Mammalian Genome

, Volume 11, Issue 5, pp 373–383 | Cite as

CpG island libraries from human Chromosomes 18 and 22: landmarks for novel genes

  • Sally H.  Cross
  • Victoria H.  Clark
  • Martin W.  Simmen
  • Wendy A.  Bickmore
  • Habib  Maroon
  • Cordelia F.  Langford
  • Nigel P.  Carter
  • Adrian P.  Bird

Abstract.

CpG islands are found at the 5′ end of approximately 60% of human genes and so are important genomic landmarks. They are concentrated in early-replicating, highly acetylated gene-rich regions. With respect to CpG island content, human Chrs 18 and 22 are very different from each other: Chr 18 appears to be CpG island poor, whereas Chr 22 appears to be CpG island rich. We have constructed and validated CpG island libraries from flow-sorted Chrs 18 and 22 and used these to estimate the difference in number of CpG islands found on these two chromosomes. These libraries contain normalized collections of sequences from the 5′ end of genes. Clones from the libraries were sequenced and compared with the sequence databases; one third matched ESTs, thus anchoring these ESTs at the 5′ end of their gene. However, it was striking that many clones either had no match or matched only existing CpG island clones. This suggests that a significant proportion of 5′ gene sequences are absent from databases, presumably either because they are difficult to clone or the gene is poorly expressed and/or has a restricted expression pattern. This point should be taken into consideration if the currently available libraries are those used for the elucidation of complete, as opposed to partial, gene sequences. The Chr 18 and 22 CpG island libraries are a sequence resource for the isolation of such 5′ gene sequences from specific human chromosomes.

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Copyright information

© Springer-Verlag New York Inc. 2000

Authors and Affiliations

  • Sally H.  Cross
    • 1
  • Victoria H.  Clark
    • 1
  • Martin W.  Simmen
    • 1
  • Wendy A.  Bickmore
    • 2
  • Habib  Maroon
    • 1
  • Cordelia F.  Langford
    • 3
  • Nigel P.  Carter
    • 3
  • Adrian P.  Bird
    • 1
  1. 1.Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UKGB
  2. 2.MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UKGB
  3. 3.The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UKGB

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