Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Sep 25;17(18):7229–7239. doi: 10.1093/nar/17.18.7229

The effect of E. coli host strain on the consensus sequence of regions of the human L1 transposon.

P J Crowther 1, A L Cartwright 1, A Hocking 1, S Jefferson 1, M D Ford 1, D M Woodcock 1
PMCID: PMC334803  PMID: 2552406

Abstract

We have used highly methylation tolerant host strains to clone hyper- and hypo-methylated genomic elements from different regions of the same family of long interspersed repetitive elements from human DNA, specifically the 1.8 kilobase (kb) and 1.2kb KpnI fragments from members of the L1 family of transposable elements in which respectively some 18% and 2.7% of cytosines are methylated in vivo in human spleen DNA. The consensus of the DNA sequences of the ends of 13 clones from the hypomethylated region of human L1 agreed exactly with the consensus derived previously from clones made using conventional host strains. However the sequences of 18 of our clones from the 5' end of the hypermethylated region differed significantly from the sequences of clones made using conventional hosts (P less than 0.0001). The 5' region of the 1.8kb L1 region is a CpG island which, in human somatic tissue, appears to be maintained in a highly methylated state, including methylation at sites other than CpG dinucleotides. The consensus sequence of this region also has features suggestive of a previously unrecognized open reading frame.

