Genome-Wide Occupancy Profile of the RNA Polymerase III Machinery in Saccharomyces cerevisiae Reveals Loci with Incomplete Transcription Complexes

Abstract

We used chromatin immunoprecipitation, followed by microarray hybridization, to determine the genome-wide distribution of the RNA polymerase (Pol) III transcription apparatus in the yeast Saccharomyces cerevisiae. The Pol III transcriptome includes all tRNA genes, previously identified non-tRNA Pol III genes, and SNR52, which encodes a small nucleolar RNA. Unexpectedly, we identify eight ETC loci that are occupied by TFIIIC but not by other components of the Pol III machinery. Some ETC loci contain stretches of DNA that are highly conserved among closely related yeast species, suggesting that they may encode functional RNAs. ETC6 is located upstream of the gene encoding the τ 91 subunit of TFIIIC, suggesting the possibility of Pol III-regulated expression of a critical Pol III factor. We also identify the ZOD1 locus, which is bound by all components of the Pol III machinery and yet does not appear to express an RNA conserved among closely related yeast species. The B block motifs and several flanking nucleotides of the ZOD1 and ETC loci are very similar to each other and are highly conserved across the yeast species. Furthermore, the unusual profile of Pol III factor association with ZOD1 and the ETC loci is perfectly preserved in a different Saccharomyces species, indicating that these loci represent novel functional entities.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/.

We thank Matthew Copeland for amplifying the PCR products representing the yeast intergenic regions, Klaus Ullmann for spotting them on glass slides, Ian Willis and Steve Hahn for antibodies, and Mark Johnston for the S. mikatae strain. We are grateful to Joseph “Rufus” Geisberg for early help in determining the Pol specificity of snRNAs and for insightful discussion. We thank Sharyl Wong for a computer program to cross-reference microarray data and gene names. We thank Joe Wade for expert technical assistance, Fred Winston for advice on yeast gene nomenclature, and Dan Hall, Paul Mason, Ned Sekinger, and Joe Wade for helpful discussions.

This study was supported by grants to K.S. from the National Institutes of Health (GM30186).