Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae

Chance M Nowak,Qing Wang,Asawari Korde,Maheshi Dassanayake,Dong-Ha Oh,David Donze

doi:10.1186/preaccept-1938943002141624

Abstract

BackgroundAssembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. These properties have been designated as `extra-transcriptional' effects of the Pol III complex. Previous coding sequence microarray studies using Pol III factor mutants to determine global effects of Pol III complex assembly on Pol II promoter activity revealed only modest effects that did not correlate with the proximity of Pol III complex binding sites.ResultsGiven our recent results demonstrating that tDNAs block progression of intergenic Pol II transcription, we hypothesized that extra-transcriptional effects within intergenic regions were not identified in the microarray study. To reconsider global impacts of Pol III complex binding, we used RNA sequencing to compare transcriptomes of wild type versus Pol III transcription factor TFIIIC depleted mutants. The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5'- and 3'-extended transcripts, and de-repression of adjacent genes and intergenic regions.ConclusionsThe results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. The results may also be relevant to synthetic biology efforts to design a minimal yeast genome.

Highlights

Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes
Mapping and analysis of RNA-Seq reads in wild type and tfc6-under-expressing strains To assess the genomic impact of RNA Pol III complex assembly on neighboring Pol II genes, we performed high-throughput RNA-Seq of ribosomal RNA depleted samples from two types of yeast strains: wild type and Tfc6p-under-expressing strains
The results presented here suggest that the presence or absence of DNA-bound Pol III complexes has a clear impact on neighboring chromosomal regions, as Pol II transcription start and termination sites near TFIIIC binding sites are altered in the tfc6 and specific B-box mutant strains

Summary

Introduction

Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. RNA polymerase III (Pol III) transcribes genes encoding small non-translated RNAs, which in the budding yeast Saccharomyces cerevisiae includes transfer RNAs (tRNAs), 5S ribosomal RNA (5S rRNA), 7SL RNA, U6 spliceosome RNA, snR52 small nucleolar RNA as well as the RNA component of RNaseP [1,2,3]. These diverse genes contain three types of promoter element arrangements. These sequences serve as binding sites for the multi-subunit transcription factor TFIIIC [4,5,6]

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