Gene dosage and stochastic effects determine the severity and direction ofuniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids

Nucleolar dominance is an epigenetic phenomenon in which one parental set o f ribosomal RNA (rRNA) genes is silenced in an interspecific hybrid. In nat ural Arabidopsis suecica, an allotetraploid (amphidiploid) hybrid of Arabid opsis thaliana and Cardaminopsis arenosa, the A. thaliana rRNA genes are re pressed. Interestingly, A. thaliana rRNA gene silencing is variable in synt hetic Arabidopsis suecica Fl hybrids. Two generations are needed for A. tha liana rRNA genes to be silenced in all lines, revealing a species-biased di rection but stochastic onset to nucleolar dominance. Backcrossing synthetic A. suecica to tetraploid A. thaliana yielded progeny with active A. thalia na rRNA genes and, in some cases, silenced C. arenosa rRNA genes, showing t hat the direction of dominance can be switched, The hypothesis that natural ly dominant rRNA genes have a superior binding affinity for a limiting tran scription factor is inconsistent with dominance switching. Inactivation of a species-specific transcription factor is argued against by showing that A . thaliana and C. arenosa rRNA genes can be expressed transiently in the ot her species. Transfected A. thaliana genes are also active in A. suecica pr otoplasts in which chromosomal A. thaliana genes are repressed. Collectivel y these data suggest that nucleolar dominance is a chromosomal phenomenon t hat results in coordinate or cooperative silencing of rRNA genes.