Abstract
Only a small proportion of the vertebrate genome codes for proteins. It would therefore be useful if genes, and in particular the sites at which transcription begins, could be identified in libraries of cloned DNA. Since many known vertebrate genes have distinctive sequences (HTF-islands) surrounding their transcription start sites1, we wished to be able to select these sequences easily and to find out how diagnostic they are for genes. HTF-islands contain a high density of non-methylated CpG (ref. 2) and can be detected in chromosomal DNA as clustered sites for certain rare-cutting (C–G) restriction enzymes3. Identification of islands in chromosomal DNA is aided by methylation which blocks C–G enzyme sites in non-island DNA. This advantage is lost in cloned DNA, where CpG methylation is absent. We have calculated, however, that even in cloned DNA most sites for certain C–G enzymes should occur in HTF-islands. We tested this prediction using the enzyme SacII and found that four out of four sites in separate cosmids from the human X chromosome were located in HTF-islands. Hybridization to Northern blots provided preliminary evidence that three of the islands were associated with genes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
1. Bird, A. P. Nature 321, 209–213 (1986). 2. Bird, A. P., Taggart, M., Frommer, M., Miller, O. J. & Macleod, D. Cell 40, 91–99 (1985). 3. Brown, W. R. A. & Bird, A. P. Nature 323, 477–481 (1986). 4. Lund, E. et ai Molec. cell. Biol 3, 2211–2220 (1983). 5. Yen, P. H., Patel, P., Chinault, A. C., Mohandas, T. & Shapiro, L. J. Proc. natn. Acad. Sci. U.S.A. 81, 1759–1763 (1984). 6. Wolf, S. F., Jolly, D. J., Lunnen, K. D., Friedman, T. & Migeon, B. R. Proc. natn. Acad. Sci. U.S.A. 81, 2806–2810 (1984). 7. Wolf, S. F. et al. Nucleic Acids Res. 12, 9333–9348 (1984). 8. Toniolo, D. et al. EMBO J. 3, 1987–1995 (1984). 9. Bird, A. P., Taggart, M. H., Nicholls, R. D. & Riggs, D. R. EMBO J. 6, 999–1004 (1987). 10. Kolsto, A.–B. et al. Nucleic Acids Res. 14, 9667–9678 (1986). 11. Van der Ploeg, L. H. T. & Flavell, R. A. Cell 19, 947–958 (1980). 12. Ish–Horowicz, D. & Burke, J. F. Nucleic Acids Res. 9, 2989–2998 (1981). 13. Maniatis, T., Fritsch, E. F. & Sambrook, J. in Molecular Cloning, a Laboratory Manual, 304–305; 314 (Cold Spring Harbor Laboratory, New York, 1982). 14. Southern, E. M. / molec. Biol. 98, 503–517 (1975). 15. Reed, K. C. & Mann, D. A. Nucleic Acids Res. 13, 7207–7221 (1985). 16. Feinberg, A. & Vogelstein, B. Analyt. Biochem. 137, 266–267 (1984). 17. Sealey, P. G., Whittaker, P. A. & Southern, E. M. Nucleic Acids Res. 13, 1905–1922 (1985). 18. Cox, R. A. Meth. Enzym. 12, 120–129 (1968). 19. Maniatis, T., Fritsch, E. F. & Sambrook, J. in Molecular Cloning, a Laboratory Manual 197–198 (Cold Spring Harbor Laboratory, New York, 1982). 20. Church, G. & Gilbert, W. Proc. natn. Acad. Sci. U.S.A. 18, 1991–1995 (1984).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Lindsay, S., Bird, A. Use of restriction enzymes to detect potential gene sequences in mammalian DNA . Nature 327, 336–338 (1987). https://doi.org/10.1038/327336a0
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1038/327336a0
- Springer Nature Limited
This article is cited by
-
Quantitative assessment of DNA methylation: potential applications for disease diagnosis, classification, and prognosis in clinical settings
Journal of Molecular Medicine (2006)
-
Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3
Nature Genetics (2005)
-
Study of Tissue-Specific CpG Methylation of DNA in Extended Genomic Loci
Biochemistry (Moscow) (2005)
-
High-resolution mapping of the Rym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2) in barley (Hordeum vulgare ssp. vulgare L.)
Theoretical and Applied Genetics (2005)