Nucleosome depletion activates poised RNA polymerase III at unconventional transcription sites in Saccharomyces cerevisiae.
RNA polymerase (pol) III, assisted by the transcription factors TFIIIC and TFIIIB, transcribes small untranslated RNAs, such as tRNAs. In addition to known pol III-transcribed genes, the Saccharomyces cerevisiae genome contains loci (ZOD1, ETC1-8) associated to incomplete pol III transcription complexes (Moqtaderi, Z., and Struhl, K. (2004) Mol. Cell. Biol. 24, 4118-4127). We show that a short segment of the ZOD1 locus, containing box A and box B promoter elements and a termination signal between them, directs the pol III-dependent production of a small RNA both in vitro and in vivo. In yeast cells, the levels of both ZOD1- and ETC5-specific transcripts were dramatically enhanced upon nucleosome depletion. Remarkably, transcription factor and pol III occupancy at the corresponding loci did not change significantly upon derepression, thus suggesting that chromatin opening activates poised pol III to transcription. Comparative genomic analysis revealed that the ZOD1 promoter is the only surviving portion of a tDNA(Ile) ancestor, whose transcription capacity has been preserved throughout evolution independently from the encoded RNA product. Similarly, another TFIIIC/TFIIIB-associated locus, close to the YGR033c open reading frame, was found to be the strictly conserved remnant of an ancient tDNA(Arg). The maintenance, by eukaryotic genomes, of chromatin-repressed, non-coding transcription units has implications for both genome expression and organization.
Guffanti
Elisa
E
Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, 43100 Parma, Italy.
Percudani
Riccardo
R
Harismendy
Olivier
O
Soutourina
Julie
J
Werner
Michel
M
Iacovella
Maria Giuseppina
MG
Negri
Rodolfo
R
Dieci
Giorgio
G
D001483:Base Sequence; D002843:Chromatin / Q000737:chemistry; D004247:DNA / Q000378:metabolism; D016681:Genome, Fungal; D008836:Micrococcal Nuclease / Q000378:metabolism; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism*; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012320:RNA Polymerase III / Q000737:chemistry* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic
D002843:Chromatin; D009707:Nucleosomes; D004247:DNA; D012320:RNA Polymerase III; D008836:Micrococcal Nuclease