title: Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress.
abstract: Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1-Ddc2 (ATR-ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription-replication fork collision.
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Jérôme
authors.initials: J
authors.lastname: Poli
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Christian-Benedikt
authors.initials: CB
authors.lastname: Gerhold
authors.affiliation: Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany;
authors.forename: Alessandro
authors.initials: A
authors.lastname: Tosi
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Nicole
authors.initials: N
authors.lastname: Hustedt
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Andrew
authors.initials: A
authors.lastname: Seeber
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Ragna
authors.initials: R
authors.lastname: Sack
authors.affiliation: Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany;
authors.forename: Franz
authors.initials: F
authors.lastname: Herzog
authors.affiliation: UPR 1142, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 30396 Montpellier, France;
authors.forename: Philippe
authors.initials: P
authors.lastname: Pasero
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;
authors.forename: Kenji
authors.initials: K
authors.lastname: Shimada
authors.affiliation: Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany;
authors.forename: Karl-Peter
authors.initials: KP
authors.lastname: Hopfner
authors.affiliation: Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Gasser
mesh_terms: D004261:DNA Replication / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: C483404:INO80 complex, S cerevisiae; D047908:Intracellular Signaling Peptides and Proteins; D009687:Nuclear Proteins; C097698:PAF1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C088937:MEC1 protein, S cerevisiae; D017346:Protein Serine-Threonine Kinases; D012319:RNA Polymerase II
keywords: INO80; RNAPII; checkpoint; genome instability; replication stress; transcription–replication interference