CpG islands are short stretches of DNA containing a high density of non–methylated CpG dinucleotides, predominantly associated with coding regions. We have constructed an affinity matrix that contains the methyl–CpG binding domain from the rat chromosomal protein MeCP2, attached to a solid support. A column containing the matrix fractionates DNA according to its degree of CpG methylation, strongly retaining those sequences that are highly methylated. Using this column, we have developed a procedure for bulk isolation of CpG islands from human genomic DNA. As CpG islands overlap with approximately 60% of human genes, the resulting CpG island library can be used to isolate full–length cDNAs and to place genes on genomic maps.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Cooper, D., Taggart, M. & Bird, A. Unmethylated domains in vertebrate DNA. Nucl. Adds Res. 11, 647–658 (1983).
Bird, A.P., Taggart, M., Frommer, M., Miller, O.J. & Macleod, D. A fraction of the mouse genome that is derived from islands of non-methylated, CpG-rich DNA. Cell 40, 91–99 (1985).
Bird, A. CpG islands as gene markers in the vertebrate nucleus. Trends Genet. 3 342–347 (1987).
Antequera, F. & Bird, A. CpG islands in DNA Methylation: Molecular Biology & Biological Significance (eds Jost, J.P. & Salute, H.P.) 169–185 (Birkhauser Verlag Basel, Switerland 1993).
Antequera, P. & Bird, A. Number of CpG islands and genes in human and mouse. Proc. natn. Acad. Sci. U.S.A. (in the press).
Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. molec. Biol. 196, 261–282 (1987).
Larsen, F., Gundersen, G., Lopez, R. & Prydz, H. CpG islands as gene markers in the human genome. Genomics 13, 1095–1107 (1992).
Brown, W.R.A. & Bird, A.P. Long-range restriction site mapping of mammalian genomic DNA. Nature 322, 477–481 (1986).
Lindsay, S. & Bird, A.P. Use of restriction enzymes to detect potential gene sequences in mammalian DNA. Nature 327, 336–338 (1987).
Lewis, J.D. et al. Purification, sequence and Cellular localisation of a novel chromosomal protein that binds to methylated DNA. Cell 69, 905–914 (1992).
Meehan, R.R., Lewis, J.D. & Bird, A.P. Characterization of MeCP2, a vertebrate DNA binding protein that binds methylated DNA. Nucl. Acids Res. 20, 5085–5092 (1992).
Nan, X., Meehan, R.R. & Bird, A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucl. Acids Res. 21, 4886–4892 (1993).
Hochuli, E., Döbeli, H. & Schacher, A. New metal chelate adsorbents selectivefor proteins and peptides containing neighbouring histidine residues. J. Chromatog. 411, 177–184 (1987).
Meehan, R.R., Lewis, J.D., McKay, S., Kleiner, E.L. & Bird, A.P. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58, 499–507 (1989).
Hendriks, R.W., Chen, Z.Y., Hinds, H., Schuurman, R.K.B. & Craig, I.W. An X chromosome inactivation assay based on differential methylation of a CpG island coupled to a VNTR polymorphism at the 5′ end of the monoamine oxidase A gene. Hum. molec. Genet. 1, 187–194 (1992).
Pfeifer, G., Tanguay, R., Steigerwald, S. & Riggs, A. In vivo footprint and methylation analysis by PCR-aided genomic sequencing: Comparison of active and Inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. Genes Devel. 4, 1277–1287 (1990).
Kenwrick, S., Levinson, B., Taylor, S., Shapiro, A. & Gitschier, J. Isolation and sequence of two genes associated with a CpG island 5′ of the factor VIII gene. Hum. molec. Genet. 1, 179–186 (1992).
Bird, A.P., Taggart, M.H., Nicholls, R.D. & Higgs, D.R., Non-methylated CpGrich islands at the human α-globin locus: implications for evolution of the α-globin pseudogene. EMBO J. 6, 999–1004 (1987).
Shemer, R., Eisenberg, S., Breslow, J.L. & Razin, A. Methylation patterns of the human ApoA-l/C-lll/A-IV gene cluster in adult and embryonic tissues suggest dynamic changes in methylation during development. J. biol. Chem. 266, 23676–23681 (1991).
Bird, A.P. & Taggart, M.H. Variable patterns of total DNA and rDNA methylation in animals. Nucl. Acids Res. 8, 1485–1497 (1980).
