Analysis of hexamer and pentamer motifs within a maize database: the presence of motif 'signatures' in functional gene categories.
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.
MacRae
A F
AF
Department of Biology, University of Missouri-St. Louis 63121, USA. SAFMACR@JINX.UMSL.EDU
Birch
R M
RM
Bange
R H
RH
D004251:DNA Transposable Elements; D016208:Databases, Factual; D008957:Models, Genetic; D011897:Random Allocation; D015183:Restriction Mapping; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements