Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana. Arabidopsis thaliana

Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large rDNA clusters, and little is known about the contribution of each to the overall transcription. Taking advantage of genome sequencing data from the 1001 Genomes Consortium we found rRNA gene sequence variation within and among accessions, including within the highly conserved ribosomal subunits, and used linkage mapping in experimental populations to assign these variants to a particular rDNA cluster unambiguously. Using these markers, we demonstrated that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via interaction between entire rDNA cluster haplotypes (alleles).