Full text

PDF
7229

Images in this article

7236Image
on p.7236

Selected References

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

  1. Bird A. P. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980 Apr 11;8(7):1499–1504. doi: 10.1093/nar/8.7.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Dover G. Molecular drive: a cohesive mode of species evolution. Nature. 1982 Sep 9;299(5879):111–117. doi: 10.1038/299111a0. [DOI] [PubMed] [Google Scholar]
  3. Fanning T. G., Singer M. F. LINE-1: a mammalian transposable element. Biochim Biophys Acta. 1987 Dec 8;910(3):203–212. doi: 10.1016/0167-4781(87)90112-6. [DOI] [PubMed] [Google Scholar]
  4. Fawcett D. H., Lister C. K., Kellett E., Finnegan D. J. Transposable elements controlling I-R hybrid dysgenesis in D. melanogaster are similar to mammalian LINEs. Cell. 1986 Dec 26;47(6):1007–1015. doi: 10.1016/0092-8674(86)90815-9. [DOI] [PubMed] [Google Scholar]
  5. Furano A. V., Robb S. M., Robb F. T. The structure of the regulatory region of the rat L1 (L1Rn, long interspersed repeated) DNA family of transposable elements. Nucleic Acids Res. 1988 Oct 11;16(19):9215–9231. doi: 10.1093/nar/16.19.9215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Hattori M., Hidaka S., Sakaki Y. Sequence analysis of a KpnI family member near the 3' end of human beta-globin gene. Nucleic Acids Res. 1985 Nov 11;13(21):7813–7827. doi: 10.1093/nar/13.21.7813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hattori M., Kuhara S., Takenaka O., Sakaki Y. L1 family of repetitive DNA sequences in primates may be derived from a sequence encoding a reverse transcriptase-related protein. Nature. 1986 Jun 5;321(6070):625–628. doi: 10.1038/321625a0. [DOI] [PubMed] [Google Scholar]
  9. Hubrich-Kühner K., Buhk H. J., Wagner H., Kröger H., Simon D. Non-C-G recognition sequences of DNA cytosine-5-methyltransferase from rat liver. Biochem Biophys Res Commun. 1989 May 15;160(3):1175–1182. doi: 10.1016/s0006-291x(89)80127-5. [DOI] [PubMed] [Google Scholar]
  10. Kazazian H. H., Jr, Wong C., Youssoufian H., Scott A. F., Phillips D. G., Antonarakis S. E. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988 Mar 10;332(6160):164–166. doi: 10.1038/332164a0. [DOI] [PubMed] [Google Scholar]
  11. Keith D. H., Singer-Sam J., Riggs A. D. Active X chromosome DNA is unmethylated at eight CCGG sites clustered in a guanine-plus-cytosine-rich island at the 5' end of the gene for phosphoglycerate kinase. Mol Cell Biol. 1986 Nov;6(11):4122–4125. doi: 10.1128/mcb.6.11.4122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Morse B., Rotherg P. G., South V. J., Spandorfer J. M., Astrin S. M. Insertional mutagenesis of the myc locus by a LINE-1 sequence in a human breast carcinoma. Nature. 1988 May 5;333(6168):87–90. doi: 10.1038/333087a0. [DOI] [PubMed] [Google Scholar]
  13. Noyer-Weidner M., Diaz R., Reiners L. Cytosine-specific DNA modification interferes with plasmid establishment in Escherichia coli K12: involvement of rglB. Mol Gen Genet. 1986 Dec;205(3):469–475. doi: 10.1007/BF00338084. [DOI] [PubMed] [Google Scholar]
  14. Nur I., Pascale E., Furano A. V. The left end of rat L1 (L1Rn, long interspersed repeated) DNA which is a CpG island can function as a promoter. Nucleic Acids Res. 1988 Oct 11;16(19):9233–9251. doi: 10.1093/nar/16.19.9233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Padgett R. W., Hutchison C. A., 3rd, Edgell M. H. The F-type 5' motif of mouse L1 elements: a major class of L1 termini similar to the A-type in organization but unrelated in sequence. Nucleic Acids Res. 1988 Jan 25;16(2):739–749. doi: 10.1093/nar/16.2.739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Raleigh E. A., Murray N. E., Revel H., Blumenthal R. M., Westaway D., Reith A. D., Rigby P. W., Elhai J., Hanahan D. McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res. 1988 Feb 25;16(4):1563–1575. doi: 10.1093/nar/16.4.1563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Raleigh E. A., Wilson G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A. 1986 Dec;83(23):9070–9074. doi: 10.1073/pnas.83.23.9070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reed K. C., Mann D. A. Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res. 1985 Oct 25;13(20):7207–7221. doi: 10.1093/nar/13.20.7207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Scott A. F., Schmeckpeper B. J., Abdelrazik M., Comey C. T., O'Hara B., Rossiter J. P., Cooley T., Heath P., Smith K. D., Margolet L. Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence. Genomics. 1987 Oct;1(2):113–125. doi: 10.1016/0888-7543(87)90003-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Servomaa K., Rytömaa T. Suicidal death of rat chloroleukaemia cells by activation of the long interspersed repetitive DNA element (L1Rn). Cell Tissue Kinet. 1988 Jan;21(1):33–43. doi: 10.1111/j.1365-2184.1988.tb00769.x. [DOI] [PubMed] [Google Scholar]
  21. Shafit-Zagardo B., Brown F. L., Maio J. J., Adams J. W. KpnI families of long, interspersed repetitive DNAs associated with the human beta-globin gene cluster. Gene. 1982 Dec;20(3):397–407. doi: 10.1016/0378-1119(82)90208-6. [DOI] [PubMed] [Google Scholar]
  22. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]
  23. Wilson V. L., Jones P. A. DNA methylation decreases in aging but not in immortal cells. Science. 1983 Jun 3;220(4601):1055–1057. doi: 10.1126/science.6844925. [DOI] [PubMed] [Google Scholar]
  24. Woodcock D. M., Crowther P. J., Diver W. P., Graham M., Bateman C., Baker D. J., Smith S. S. RglB facilitated cloning of highly methylated eukaryotic DNA: the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase. Nucleic Acids Res. 1988 May 25;16(10):4465–4482. doi: 10.1093/nar/16.10.4465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Woodcock D. M., Crowther P. J., Diver W. P. The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun. 1987 Jun 15;145(2):888–894. doi: 10.1016/0006-291x(87)91048-5. [DOI] [PubMed] [Google Scholar]
  26. Woodcock D. M., Crowther P. J., Doherty J., Jefferson S., DeCruz E., Noyer-Weidner M., Smith S. S., Michael M. Z., Graham M. W. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 1989 May 11;17(9):3469–3478. doi: 10.1093/nar/17.9.3469. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES