchison, R. Gregory, N.D. Allen, and R. Feil. 1999. Parental allele-specific chromatin configuration in a boundary-imprinting-control element upstream of the mouse H19 gene. Mol. Cell. Biol. 19: 2556-2566.
15. Lee, J., J. Pintar, and A. Efstratiadis. 1990. Pattern of the insulin-like growth factor II gene expression during early mouse embryogenesis. Development 110: 151-159.
16. Leighton, P.A., R.S. Ingram, J. Eggenschwiler, A. Efstratiadis, and S.M. Tilghman. 1995a. Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375: 34-39.
17. Leighton, P.A., J.R. Saam, R.S. Ingram, C.L. Stewart, and S.M. Tilghman. 1995b. An enhancer deletion affects both H19 and Igf2 expression. Genes Dev. 9: 2079-2089.
18. Li, Q., S. Harju, and K.R. Peterson. 1999. Locus control regions. Trends Genet. 15: 403-408.
19. Oeltjen, J.C., T.M. Malley, D.M. Muzny, W. Miller, R.A. Gibbs, and J.W. Belmont. 1997. Large-scale comparative sequence analysis of the human and marine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Res. 7: 315-329.
20. Sasaki, H., P.A. Jones, J.R. Chaillet, A.C. Ferguson-Smith, S.C. Barton, W. Reik, and M.A. Surani. 1992. Parental imprinting: Potentially active chromatin of the repressed maternal allele of the mouse insulin-like growth factor II (Igf2) gene. Genes Dev. 6: 1843-1856.
21. Schmidt, J.V., J.M. Levorse, and S.M. Tilghman. 1999. Enhancer competition between H19 and Igf2 does not mediate their imprinting. Proc. Natl. Acad. Sci. USA 96: 9733-9738.
22. Stadnick, M.P., F.M. Pieracci, M.J. Cranston, E. Taksel, J.L. Thorvaldsen, and M.S. Bartolomei. 1999. Role of a 461-bp G-rich repetitive element in H19 transgene imprinting. Dev. Genes Evol. 209: 239-248.
23. Stylianopoulou, F., A. Efstratiadis, J. Herbert, and J. Pintar. 1988. Pattern of the insulin-like growth factor II gene expression during rat embryogenesis. Development 103: 497-506.
24. Thacker, C., M.A. Marra, A. Jones, D.L. Baillie, and A.M. Rose. 1999. Functional genomics in Caenorhabditis elegans: An approach involving comparisons of sequences from related nematodes. Genome Res. 9: 348-359.
25. Thorvaldsen, J.L., K.L. Duran, K.L., and M.S. Bartolomei. 1998. Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev. 12: 3693-3702.
26. Tremblay, K.D., J.R. Saam, R.S. Ingram, S.M. Tilghman, and M.S. Bartolomei. 1995. A paternal-specific methylation imprint marks the alleles of the mouse H19 gene. Nature Genet. 9: 407-413.
27. Webber, A.L., R.S. Ingram, J.M. Levorse, and S.M. Tilghman. 1998. Location of enhancers is essential for the imprinting of H19 and Igf2. Nature 391: 711-715.
28. Yoo-Warren, H., V. Pachnis, R.S. Ingram, and S.M. Tilghman. 1988. Two regulatory domains flank the mouse H19 gene. Mol. Cell. Biol. 8: 4707-4715.