Strand-Specific Analysis Shows Protein Binding at Replication Forks and PCNA Unloading from Lagging Strands when Forks Stall

• Published in: Molecular cell Vol. 56; no. 4; pp. 551 - 563
• Main Authors: Yu, Chuanhe, Gan, Haiyun, Han, Junhong, Zhou, Zhi-Xiong, Jia, Shaodong, Chabes, Andrei, Farrugia, Gianrico, Ordog, Tamas, Zhang, Zhiguo
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 20-11-2014
• Subjects: 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
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2014.09.017

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.
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•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.