Abstract
Several transposable elements (TEs) have been reported in association with genes in maize and other plants. In this study we found, based on statistical analyses of 951 DNA sequences within a maize computer database, that short hexamer and pentamer DNA motifs from the Activator (Ac) and from the Tourist TEs, respectively, were also associated with maize genes. Moreover, these two short hexamer and pentamer TE motifs were nonrandomly and nearly nonrandomly distributed, respectively, with respect to particular biochemical functions of those maize genes. To determine whether this distribution may be unique to TE motifs, or may be more widespread among hexamers/pentamers in general, we similarly studied six additional hexamer or pentamer sequences not derived from TEs. These also showed nonrandom distribution with respect to functional gene categories in the maize database. However, each of the total of eight short sequence motifs we studied differed in its pattern of association with distinct sets of functional gene categories; that is, there was a unique ‘signature’ for each of the hexamers and pentameters tested. Potential biological hypotheses to explain these findings are discussed.
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Alfenito, M.R. & J.A. Birchler, 1993. Molecular characterization of a maize B chromosome centric sequence. Genetics 135: 589–597.
Becker, H.A. & R. Kunze, 1996. Binding sites for maize nuclear proteins in the subterminal regions of the transposable element Activator. Mol. Gen. Genet. 251: 428–435.
Becker, H.A. & R. Kunze, 1997. Maize Activator transposase has a bipartite DNA binding domain that recognizes subterminal sequences and the terminal inverted repeats. Mol. Gen. Genet. 254: 219–230.
Bravo-Angel, A.M., H.A. Becker, R. Kunze, B. Hohn & W.H. Shen, 1995. The binding motifs for Ac transposase are absolutely required for excision of Ds1 in maize. Mol. Gen. Genet. 248: 527–534.
Bult, C.J., O. White, G.J. Olsen et al. (40 co-authors), 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058–1073.
Bureau, T.E., P.C. Ronald & S.R. Wessler, 1996. A computerbased systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl. Acad. Sci. USA 93: 8524–8529.
Bureau, T.E. & S.R. Wessler, 1992. Tourist: A large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4: 1283–1294.
Bureau, T.E. & S.R. Wessler, 1994a. Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc. Natl. Acad. Sci. USA 91: 1411–1415.
Bureau, T.E. & S.R. Wessler, 1994b. Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6: 907–916.
Cochran, W.G., 1954. Some methods for strengthening the common ξ2 test. Biometrics 10: 417–451.
Devereux, J., P. Haeberli & O. Smithies, 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387–395.
Fleischmann, R.D., M.D. Adams, O. White et al. (40 co-authors), 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496–512.
Fraser, C.M., J.D. Gocayne, O. White et al. (29 co-authors), 1995. The minimal gene complement of Mycoplasma genitalium. Science 270: 397–403.
Kunze, R., 1996. The maize transposable element Activator (Ac). Curr. Top. Microbio. Immunol. 204: 161–194.
Kunze, R. & P. Stralinger, 1989. The putative transposase of transposable element Ac from Zea mays L. interacts with subterminal sequences of Ac. EMBO J. 8: 3177–3185.
MacRae, A.F., 1998. A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook). Genome 41: 553–559.
Marks, M.D., J.S. Lindell & B.A. Larkins, 1985. Nucleotide sequence analysis of zein mRNAs from maize endosperm. J. Biol. Chem. 260: 16451–16459.
Mathews, C.K. & K.E. Van Holde, 1996. Biochemistry. 2nd edition, Benjamin/Cummings Menlo Park, California.
Pearson, W.R. & D.J. Lipman, 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85: 2444–2448.
Pozueta-Romero, J., G. Houlne & R. Schantz, 1996. Nonautonomous inverted repeat Alien transposable elements are associated with genes of both monocotyledonous and dicotyledonous plants. Gene 171: 147–153.
Wessler, S.R., T.E. Bureau & S.E. White, 1995. LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814–821.
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MacRae, A.F., Birch, R.M. & Bange, R.H. Analysis of hexamer and pentamer motifs within a maize database: the presence of motif ‘signatures’ in functional gene categories. Genetica 105, 19–29 (1999). https://doi.org/10.1023/A:1003559310976
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DOI: https://doi.org/10.1023/A:1003559310976