RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: Tests of transcription factor involvement in nucleolar dominance

In interspecific hybrids or allopolyploids, often one parental set of ribos omal RNA genes is transcribed and the other is silent, an epigenetic phenom enon known as nucleolar dominance. Silencing is enforced by cytosine methyl ation and histone deacetylation, but the initial discrimination mechanism i s unknown. One hypothesis is that a species-specific transcription factor i s inactivated, thereby silencing one set of rRNA genes. Another is that dom inant rRNA genes have higher binding affinities for limiting transcription factors. A third suggests that selective methylation of underdominant rRNA genes blocks transcription factor binding. We tested these hypotheses using Brassica napus (canola), an allotetraploid derived from B. rapa and B. ole racea in which only B. rapa rRNA genes are transcribed. B. oleracea and B. rapa rRNA genes were active when transfected into protoplasts of the other species, which argues against the species-specific transcription factor mod el. B. oleracea and B. rapa rRNA genes also competed equally for the pol I transcription machinery in vitro and in vivo. Cytosine methylation had no e ffect on rRNA gene transcription in vitro, which suggests that transcriptio n factor binding was unimpaired. These data are inconsistent with the preva iling models and point to discrimination mechanisms that are likely to act at a chromosomal level.