Nucleic Acids Research, Vol 27, Issue 10 2099-2107, Copyright © 1999 by Oxford University Press
SH Cross, VH Clark and AP Bird
Positional cloning is a powerful method for the identification of genes.
Using genetic and physical mapping methods the genomic region within which
a particular gene is located can relatively easily be narrowed down to a
comparatively small area contained within cosmid, PAC or BAC clones. It is
then a matter of identifying genes within these clones. Here we describe
the appli-cation of a technique, which has been successfully used for the
bulk purification of CpG islands from whole genomes, to the isolation of
CpG island sequences from such clones. As CpG islands overlap transcription
units they can be used to isolate full-length cDNAs for associated genes,
either by probing cDNA libraries or by searching databases. CpG islands are
linked with approximately 60% of human genes and because their isolation is
independent of the expression profile of these genes this approach would
complement other expression-based methods of gene identification. By
applying this technique to a cosmid clone known to contain the PAX6 gene we
successfully isolated the CpG island for this gene along with other CpG
island-like sequences. Closer examination revealed that an extensive
genomic region around the 5'-end of PAX6 is unusual with regard to
methylation and GC content. CpG island sequences were also successfully
isolated from a PAC clone carrying the MBD1 gene. These included the
complete CpG island containing the first exon and regulatory sequences from
MBD1.
ARTICLES
Isolation of CpG islands from large genomic clones
Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK. sally.cross@hgu.mrc.ac.uk
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  I. Zighelboim, P. J. Goodfellow, A. P. Schmidt, K. C. Walls, M. A. Mallon, D. G. Mutch, P. S. Yan, T. H.-M. Huang, and M. A. Powell Differential Methylation Hybridization Array of Endometrial Cancers Reveals Two Novel Cancer-Specific Methylation Markers Clin. Cancer Res., May 15, 2007; 13(10): 2882 - 2889. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Sun, S. K. Palaniswamy, T. T. Pohar, V. X. Jin, T. H.-M. Huang, and R. V. Davuluri MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data Nucleic Acids Res., January 1, 2006; 34(suppl_1): D98 - D103. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. E. Heisler, D. Torti, P. C. Boutros, J. Watson, C. Chan, N. Winegarden, M. Takahashi, P. Yau, T. H.-M. Huang, P. J. Farnham, et al. CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome Nucleic Acids Res., May 23, 2005; 33(9): 2952 - 2961. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Murrell, V. K. Rakyan, and S. Beck From genome to epigenome Hum. Mol. Genet., April 15, 2005; 14(suppl_1): R3 - R10. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Tateno, N. Saitou, K. Okubo, H. Sugawara, and T. Gojobori DDBJ in collaboration with mass-sequencing teams on annotation Nucleic Acids Res., January 1, 2005; 33(suppl_1): D25 - D28. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. F. Jorgensen, I. Ben-Porath, and A. P. Bird Mbd1 Is Recruited to both Methylated and Nonmethylated CpGs via Distinct DNA Binding Domains Mol. Cell. Biol., April 15, 2004; 24(8): 3387 - 3395. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. A. Samad, A. Srinivasan, L. A. Karchewski, S.-J. Jeong, J. A. Campagna, R.-R. Ji, D. A. Fabrizio, Y. Zhang, H. Y. Lin, E. Bell, et al. DRAGON: A Member of the Repulsive Guidance Molecule-Related Family of Neuronal- and Muscle-Expressed Membrane Proteins Is Regulated by DRG11 and Has Neuronal Adhesive Properties J. Neurosci., February 25, 2004; 24(8): 2027 - 2036. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. B. Bajic and S. H. Seah Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units Genome Res., August 1, 2003; 13(8): 1923 - 1929. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. B. Bajic and S. H. Seah Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes Nucleic Acids Res., July 1, 2003; 31(13): 3560 - 3563. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Xu and S. S. Korban A Cluster of Four Receptor-Like Genes Resides in the Vf Locus That Confers Resistance to Apple Scab Disease Genetics, December 1, 2002; 162(4): 1995 - 2006. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Shin Voo, D. L. Carlone, B. M. Jacobsen, A. Flodin, and D. G. Skalnik Cloning of a Mammalian Transcriptional Activator That Binds Unmethylated CpG Motifs and Shares a CXXC Domain with DNA Methyltransferase, Human Trithorax, and Methyl-CpG Binding Domain Protein 1 Mol. Cell. Biol., March 15, 2000; 20(6): 2108 - 2121. [Abstract] [Full Text]
|
|
|
|
 |
|
 G. G. Mahairas, J. C. Wallace, K. Smith, S. Swartzell, T. Holzman, A. Keller, R. Shaker, J. Furlong, J. Young, S. Zhao, et al. Sequence-tagged connectors: A sequence approach to mapping and scanning the human genome PNAS, August 17, 1999; 96(17): 9739 - 9744. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Stopa, D. Anhuf, L. Terstegen, P. Gatsios, A. M. Gressner, and S. Dooley Participation of Smad2, Smad3, and Smad4 in Transforming Growth Factor beta (TGF-beta )-induced Activation of Smad7. THE TGF-beta RESPONSE ELEMENT OF THE PROMOTER REQUIRES FUNCTIONAL Smad BINDING ELEMENT AND E-BOX SEQUENCES FOR TRANSCRIPTIONAL REGULATION J. Biol. Chem., September 15, 2000; 275(38): 29308 - 29317. [Abstract] [Full Text] [PDF]
|
|