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In Arabidopsis thaliana, ∼8 million of the genome's ∼130 million basepairs are devoted to two chromosomal loci, NOR2 and NOR4. At these loci, the genes encoding the precursor transcripts of 18S, 5.8S and 25S ribosomal RNA are clustered. These gene clusters are remarkable in many ways. The ∼375 ribosomal RNA (rRNA) genes at each NOR evolve rapidly, yet do so in almost perfect synchrony with one another, a phenomenon known as concerted evolution. The rRNA genes have their own transcription system, namely that of RNA polymerase I (pol I). Transcription factors of the pol I system co-evolve with the rapidly evolving promoter sequences in an evolutionary duet of molecular recognition. At times, the rRNA genes are the most active genes in the nucleus and at other times, their transcripts are virtually undetectable. When activated, rRNA genes are the driving force for the formation of one of the cell's most recognizable features, the nucleolus. Yet rRNA genes can be silenced by mysterious (epi)genetic forces of repression in response to inter-species genetic hybridization, a phenomenon known as nucleolar dominance. The wide range of biological questions for which rRNA genes are well-suited has made these genes the focus of studies in diverse eukaryotes. Research using Arabidopsis has contributed to the understanding of eukaryotic rRNA gene chromosomal organization, evolution, transcription and epigenetic regulation. Insights gleaned from studying Arabidopsis and its relatives, in the broader context of eukaryotic rRNA gene regulation, are the focus of this review.

Transcription and Tyranny in the Nucleolus: The Organization, Activation, Dominance and Repression of Ribosomal RNA Genes.