PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes

• Published in: Nature communications 2017-04, Vol.8 (1), p.15025-15025, Article 15025
• Main Authors: Tran, Phong Lan Thao, Pohl, Thomas J., Chen, Chi-Fu, Chan, Angela, Pott, Sebastian, Zakian, Virginia A.
• Format: Article
• Language: English
• Subjects: 45/15; 45/41; 631/337/1427; 631/337/151/2357; Biochemistry, Molecular Biology; DNA Damage; DNA Helicases - genetics; DNA Helicases - metabolism; DNA Replication; DNA, Fungal - genetics; DNA, Fungal - metabolism; Gene Expression Regulation, Fungal; Genes; Genome, Fungal; Genomes; Genomic Instability; Humanities and Social Sciences; Laboratories; Life Sciences; Mitochondrial DNA; multidisciplinary; Mutation; Nucleic Acid Conformation; Protein Binding; Proteins; Recombinational DNA Repair; RNA polymerase; RNA, Transfer - genetics; RNA, Transfer - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Telomerase; Transfer RNA; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms15025

Saccharomyces cerevisiae encodes two Pif1 family DNA helicases, Pif1 and Rrm3. Rrm3 promotes DNA replication past stable protein complexes at tRNA genes (tDNAs). We identify a new role for the Pif1 helicase: promotion of replication and suppression of DNA damage at tDNAs. Pif1 binds multiple tDNAs, and this binding is higher in rrm3 Δ cells. Accumulation of replication intermediates and DNA damage at tDNAs is higher in pif1 Δ rrm3 Δ than in rrm3 Δ cells. DNA damage at tDNAs in the absence of these helicases is suppressed by destabilizing R-loops while Pif1 and Rrm3 binding to tDNAs is increased upon R-loop stabilization. We propose that Rrm3 and Pif1 promote genome stability at tDNAs by displacing the stable multi-protein transcription complex and by removing R-loops. Thus, we identify tDNAs as a new source of R-loop-mediated DNA damage. Given their large number and high transcription rate, tDNAs may be a potent source of genome instability. The budding yeast genome encodes two Pif1 family helicases, Pif1 and Rrm3, previously shown to have distinct functions in the maintenance of telomeres and other aspects of genome stability. Here the authors identify a role for Pif1 (and Rrm3) in promoting DNA replication and suppressing R-loop mediated DNA damage at tRNA genes.