SIRF: Quantitative in situ analysis of protein interactions at DNA replication forks

DNA replication reactions are central to diverse cellular processes including development, cancer etiology, drug treatment, and resistance. Many proteins and pathways exist to ensure DNA replication fidelity and protection of stalled or damaged replication forks. Consistently, mutations in proteins...

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Published inThe Journal of cell biology Vol. 217; no. 4; pp. 1521 - 1536
Main Authors Roy, Sunetra, Luzwick, Jessica W, Schlacher, Katharina
Format Journal Article
LanguageEnglish
Published United States Rockefeller University Press 02.04.2018
Subjects
Aging
Animals
Binding Sites
Blood diseases
Breast Neoplasms - genetics
Breast Neoplasms - metabolism
Cancer
Chemical synthesis
Deoxyribonucleic acid
DNA
DNA biosynthesis
DNA Breaks, Double-Stranded
DNA Replication
DNA, Neoplasm - biosynthesis
DNA, Neoplasm - genetics
Embryogenesis
Embryonic growth stage
Etiology
Female
Fibroblasts - metabolism
Humans
Immunity
Immunity (Disease)
Kinetics
Male
MCF-7 Cells
Mice, Inbred C57BL
Microscopy, Fluorescence
Molecular biology
Mutation
Organic chemistry
Protein Binding
Protein interaction
Proteins
Quantitation
Quantitative analysis
Replication
Replication forks
Sensitivity analysis
Single-Cell Analysis - methods
Substance abuse treatment
Tumor Suppressor p53-Binding Protein 1 - genetics
Tumor Suppressor p53-Binding Protein 1 - metabolism
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Abstract DNA replication reactions are central to diverse cellular processes including development, cancer etiology, drug treatment, and resistance. Many proteins and pathways exist to ensure DNA replication fidelity and protection of stalled or damaged replication forks. Consistently, mutations in proteins involved in DNA replication are implicated in diverse diseases that include defects during embryonic development and immunity, accelerated aging, increased inflammation, blood disease, and cancer. Thus, tools for efficient quantitative analysis of protein interactions at active and stalled replication forks are key for advanced and accurate biological understanding. Here we describe a sensitive single-cell-level assay system for the quantitative analysis of protein interactions with nascent DNA. Specifically, we achieve robust in situ analysis of protein interactions at DNA replication forks (SIRF) using proximity ligation coupled with 5'-ethylene-2'-deoxyuridine click chemistry suitable for multiparameter analysis in heterogeneous cell populations. We provide validation data for sensitivity, accuracy, proximity, and quantitation. Using SIRF, we obtained new insight on the regulation of pathway choice by 53BP1 at transiently stalled replication forks.
AbstractList Roy et al. describe a novel assay to measure direct protein associations at active and stalled DNA replication forks, called in situ analysis of protein interactions at DNA replication forks. The EdU-chase, click-chemistry, and PLA-composite system is quantitative, sensitive, and effective, with single-cell resolution suitable for concomitant multiparameter analysis. DNA replication reactions are central to diverse cellular processes including development, cancer etiology, drug treatment, and resistance. Many proteins and pathways exist to ensure DNA replication fidelity and protection of stalled or damaged replication forks. Consistently, mutations in proteins involved in DNA replication are implicated in diverse diseases that include defects during embryonic development and immunity, accelerated aging, increased inflammation, blood disease, and cancer. Thus, tools for efficient quantitative analysis of protein interactions at active and stalled replication forks are key for advanced and accurate biological understanding. Here we describe a sensitive single-cell–level assay system for the quantitative analysis of protein interactions with nascent DNA. Specifically, we achieve robust in situ analysis of protein interactions at DNA replication forks (SIRF) using proximity ligation coupled with 5′-ethylene-2′-deoxyuridine click chemistry suitable for multiparameter analysis in heterogeneous cell populations. We provide validation data for sensitivity, accuracy, proximity, and quantitation. Using SIRF, we obtained new insight on the regulation of pathway choice by 53BP1 at transiently stalled replication forks.
DNA replication reactions are central to diverse cellular processes including development, cancer etiology, drug treatment, and resistance. Many proteins and pathways exist to ensure DNA replication fidelity and protection of stalled or damaged replication forks. Consistently, mutations in proteins involved in DNA replication are implicated in diverse diseases that include defects during embryonic development and immunity, accelerated aging, increased inflammation, blood disease, and cancer. Thus, tools for efficient quantitative analysis of protein interactions at active and stalled replication forks are key for advanced and accurate biological understanding. Here we describe a sensitive single-cell-level assay system for the quantitative analysis of protein interactions with nascent DNA. Specifically, we achieve robust in situ analysis of protein interactions at DNA replication forks (SIRF) using proximity ligation coupled with 5'-ethylene-2'-deoxyuridine click chemistry suitable for multiparameter analysis in heterogeneous cell populations. We provide validation data for sensitivity, accuracy, proximity, and quantitation. Using SIRF, we obtained new insight on the regulation of pathway choice by 53BP1 at transiently stalled replication forks.
Author Schlacher, Katharina
Luzwick, Jessica W
Roy, Sunetra
AuthorAffiliation Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX
AuthorAffiliation_xml – name: Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX
Author_xml – sequence: 1
  givenname: Sunetra
  surname: Roy
  fullname: Roy, Sunetra
  organization: Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX
– sequence: 2
  givenname: Jessica W
  surname: Luzwick
  fullname: Luzwick, Jessica W
  organization: Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX
– sequence: 3
  givenname: Katharina
  orcidid: 0000-0001-7226-6391
  surname: Schlacher
  fullname: Schlacher, Katharina
  email: kschlacher@mdanderson.org
  organization: Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX kschlacher@mdanderson.org
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29475976$$D View this record in MEDLINE/PubMed
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Snippet DNA replication reactions are central to diverse cellular processes including development, cancer etiology, drug treatment, and resistance. Many proteins and...
Roy et al. describe a novel assay to measure direct protein associations at active and stalled DNA replication forks, called in situ analysis of protein...
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SourceType Open Access Repository
Aggregation Database
Index Database
StartPage 1521
SubjectTerms Aging
Animals
Binding Sites
Blood diseases
Breast Neoplasms - genetics
Breast Neoplasms - metabolism
Cancer
Chemical synthesis
Deoxyribonucleic acid
DNA
DNA biosynthesis
DNA Breaks, Double-Stranded
DNA Replication
DNA, Neoplasm - biosynthesis
DNA, Neoplasm - genetics
Embryogenesis
Embryonic growth stage
Etiology
Female
Fibroblasts - metabolism
Humans
Immunity
Immunity (Disease)
Kinetics
Male
MCF-7 Cells
Mice, Inbred C57BL
Microscopy, Fluorescence
Molecular biology
Mutation
Organic chemistry
Protein Binding
Protein interaction
Proteins
Quantitation
Quantitative analysis
Replication
Replication forks
Sensitivity analysis
Single-Cell Analysis - methods
Substance abuse treatment
Tumor Suppressor p53-Binding Protein 1 - genetics
Tumor Suppressor p53-Binding Protein 1 - metabolism
Title SIRF: Quantitative in situ analysis of protein interactions at DNA replication forks
URI https://www.ncbi.nlm.nih.gov/pubmed/29475976
https://www.proquest.com/docview/2078828698
https://pubmed.ncbi.nlm.nih.gov/PMC5881507
Volume 217
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