Long, E.O. & Dawid, I.B. Repeated genes in eukaryotes. A. Rev. Biochem. 49, 727–764 (1980).
Cooke, H.J. & Smith, B.A. Variability at the telomeres of the human X/Y pseudoautosomal region. Cold Spring Harbor Symp. Quant. Biol. 51, 213–219 (1986).
Baens, M., Chaffanet, M., Cassiman, J.J., Vandenberghe, H. & Marynen, P. Construction and Evaluation of a hncDNA library of human 12p transcribed sequences derived from a somatic-cell hybrid. Genomics 16, 214–218 (1993).
Fearnley, I.M., Finel, M., Skehel, J.M. & Walker, J.E. NADH: ubiquinone oxidoreductase from bovine heart mitochondria: cDNA sequences of the import precursors of the nuclear encoded 39 kDa and 42 kDa subunits.J. Biochem. 278, 821–829 (1991).
Adams, M.D., Soares, M.B., Kerlavage, A.R., Fields, C. & Venter, J.C. Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library. Nature Genet. 4, 373–380 (1993).
Vanspronsen, A., Nahmias, C., Krief, S., Briendsutren, M.M., Strosberg, A.D. & Emorine, L.J. The promoter and intron-exon structure of the human and mouse β-3-adrenergic-receptor genes. Eur. J. Biochem. 213, 1117–1124 (1993).
Dawid, I.B. 5-methylcytidylcacid: absence from mitochondrial DNA of frogs and HeLa cells. Science 184, 80–81 (1974).
Lavia, P., Macleod, D. & Bird, A.P. Coincident start sites for divergent transcripts at a randomly selected CpG-rich island of mouse. EMBO J. 6, 2773–2779 (1987).
Larsen, F., Solheim, J., Kristensen, T., Kolstø, A.B. & Prydz, H. A tight cluster of five unrelated human genes on chromosome 16q22.1. Hum. molec. Genet. 2, 1589–1595 (1993).
Studier, F.W., Rosenberg, A.H., Dunn, J.J. & Dubendorff, J.W. Use of T7 RNA polymerase to direct expression of cloned genes. Meth. Enzymol. 185, 60–89 (1990).
Tolan, D.R. & Penhoet, E.E. Characterization of the human aldolase B gene. Molec. Biol. Med. 3, 245–264 (1983).
Lawn, R.M., Adelman, J., Dull, T.J., Gross, M., Goeddel, D. & Ullrich, A. DNA sequence of 2 closely linked human-leukocyte interferon genes.Science 212, 1159–1162 (1981).
Abbott, C. & Povey, S. Development of human chromosome-specific PCR primers for characterization of somatic cell hybrids. Genomics 9, 73–77 (1991).
Ponce, M.R. & Micol, J.L. PCR amplification of long DNA fragments. Nucl. Acids Res. 20, 623 (1992).
Cross, S., Kovarik, P., Schmidtke, J. & Bird, A. Nonmethylated islands in fish genomes are GC-poor. Nucl. Acids Res. 19, 1469–1474 (1991).
Feinberg, A.P. & Vogelstein, B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6–13 (1983).
Devereux, J., Haeberli, P. & Smithies, O. A comprehensive set of sequence-analysis programs for the VAX. Nucl. Adds Res. 12, 387–395 (1984).
States, D.J., Gish, W. & Altschul, F. Improved sensitivity of nucleic acid database similarity searches using application specific scoring matrices. Methods: Compan. Meth. Enzymol. 3, 66–70 (1991).
McCombie, W.R. et al. Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome-4p16.3. Nature Genet. 1, 348–353 (1992).
Britten, R.J., Baron, W.F., Stout, D.B. & Davidson, E.H. Sources and evolution of human Alu repeated sequences. Proc. natn. Acad. Sci. U.S.A. 85, 4770–4774 (1988).
Deininger, P.L., Jolly, D.J., Rubin, C.M., Friedmann, T. & Schmid, C.W. Base sequence studies of 300 nucleottde renatured repeated human DNA clones. J. molec. Biol. 151, 17–33 (1981).
Shafit-Zagardo, B., Brown, F.L., Maio, J.J. & Adam, J.W. Kpnl families of long, interspersed repetitive DNAs associated with the b-globingene cluster. Gene 20, 397–407 (1982).
About this article
Identification and expression of alternatively spliced novel isoforms of cancer associated MYD88 lacking death domain in mouse
Molecular Biology Reports (2018)