Abstract
We have used a combination of BsuE methyltransferase (M-BsuE) and NotI restriction enzyme to cut genomic DNA at a subset of NotI sites. The usefulness of this system is shown in a re-examination of the restriction map of the human MHC. Combinations of methylases and restriction enzymes can be used to generate cuts at different frequencies in genomic DNA, such that they generate ends complementary to NotI ends, and can be used in conjunction with NotI linking clones in chromosome jumping experiments. These enzyme combinations have the potential to produce cutting sites in genomic DNA spaced at intervals favorable for extensive mapping, fragment enrichment, and cloning efforts.
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- Abe K., Wei J. F., Wei F. S., Hsu Y. C., Uehara H., Artzt K., Bennett D. Searching for coding sequences in the mammalian genome: the H-2K region of the mouse MHC is replete with genes expressed in embryos. EMBO J. 1988 Nov;7(11):3441–3449. doi: 10.1002/j.1460-2075.1988.tb03218.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
- Burke D. T., Carle G. F., Olson M. V. Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science. 1987 May 15;236(4803):806–812. doi: 10.1126/science.3033825. [DOI] [PubMed] [Google Scholar]
- Carroll M. C., Katzman P., Alicot E. M., Koller B. H., Geraghty D. E., Orr H. T., Strominger J. L., Spies T. Linkage map of the human major histocompatibility complex including the tumor necrosis factor genes. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8535–8539. doi: 10.1073/pnas.84.23.8535. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chu G., Vollrath D., Davis R. W. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986 Dec 19;234(4783):1582–1585. doi: 10.1126/science.3538420. [DOI] [PubMed] [Google Scholar]
- Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Collins F. S., Weissman S. M. Directional cloning of DNA fragments at a large distance from an initial probe: a circularization method. Proc Natl Acad Sci U S A. 1984 Nov;81(21):6812–6816. doi: 10.1073/pnas.81.21.6812. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Das H. K., Lawrance S. K., Weissman S. M. Structure and nucleotide sequence of the heavy chain gene of HLA-DR. Proc Natl Acad Sci U S A. 1983 Jun;80(12):3543–3547. doi: 10.1073/pnas.80.12.3543. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dunham I., Sargent C. A., Trowsdale J., Campbell R. D. Molecular mapping of the human major histocompatibility complex by pulsed-field gel electrophoresis. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7237–7241. doi: 10.1073/pnas.84.20.7237. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
- Gaido M. L., Prostko C. R., Strobl J. S. Isolation and characterization of BsuE methyltransferase, a CGCG specific DNA methyltransferase from Bacillus subtilis. J Biol Chem. 1988 Apr 5;263(10):4832–4836. [PubMed] [Google Scholar]
- Hardy D. A., Bell J. I., Long E. O., Lindsten T., McDevitt H. O. Mapping of the class II region of the human major histocompatibility complex by pulsed-field gel electrophoresis. Nature. 1986 Oct 2;323(6087):453–455. doi: 10.1038/323453a0. [DOI] [PubMed] [Google Scholar]
- Ikawa S., Shibata T., Ando T., Saito H. Genetic studies on site-specific endodeoxyribonucleases in Bacillus subtilis: multiple modification and restriction systems in transformants of Bacillus subtilis 168. Mol Gen Genet. 1980 Feb;177(3):359–368. doi: 10.1007/BF00271474. [DOI] [PubMed] [Google Scholar]
- Kandpal R. P., Ward D. C., Weissman S. M. Selective enrichment of a large size genomic DNA fragment by affinity capture: an approach for genome mapping. Nucleic Acids Res. 1990 Apr 11;18(7):1789–1795. doi: 10.1093/nar/18.7.1789. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kappes D., Strominger J. L. Human class II major histocompatibility complex genes and proteins. Annu Rev Biochem. 1988;57:991–1028. doi: 10.1146/annurev.bi.57.070188.005015. [DOI] [PubMed] [Google Scholar]
- Koller B. H., Geraghty D. E., Shimizu Y., DeMars R., Orr H. T. HLA-E. A novel HLA class I gene expressed in resting T lymphocytes. J Immunol. 1988 Aug 1;141(3):897–904. [PubMed] [Google Scholar]
- Koller B. H., Geraghty D., Orr H. T., Shimizu Y., DeMars R. Organization of the human class I major histocompatibility complex genes. Immunol Res. 1987;6(1-2):1–10. doi: 10.1007/BF02918100. [DOI] [PubMed] [Google Scholar]
