R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1

Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-...

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Published inNature protocols Vol. 14; no. 5; pp. 1661 - 1685
Main Authors Chen, Jia-Yu, Zhang, Xuan, Fu, Xiang-Dong, Chen, Liang
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.05.2019
Nature Publishing Group
Subjects
631/1647/2217/2088
631/337/572
631/61/212
Analytical Chemistry
Animals
Biological activity
Biological Techniques
Biomedical and Life Sciences
Cell Line
Cell lines
Chromatin
Chromatin Immunoprecipitation - methods
Chromosome Mapping - methods
Computational Biology/Bioinformatics
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA damage
DNA repair
DNA structure
DNA-directed RNA polymerase
Gene expression
Gene mapping
Genetic aspects
Genetic research
Genomes
Genomic instability
Genomics
Hybrid structures
Hybrids
Hydrolases
Immunoprecipitation
Life Sciences
Mapping
Methods
Microarrays
Monoclonal antibodies
Mutation
Myelodysplastic syndrome
Organic Chemistry
Protocol
R-loops
Ribonuclease H - chemistry
Ribonuclease H - genetics
Ribonuclease H - metabolism
Ribonucleic acid
RNA
RNA - chemistry
RNA - genetics
RNA polymerase
RNA polymerase II
Splicing
Splicing factors
Stability
Structure
Transcription
United States
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Abstract Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA–DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA–DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS). This protocol describes the steps in R-ChIP, a procedure based on chromatin immunoprecipitation (ChIP) of an exogenously expressed mutant RNASEH1 to capture the genome-wide distribution of R-loops.
AbstractList Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA-DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA-DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS). This protocol describes the steps in R-ChIP, a procedure based on chromatin immunoprecipitation (ChIP) of an exogenously expressed mutant RNASEH1 to capture the genome-wide distribution of R-loops.
Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA–DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA–DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS).
Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA-DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA-DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS).Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA-DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA-DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS).
Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription, replication and genome instability. Here, we provide a detailed protocol for a newly developed strategy, named R-ChIP, for robust capture of R-loops genome-wide. Distinct from R-loop-mapping methods based on the monoclonal antibody S9.6, which recognizes RNA–DNA hybrid structures, R-ChIP involves expression of an exogenous catalytically inactive RNASEH1 in cells to bind RNA–DNA hybrids but not resolve them. This is followed by chromatin immunoprecipitation (ChIP) of the tagged RNASEH1 and construction of a strand-specific library for deep sequencing. It takes ~3 weeks to establish a stable cell line expressing the mutant enzyme and 5 more days to proceed with the R-ChIP protocol. In principle, R-ChIP is applicable to both cell lines and animals, as long as the catalytically inactive RNASEH1 can be expressed to study the dynamics of R-loop formation and resolution, as well as its impact on the functionality of the genome. In our recent studies with R-ChIP, we showed an intimate spatiotemporal relationship between R-loops and RNA polymerase II pausing/pause release, as well as linking augmented R-loop formation to DNA damage response induced by driver mutations of key splicing factors associated with myelodysplastic syndrome (MDS). This protocol describes the steps in R-ChIP, a procedure based on chromatin immunoprecipitation (ChIP) of an exogenously expressed mutant RNASEH1 to capture the genome-wide distribution of R-loops.
Audience Academic
Author Fu, Xiang-Dong
Chen, Liang
Zhang, Xuan
Chen, Jia-Yu
AuthorAffiliation 2 Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
1 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/30996261$$D View this record in MEDLINE/PubMed
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ObjectType-Feature-2
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Author contributions
L.C. and X.-D.F. conceived the idea; L.C. and J.-Y.C. codeveloped the R-ChIP method and data analysis pipeline; L.C. and X.Z. performed the experiments. J.-Y.C. performed bioinformatics analysis with assistance from L.C.; L.C., J.-Y.C. and X.-D.F. wrote the manuscript.
ORCID 0000-0001-5499-8732
0000-0001-9449-9321
0000-0002-6748-9416
OpenAccessLink https://www.ncbi.nlm.nih.gov/pmc/articles/6604627
PMID 30996261
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Snippet Nascent RNA may form a three-stranded structure with DNA, called an R-loop, which has been linked to fundamental biological processes such as transcription,...
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proquest
gale
pubmed
crossref
springer
SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 1661
SubjectTerms 631/1647/2217/2088
631/337/572
631/61/212
Analytical Chemistry
Animals
Biological activity
Biological Techniques
Biomedical and Life Sciences
Cell Line
Cell lines
Chromatin
Chromatin Immunoprecipitation - methods
Chromosome Mapping - methods
Computational Biology/Bioinformatics
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA damage
DNA repair
DNA structure
DNA-directed RNA polymerase
Gene expression
Gene mapping
Genetic aspects
Genetic research
Genomes
Genomic instability
Genomics
Hybrid structures
Hybrids
Hydrolases
Immunoprecipitation
Life Sciences
Mapping
Methods
Microarrays
Monoclonal antibodies
Mutation
Myelodysplastic syndrome
Organic Chemistry
Protocol
R-loops
Ribonuclease H - chemistry
Ribonuclease H - genetics
Ribonuclease H - metabolism
Ribonucleic acid
RNA
RNA - chemistry
RNA - genetics
RNA polymerase
RNA polymerase II
Splicing
Splicing factors
Stability
Structure
Transcription
Title R-ChIP for genome-wide mapping of R-loops by using catalytically inactive RNASEH1
URI https://link.springer.com/article/10.1038/s41596-019-0154-6
https://www.ncbi.nlm.nih.gov/pubmed/30996261
https://www.proquest.com/docview/2216766684
https://www.proquest.com/docview/2211326538
https://pubmed.ncbi.nlm.nih.gov/PMC6604627
Volume 14
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