title: Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall.
abstract: In eukaryotic cells, DNA replication proceeds with continuous synthesis of leading-strand DNA and discontinuous synthesis of lagging-strand DNA. Here we describe a method, eSPAN (enrichment and sequencing of protein-associated nascent DNA), which reveals the genome-wide association of proteins with leading and lagging strands of DNA replication forks. Using this approach in budding yeast, we confirm the strand specificities of DNA polymerases delta and epsilon and show that the PCNA clamp is enriched at lagging strands compared with leading-strand replication. Surprisingly, at stalled forks, PCNA is unloaded specifically from lagging strands. PCNA unloading depends on the Elg1-containing alternative RFC complex, ubiquitination of PCNA, and the checkpoint kinases Mec1 and Rad53. Cells deficient in PCNA unloading exhibit increased chromosome breaks. Our studies provide a tool for studying replication-related processes and reveal a mechanism whereby checkpoint kinases regulate strand-specific unloading of PCNA from stalled replication forks to maintain genome stability.
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Chuanhe
authors.initials: C
authors.lastname: Yu
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Haiyun
authors.initials: H
authors.lastname: Gan
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Junhong
authors.initials: J
authors.lastname: Han
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Zhi-Xiong
authors.initials: ZX
authors.lastname: Zhou
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
authors.forename: Shaodong
authors.initials: S
authors.lastname: Jia
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
authors.forename: Andrei
authors.initials: A
authors.lastname: Chabes
authors.affiliation: Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Gianrico
authors.initials: G
authors.lastname: Farrugia
authors.affiliation: Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Tamas
authors.initials: T
authors.lastname: Ordog
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA. Electronic address: zhang.zhiguo@mayo.edu.
authors.forename: Zhiguo
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D047369:Chromatin Immunoprecipitation; D015825:Chromosomes, Fungal / Q000235:genetics; D004249:DNA Damage; D004257:DNA Polymerase II / Q000378:metabolism; D004258:DNA Polymerase III / Q000378:metabolism; D004261:DNA Replication; D004271:DNA, Fungal / Q000096:biosynthesis* / Q000235:genetics; D042822:Genomic Instability; D018809:Proliferating Cell Nuclear Antigen / Q000378:metabolism*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D054875:Ubiquitination
chemical_list: D004271:DNA, Fungal; D018809:Proliferating Cell Nuclear Antigen; D029701:Saccharomyces cerevisiae Proteins; D004257:DNA Polymerase II; D004258:DNA Polymerase III