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

Abstract

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 chromoso-mal 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. Organization and expression of rRNA genes rRNA genes and the nucleolus When one peers at a cell nucleus through a microscope (or in a textbook) one's gaze is invariably drawn to its darkest, most dense feature-the nucleolus. The nucleolus is the place where ribosomes are assembled from four rRNAs, transcribed by RNA polymerase I (18S, 5.8S, 25S rRNAs) and RNA polymerase III (5S RNA), and approximately 85 proteins whose mRNAs are transcribed by RNA poly-merase II (Scheer and Weisenberger, 1994; Shaw and Jordan, 1995). Ribosome assembly is orchestrated by a host of small nucleolar RNAs (snoRNAs), each associated with sets of specific proteins (Kiss, 2001; Ni et al., 1997; Tollervey and Kiss, 1997). These small nucleolar ribonucle-oprotein complexes (snoRPs) mediate pre-rRNA cleavage events and specify sites of post-transcriptional modifications that include RNA methylation and pseudouridylation (Leary and Huang, 2001). It is increasingly clear that the nucleolus is a hub of intracellular trafficking and RNA processing , not only for ribosomal RNAs, but also for tRNAs and mRNAs (Pederson, 1998). The fact that the nucleolus is so dense with macromolecules, processing complexes, and ribosomal subunits in various stages of assembly is what accounts for its prominence under the microscope (Wachtler and Stahl, 1993).