Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Feb 25;20(4):727–733. doi: 10.1093/nar/20.4.727

Methylation and sequence analysis around EagI sites: identification of 28 new CpG islands in XQ24-XQ28.

C Tribioli 1, F Tamanini 1, C Patrosso 1, L Milanesi 1, A Villa 1, R Pergolizzi 1, E Maestrini 1, S Rivella 1, S Bione 1, M Mancini 1
PMCID: PMC312011  PMID: 1542569

Abstract

Thirty-two probes for CpG islands of the distal long arm of the human X chromosome have been identified. From a genomic library of DNA of the hamster-human cell hybrid X3000.1 digested with the rare cutter restriction enzyme EagI, 53 different human clones have been isolated and characterized by methylation and sequence analysis. The characteristic pattern of DNA methylation of CpG islands at the 5' end of genes of the X chromosome has been used to distinguish between EagI sites in CpG islands versus isolated EagI sites. The sequence analysis has confirmed and completed the characterization showing that sequences at the 5' end of known genes were among the clones defined CpG islands and that the non-CpG islands clones were mostly repetitive sequences with a non-methylated or variably methylated EagI site. Thus, since clones corresponding to repetitive sequences can be easily identified by sequencing, such libraries are a very good source of CpG islands. The methylation analysis of 28 different new probes allows to state that demethylation of CpG islands of the active X and methylation of those on the inactive X chromosome are the general rule. Moreover, the finding, in all instances, of methylation differences between male and female DNA is in very strong support of the notion that most genes of the distal long arm of the X chromosome are subject to X inactivation.

