Abstract
PCR primers of arbitrary nucleotide sequence have identified DNA polymorphisms useful for genetic mapping in a large variety of organisms. Although technically very powerful, the use of arbitrary primers for genome mapping has the disadvantage of characterizing DNA sequences of unknown function. Thus, there is no reason to anticipate that DNA fragments amplified by use of arbitrary primers will be enriched for either transcribed or promoter sequences that may be conserved in evolution. For these reasons, we modified the arbitrarily primed PCR method by using oligonucleotide primers derived from conserved promoter elements and protein motifs. Twenty-nine of these primers were tested individually and in pairwise combinations for their ability to amplify genomic DNA from a variety of species including various inbred strains of laboratory mice and Mus spretus. Using recombinant inbred strains of mice, we determined the chromosomal location of 27 polymorphic fragments in the mouse genome. The results demonstrated that motif sequence-tagged PCR products are reliable markers for mapping the mouse genome and that motif primers can also be used for genomic fingerprinting of many divergent species.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Birkenmeier, E.H. and Gordon, J.I.: Developmental regulation of a gene that encodes a cysteine-rich intestinal protein and maps near the murine immunoglobulin heavy chain locus. Proc Natl Acad Sci USA 83: 2516–2520, 1986.
Cao, Z., Umek, R.M., and McKnight, S.L.: Regulated expression of three C/EBP isoforms during adipose conversion of 3T3-L1 cells. Genes Dev 5: 1538–1552, 1991.
Cereghini, S., Raymondjean, M., Carranca, A.G., Herbomel, P., and Yaniv, M.: Factors involved in control of tissue-specific expression of albumin gene. Cell 50: 627–638, 1987.
Chang, C.-J., Chen, T.-T., Lei, H.-Y., Chen, D.-S., and Lee, S.-C.: Molecular cloning of a transcription factor, AGP/EBP, that belongs to members of the C/EBP family. Mol Cell Biol 10: 6642–6653, 1990.
Christy, R.J., Kaestner, K.H., Geiman, D.E., and Lane, M.D.: CCAAT/enhancer binding protein gene promoter; binding of nuclear factors during differentiation of 3T3-L1 preadipocytes. Proc Natl Acad Sci USA 88: 2593–2597, 1991.
Cotter, F.E., Hampton, G.M., Nasipuri, S., Bodmer, W.F., and Young, B.D.: Rapid isolation of human chromosome-specific DNA probes from a somatic cell hybrid. Genomics 7: 257–263, 1990.
Cox, R.D., Copeland, N.G., Jenkins, N.A., and Lehrach, H.: Interspersed repetitive element polymerase chain reaction product mapping using a mouse interspecific backcross. Genomics 10: 375–384, 1991.
Dorit, R.L., Schoenbach, L., and Gilbert, W.: How big is the universe of exons? Science 250: 1377–1382, 1990.
Gwynn, B., Lyford, K.A., and Birkenmeier, E.H.: Sequence conservation and structural organization of the glycerol-3-phosphate dehydrogenase promoter in mice and humans. Mol Cell Biol 10: 5244–5256, 1990.
Kamb, A., Weir, M., Rudy, B., Varmus, H., Kenyon, C.: Identification of genes from pattern formation, tyrosine kinase, and potassium channel families by DNA amplification. Proc Natl Acad Sci USA 86: 4372–4376, 1989.
Karlsson, O., Thor, S., Norberg, T., Ohlsson, H., and Edlund, T.: Insulin gene enhancer binding protein Isl-1 is a member of a novel class of proteins containing both a homeo- and a Cys-His domain. Nature 344: 879–882, 1990.
Ledbetter, S.A., Nelson, D.L., Warren, S.T., and Ledbetter, D.H.: Rapid isolation of DNA probes within specific chromosome regions by interspersed repetitive sequence polymerase chain reaction. Genomics 6: 475–481, 1990.
Love, J.M., Knight, A.M., McAleer, M.A., and Todd, J.A.: Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellites. Nucleic Acids Res 18: 4123–4130, 1990.
Nadeau, J.H., Bedigian, H.G., Bouchard, G., Denial, T., Kosowsky, M., Norberg, R., Pugh, S., Sargeant, E., Turner, R., and Paigen, B.: Multilocus markers for mouse genome analysis: PCR amplification based on single primers of arbitrary nucleotide sequence. Mammalian Genome 3: 55–64, 1992.
Nelson, D.L., Ledbetter, S.A., Corbo, L., Victoria, M.F., Ramirez-Solis, R., Webster, T.D., Ledbetter, D.H., and Caskey, C.T.: Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci USA 86: 6686–6690, 1989.
Parker, J.D., Rabinovitch, P.S., and Burmer, G.C.: Targeted gene walking polymerase chain reaction. Nucleic Acids Res 19: 3055–3060, 1991.
Roman, C., Platero, J.S., Shuman, J., and Calame, K.: Ig/EBP-1: a ubiquitously expressed immunoglobulin enhancer binding protein that is similar to C/EBP and heterodimerizes with C/EBP. Genes Dev 4: 1404–1415, 1990.
Sawadogo, M. and Van Dyke, M.W.: A rapid method for the purification of deprotected oligodeoxynucleotides. Nucleic Acids Res 19: 674, 1991.
Serikawa, T., Montagutelli, X., Simon-Chazottes, D., and Guénet, J.-L.: Polymorphisms revealed by PCR with single, short sized, arbitrary primers are reliable markers for mouse and rat gene mapping. Mammalian Genome 3: 65–72, 1992.
Silver, J.: Confidence limits for estimates of gene linkage based on analysis of recombinant inbred strains. J Hered 76: 436–440, 1985.
Taylor, B.A.: Recombinant inbred strains: use in gene mapping. In H.C. Morse (ed.), Origins of Inbred Mice, pp. 423–438, Academic Press, New York, 1978.
Weber, J.L. and May, P.E.: Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44: 388–396, 1989.
Welsh, J. and McClelland, M.: Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18: 7213–7218, 1990.
Welsh, J. and McClelland, M.: Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Res 19: 5275–5279, 1991.
Welsh, J., Petersen, C., and McClelland, M.: Polymorphisms generated by arbitrarily primed PCR in the mouse: application to strain identification and genetic mapping. Nucleic Acids Res 19: 303–306, 1991.
Williams, J.G.K., Kubelik. A.R., Livak, K.J., Rafalski, J.A., and Tingey, S.V.: DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18: 6531–6535, 1990.
Williams, S.C., Cantwell, C.A., and Johnson, P.F.: A family of C/EBP-related proteins capable of forming covalently linked leucine zipper dimers in vitro. Genes Dev 5: 1553–1567, 1991.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Birkenmeier, E.H., Schneider, U. & Thurston, S.J. Fingerprinting genomes by use of PCR with primers that encode protein motifs or contain sequences that regulate gene expression. Mammalian Genome 3, 537–545 (1992). https://doi.org/10.1007/BF00350618
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00350618