Abundance of oligo-dC/oligo-dG runs in the genomes of maize and other eukaryotes

The existence of "specious positive" genomic sequences, clones for which are frequently recovered by annealing of oligo-dC/oligo-dG tails in cDNA plasmids to genomic sequences (see MNL 60:72, 1986), has been further investigated. Quantification of the frequency of such sequences in maize DNA was performed by plating a maize phage-l genomic DNA library at several dilutions and challenging for positive plaques with 32P end-labelled synthetic oligo-dC probe. The result is that 2% of all clones from such a library (average insert size 15,000 ntp) contain at least one oligo-dC/oligo-dG run. Such clones are readily detectable after brief radioautographic exposures and appear as strong positives on an overnight radioautogram. Of twelve specious positive clones recovered as phage which were examined on Southern transfers, one contained two positive fragments, suggesting the possibility that there may be some clustering of such regions in the genome. It thus appears that oligo-dC/oligo-dG runs are a widely distributed component of the maize genome.

We felt it would be of interest to determine whether this situation was peculiar to maize. Accordingly, we have examined the occurrence of such regions in other selected eukaryote genomes by comparing the relative intensity of hybridization to the synthetic probe of their DNAs with that seen for maize DNA. While the exact relative quantification is still preliminary, it is evident that such sequences are a widespread feature of higher eukaryote genomes, although their abundance varies considerably. Among monocotyledonous plants, wheat (Triticum aestivum), the closest relative to maize examined, has about three times the maize abundance per unit weight of DNA of oligo-dC probe positive sequences. Of other selected monocots, Allium cepa has about one-third the oligo-dC probe positive sequence abundance of maize, while Yucca schidigera and Asparagus officinalis have 4-5 times the abundance of maize. Abundancy differences may occur over short evolutionary distances, since in the genus Lilium the species L. speciosum shows four times the abundance of oligo-dC probe positive sequences as L. henryi or L. longiflorum. Oligo-dC probe positive sequences are also a feature of some dicotyledonous plant genomes, occurring in Nicotiana tabacum and Hypochaeris radicata with about twice the abundance seen in maize. In addition, they are present at significant levels in some animal genomes, such as D. melanogaster (at comparable concentration to maize) and salmon sperm DNA (Salmo ssp.) (at very high abundance; at least 25 times that seen in maize). Oligo-dC probe positive sequences are however relatively rare in some eukaryotic DNAs, such as those of Phaseolus vulgaris and Bos taurus, both of which show less than one-tenth the maize abundance; and they are entirely absent from the DNA of the prokaryotes E. coli and phage l.

The biological significance of these sequences, if any, remains to be elucidated. Two sets of observations do suggest that their presence could have some impact on the genome. The presence of such short oligo-dC/oligo-dG runs has been shown to induce altered conformation upon neighboring regions when the DNA is placed under torsional stress (Kowhi-Shigematsu and Kowhi, Cell 43:199, 1985). Such runs also may positively influence the level of action of meiotic recombinase enzymes on DNAs containing them (Hotta & Bouchard, unpublished). In any event, as we have previously noted, the existence of such sites presents an important practical problem for workers using heterologous plasmid probes containing inserts with oligo-dC/oligo-dG tails (as many cDNA plasmids do) for the purpose of recovering maize genomic clones containing genes with sequence homology to those inserts. This caveat from maize should now be generalized to a number of other organisms, a number of which also have some degree of genetic interest.

Robert A. Bouchard, Michael McKeown and John S. Parker

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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