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Restriction fragments of yeast rDNA retained by purified RNA polymerases on nitrocellulose filters were analysed by gel electrophoresis. The EcoRI fragment B was preferentially retained by RNA polymerase I, but not by RNA polymerase III. The in vivo initiation sites for both polymerases are located within this fragment. Further analysis indicated that the preferred binding site for RNA polymerase I is highly AT-rich regions rather than a true promoter. The reported selective in vitro transcription of rDNA by purified yeast RNA polymerase I could then be explained by this preferential binding.

Yeast RNA polymerase I binds preferentially to A+T-rich linkers in rDNA