Full text

PDF
727

Images in this article

728Image
on p.728

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Ansorge W., Sproat B., Stegemann J., Schwager C., Zenke M. Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis. Nucleic Acids Res. 1987 Jun 11;15(11):4593–4602. doi: 10.1093/nar/15.11.4593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bates G. P., MacDonald M. E., Baxendale S., Youngman S., Lin C., Whaley W. L., Wasmuth J. J., Gusella J. F., Lehrach H. Defined physical limits of the Huntington disease gene candidate region. Am J Hum Genet. 1991 Jul;49(1):7–16. [PMC free article] [PubMed] [Google Scholar]
  4. Bird A. P. Two classes of observed frequency for rare-cutter sites in CpG islands. Nucleic Acids Res. 1989 Nov 25;17(22):9485–9485. doi: 10.1093/nar/17.22.9485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Crowther P. J., Doherty J. P., Linsenmeyer M. E., Williamson M. R., Woodcock D. M. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains. Nucleic Acids Res. 1991 May 11;19(9):2395–2401. doi: 10.1093/nar/19.9.2395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Davies K. Human genetics. The essence of inactivity. Nature. 1991 Jan 3;349(6304):15–16. doi: 10.1038/349015a0. [DOI] [PubMed] [Google Scholar]
  7. Dietrich A., Kioschis P., Monaco A. P., Gross B., Korn B., Williams S. V., Sheer D., Heitz D., Oberle I., Toniolo D. Molecular cloning and analysis of the fragile X region in man. Nucleic Acids Res. 1991 May 25;19(10):2567–2572. doi: 10.1093/nar/19.10.2567. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Estivill X., Farrall M., Scambler P. J., Bell G. M., Hawley K. M., Lench N. J., Bates G. P., Kruyer H. C., Frederick P. A., Stanier P. A candidate for the cystic fibrosis locus isolated by selection for methylation-free islands. 1987 Apr 30-May 6Nature. 326(6116):840–845. doi: 10.1038/326840a0. [DOI] [PubMed] [Google Scholar]
  9. Filippi M., Tribioli C., Toniolo D. Linkage and sequence conservation of the X-linked genes DXS253E (P3) and DXS254E (GdX) in mouse and man. Genomics. 1990 Jul;7(3):453–457. doi: 10.1016/0888-7543(90)90184-v. [DOI] [PubMed] [Google Scholar]
  10. Gardiner-Garden M., Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261–282. doi: 10.1016/0022-2836(87)90689-9. [DOI] [PubMed] [Google Scholar]
  11. Gardiner K., Horisberger M., Kraus J., Tantravahi U., Korenberg J., Rao V., Reddy S., Patterson D. Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distributions. EMBO J. 1990 Jan;9(1):25–34. doi: 10.1002/j.1460-2075.1990.tb08076.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Grant S. G., Chapman V. M. Mechanisms of X-chromosome regulation. Annu Rev Genet. 1988;22:199–233. doi: 10.1146/annurev.ge.22.120188.001215. [DOI] [PubMed] [Google Scholar]
  13. Harada F., Tsukada N., Kato N. Isolation of three kinds of human endogenous retrovirus-like sequences using tRNA(Pro) as a probe. Nucleic Acids Res. 1987 Nov 25;15(22):9153–9162. doi: 10.1093/nar/15.22.9153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Heitz D., Rousseau F., Devys D., Saccone S., Abderrahim H., Le Paslier D., Cohen D., Vincent A., Toniolo D., Della Valle G. Isolation of sequences that span the fragile X and identification of a fragile X-related CpG island. Science. 1991 Mar 8;251(4998):1236–1239. doi: 10.1126/science.2006411. [DOI] [PubMed] [Google Scholar]
  15. Hohjoh H., Minakami R., Sakaki Y. Selective cloning and sequence analysis of the human L1 (LINE-1) sequences which transposed in the relatively recent past. Nucleic Acids Res. 1990 Jul 25;18(14):4099–4104. doi: 10.1093/nar/18.14.4099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kariya Y., Kato K., Hayashizaki Y., Himeno S., Tarui S., Matsubara K. Revision of consensus sequence of human Alu repeats--a review. Gene. 1987;53(1):1–10. doi: 10.1016/0378-1119(87)90087-4. [DOI] [PubMed] [Google Scholar]
  17. Maestrini E., Rivella S., Tribioli C., Purtilo D., Rocchi M., Archidiacono N., Toniolo D. Probes for CpG islands on the distal long arm of the human X chromosome are clustered in Xq24 and Xq28. Genomics. 1990 Dec;8(4):664–670. doi: 10.1016/0888-7543(90)90253-q. [DOI] [PubMed] [Google Scholar]
  18. Manoni M., Tribioli C., Lazzari B., DeBellis G., Patrosso C., Pergolizzi R., Pellegrini M., Maestrini E., Rivella S., Vezzoni P. The nucleotide sequence of a CpG island demonstrates the presence of the first exon of the gene encoding the human lysosomal membrane protein lamp2 and assigns the gene to Xq24. Genomics. 1991 Mar;9(3):551–554. doi: 10.1016/0888-7543(91)90424-d. [DOI] [PubMed] [Google Scholar]
  19. Nussbaum R. L., Airhart S. D., Ledbetter D. H. A rodent-human hybrid containing Xq24-qter translocated to a hamster chromosome expresses the Xq27 folate-sensitive fragile site. Am J Med Genet. 1986 Jan-Feb;23(1-2):457–466. doi: 10.1002/ajmg.1320230137. [DOI] [PubMed] [Google Scholar]
  20. Patterson M., Schwartz C., Bell M., Sauer S., Hofker M., Trask B., van den Engh G., Davies K. E. Physical mapping studies on the human X chromosome in the region Xq27-Xqter. Genomics. 1987 Dec;1(4):297–306. doi: 10.1016/0888-7543(87)90028-0. [DOI] [PubMed] [Google Scholar]
  21. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Poustka A., Dietrich A., Langenstein G., Toniolo D., Warren S. T., Lehrach H. Physical map of human Xq27-qter: localizing the region of the fragile X mutation. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8302–8306. doi: 10.1073/pnas.88.19.8302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Schmid C. W. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res. 1991 Oct 25;19(20):5613–5617. doi: 10.1093/nar/19.20.5613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ullu E., Weiner A. M. Human genes and pseudogenes for the 7SL RNA component of signal recognition particle. EMBO J. 1984 Dec 20;3(13):3303–3310. doi: 10.1002/j.1460-2075.1984.tb02294.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Verkerk A. J., Pieretti M., Sutcliffe J. S., Fu Y. H., Kuhl D. P., Pizzuti A., Reiner O., Richards S., Victoria M. F., Zhang F. P. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell. 1991 May 31;65(5):905–914. doi: 10.1016/0092-8674(91)90397-h. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES