title: Retrotransposon profiling of RNA polymerase III initiation sites.
abstract: Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III-transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III-transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes.
authors.affiliation: Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697, USA.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Qi
authors.forename: Kenneth
authors.initials: K
authors.lastname: Daily
authors.forename: Kim
authors.initials: K
authors.lastname: Nguyen
authors.forename: Haoyi
authors.initials: H
authors.lastname: Wang
authors.forename: David
authors.initials: D
authors.lastname: Mayhew
authors.forename: Paul
authors.initials: P
authors.lastname: Rigor
authors.forename: Sholeh
authors.initials: S
authors.lastname: Forouzan
authors.forename: Mark
authors.initials: M
authors.lastname: Johnston
authors.forename: Robi David
authors.initials: RD
authors.lastname: Mitra
authors.forename: Pierre
authors.initials: P
authors.lastname: Baldi
authors.forename: Suzanne
authors.initials: S
authors.lastname: Sandmeyer
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004258:DNA Polymerase III / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D020411:Oligonucleotide Array Sequence Analysis; D011995:Recombination, Genetic; D018626:Retroelements / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D035361:Transcription Factor TFIIIB / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: C491232:POL3 protein, S cerevisiae; D018626:Retroelements; D029701:Saccharomyces cerevisiae Proteins; D035361:Transcription Factor TFIIIB; D004258:DNA Polymerase III