Spatial organization of transcription by RNA polymerase III

Abstract

RNA polymerase III (pol III) transcribes many essential, small, noncoding RNAs, including the 5S rRNAs and tRNAs. While most pol III-transcribed genes are found scattered throughout the linear chromosome maps or in multiple linear clusters, there is increasing evidence that many of these genes prefer to be spatially clustered, often at or near the nucleolus. This association could create an environment that fosters the coregulation of transcription by pol III with transcription of the large ribosomal RNA repeats by RNA polymerase I (pol I) within the nucleolus. Given the high number of pol III-transcribed genes in all eukaryotic genomes, the spatial organization of these genes is likely to affect a large portion of the other genes in a genome. In this Survey and Summary we analyze the reports regarding the spatial organization of pol III genes and address the potential influence of this organization on transcriptional regulation.

Figure 1

In situ hybridization using short, oligonucleotide probes reveals that tRNA genes (red) overlap 5S genes (green) at the nucleolus. DAPI staining of chromatin is shown in blue. tRNA genes and 5S genes are both transcribed by RNA polymerase III and they also share the same transcription factors, although 5S genes require one additional factor, TFIIIA. Gene colors in the line drawings correspond to image pseudocoloring, while protein colors are arbitrary. Co-localization of tRNA and 5S genes may provide a basis for coregulation of their transcription with one another. Further, nucleolar co-localization of these genes might facilitate allows coordination of transcription with another heavily expressed component of the protein synthesis machinery, the large ribosomal RNA gene repeats that are by RNA polymerase I. With the current resolution it is not possible to conclusively interpret whether signals from tRNA and 5S genes are coincident or adjacent. Figure courtesy of Martin Thompson.