title: Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  Given 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.
  
  
  CONCLUSIONS
  The 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.
authors.forename: Qing
authors.initials: Q
authors.lastname: Wang
authors.forename: Chance M
authors.initials: CM
authors.lastname: Nowak
authors.forename: Asawari
authors.initials: A
authors.lastname: Korde
authors.forename: Dong-Ha
authors.initials: DH
authors.lastname: Oh
authors.forename: Maheshi
authors.initials: M
authors.lastname: Dassanayake
authors.forename: David
authors.initials: D
authors.lastname: Donze
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000235:genetics; D002874:Chromosome Mapping; D021901:DNA, Intergenic / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D056426:Genetic Loci; D016681:Genome, Fungal; D005838:Genotype; D016366:Open Reading Frames / Q000235:genetics; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012320:RNA Polymerase III / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics*; D017423:Sequence Analysis, RNA; D019474:Transcription Factors, TFIII / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D059467:Transcriptome; D000098832:Transcription Factor TFIIIC
chemical_list: D002843:Chromatin; D021901:DNA, Intergenic; D019474:Transcription Factors, TFIII; D000098832:Transcription Factor TFIIIC; D012319:RNA Polymerase II; D012320:RNA Polymerase III