- Koller B. H., Sidwell B., DeMars R., Orr H. T. Isolation of HLA locus-specific DNA probes from the 3'-untranslated region. Proc Natl Acad Sci U S A. 1984 Aug;81(16):5175–5178. doi: 10.1073/pnas.81.16.5175. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Koob M., Szybalski W. Cleaving yeast and Escherichia coli genomes at a single site. Science. 1990 Oct 12;250(4978):271–273. doi: 10.1126/science.2218529. [DOI] [PubMed] [Google Scholar]
- Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
- Lawrance S. K., Das H. K., Pan J., Weissman S. M. The genomic organisation and nucleotide sequence of the HLA-SB(DP) alpha gene. Nucleic Acids Res. 1985 Oct 25;13(20):7515–7528. doi: 10.1093/nar/13.20.7515. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lawrance S. K., Smith C. L. Megabase scale restriction fragment length polymorphisms in the human major histocompatibility complex. Genomics. 1990 Oct;8(2):394–399. doi: 10.1016/0888-7543(90)90299-a. [DOI] [PubMed] [Google Scholar]
- Lawrance S. K., Smith C. L., Srivastava R., Cantor C. R., Weissman S. M. Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis. Science. 1987 Mar 13;235(4794):1387–1390. doi: 10.1126/science.3029868. [DOI] [PubMed] [Google Scholar]
- Maher L. J., 3rd, Wold B., Dervan P. B. Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science. 1989 Aug 18;245(4919):725–730. doi: 10.1126/science.2549631. [DOI] [PubMed] [Google Scholar]
- McClelland M., Kessler L. G., Bittner M. Site-specific cleavage of DNA at 8- and 10-base-pair sequences. Proc Natl Acad Sci U S A. 1984 Feb;81(4):983–987. doi: 10.1073/pnas.81.4.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nedwin G. E., Naylor S. L., Sakaguchi A. Y., Smith D., Jarrett-Nedwin J., Pennica D., Goeddel D. V., Gray P. W. Human lymphotoxin and tumor necrosis factor genes: structure, homology and chromosomal localization. Nucleic Acids Res. 1985 Sep 11;13(17):6361–6373. doi: 10.1093/nar/13.17.6361. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nelson M., Christ C., Schildkraut I. Alteration of apparent restriction endonuclease recognition specificities by DNA methylases. Nucleic Acids Res. 1984 Jul 11;12(13):5165–5173. doi: 10.1093/nar/12.13.5165. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Oda K., Marmur J. Purification and properties of deoxyribonucleic acid methylase from Bacillus subtilis. Biochemistry. 1966 Feb;5(2):761–773. doi: 10.1021/bi00866a051. [DOI] [PubMed] [Google Scholar]
- Qiang B. Q., McClelland M., Poddar S., Spokauskas A., Nelson M. The apparent specificity of NotI (5'-GCGGCCGC-3') is enhanced by M.FnuDII or M.BepI methyltransferases (5'-mCGCG-3'): cutting bacterial chromosomes into a few large pieces. Gene. 1990 Mar 30;88(1):101–105. doi: 10.1016/0378-1119(90)90065-y. [DOI] [PubMed] [Google Scholar]
- Ragoussis J., Bloemer K., Pohla H., Messer G., Weiss E. H., Ziegler A. A physical map including a new class I gene (cda12) of the human major histocompatibility complex (A2/B13 haplotype) derived from a monosomy 6 mutant cell line. Genomics. 1989 Apr;4(3):301–308. doi: 10.1016/0888-7543(89)90334-0. [DOI] [PubMed] [Google Scholar]
- Smith H. O., Birnstiel M. L. A simple method for DNA restriction site mapping. Nucleic Acids Res. 1976 Sep;3(9):2387–2398. doi: 10.1093/nar/3.9.2387. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spies T., Bresnahan M., Strominger J. L. Human major histocompatibility complex contains a minimum of 19 genes between the complement cluster and HLA-B. Proc Natl Acad Sci U S A. 1989 Nov;86(22):8955–8958. doi: 10.1073/pnas.86.22.8955. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Srivastava R., Chorney M. J., Lawrance S. K., Pan J., Smith Z., Smith C. L., Weissman S. M. Structure, expression, and molecular mapping of a divergent member of the class I HLA gene family. Proc Natl Acad Sci U S A. 1987 Jun;84(12):4224–4228. doi: 10.1073/pnas.84.12.4224. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Svejgaard A., Platz P., Ryder L. P. HLA and disease 1982--a survey. Immunol Rev. 1983;70:193–218. doi: 10.1111/j.1600-065x.1983.tb00715.x. [DOI] [PubMed] [Google Scholar]
- Swaroop A., Weissman S. M. Charon BS(+) and (-), versatile lambda phage vectors for constructing directional cDNA libraries and their efficient transfer to plasmids. Nucleic Acids Res. 1988 Sep 12;16(17):8739–8739. doi: 10.1093/nar/16.17.8739. [DOI] [PMC free article] [PubMed] [Google Scholar]
- van Seventer G. A., Spits H., Yssel H., Melief C. J., Ivanyi P. Differential recognition by human cytotoxic T cell clones of human M1 fibroblasts transfected with an HLA-B7 gene (JY150) suggests the existence of two different HLA-B7 alleles in the cell line JY (HLA-A2,2;B7,7;Cw-,-;DR4,w6). J Immunol. 1988 Jul 15;141(2):417–422. [PubMed] [Google Scholar]



