Strand-Specific Analysis Shows Protein Binding at Replication Forks and PCNA Unloading from Lagging Strands when Forks Stall
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...
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Published in | Molecular cell Vol. 56; no. 4; pp. 551 - 563 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
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United States
Elsevier Inc
20.11.2014
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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.
[Display omitted]
•eSPAN is a method to detect proteins with strand specificity at replication forks•PCNA is unloaded from lagging strands when forks stall under replication stress•PCNA unloading depends on Elg1, PCNA ubiquitylation, and checkpoint kinases•PCNA unloading contributes to genome stability maintenance
DNA replication proceeds with continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand. Yu et al. describe eSPAN, a method to measure relative amounts of proteins on the leading and lagging strands of replication forks, which they use to show that PCNA is unloaded from lagging strands of stalled forks. |
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AbstractList | 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. 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. 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. [Display omitted] •eSPAN is a method to detect proteins with strand specificity at replication forks•PCNA is unloaded from lagging strands when forks stall under replication stress•PCNA unloading depends on Elg1, PCNA ubiquitylation, and checkpoint kinases•PCNA unloading contributes to genome stability maintenance DNA replication proceeds with continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand. Yu et al. describe eSPAN, a method to measure relative amounts of proteins on the leading and lagging strands of replication forks, which they use to show that PCNA is unloaded from lagging strands of stalled forks. |
Author | Jia, Shaodong Han, Junhong Zhang, Zhiguo Gan, Haiyun Farrugia, Gianrico Zhou, Zhi-Xiong Yu, Chuanhe Chabes, Andrei Ordog, Tamas |
AuthorAffiliation | 4 Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA 1 Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA 2 Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden 3 Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA |
AuthorAffiliation_xml | – name: 3 Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – name: 4 Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – name: 1 Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – name: 2 Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden |
Author_xml | – sequence: 1 givenname: Chuanhe surname: Yu fullname: Yu, Chuanhe organization: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 2 givenname: Haiyun surname: Gan fullname: Gan, Haiyun organization: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 3 givenname: Junhong surname: Han fullname: Han, Junhong organization: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 4 givenname: Zhi-Xiong surname: Zhou fullname: Zhou, Zhi-Xiong organization: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 5 givenname: Shaodong surname: Jia fullname: Jia, Shaodong organization: Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden – sequence: 6 givenname: Andrei surname: Chabes fullname: Chabes, Andrei organization: Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden – sequence: 7 givenname: Gianrico surname: Farrugia fullname: Farrugia, Gianrico organization: Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 8 givenname: Tamas surname: Ordog fullname: Ordog, Tamas organization: Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA – sequence: 9 givenname: Zhiguo surname: Zhang fullname: Zhang, Zhiguo email: zhang.zhiguo@mayo.edu organization: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA |
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SubjectTerms | Chromatin Immunoprecipitation Chromosomes, Fungal - genetics DNA Damage DNA Polymerase II - metabolism DNA Polymerase III - metabolism DNA Replication DNA, Fungal - biosynthesis DNA, Fungal - genetics Genomic Instability Proliferating Cell Nuclear Antigen - metabolism Protein Binding Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae Proteins - metabolism Sequence Analysis, DNA Ubiquitination |
Title | Strand-Specific Analysis Shows Protein Binding at Replication Forks and PCNA Unloading from Lagging Strands when Forks Stall |
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