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R-Loops

Overview of attention for book
Cover of 'R-Loops'

Table of Contents

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    Book Overview
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    Chapter 1 Direct R-Loop Visualization on Genomic DNA by Native Automated Electron Microscopy
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    Chapter 2 Detection of R-Loop Structures by Immunofluorescence Using the S9.6 Monoclonal Antibody
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    Chapter 3 R-Loop Detection in Bacteria
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    Chapter 4 Detection of R-Loops by In Vivo and In Vitro Cytosine Deamination in Saccharomyces cerevisiae
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    Chapter 5 Identification of RNA–DNA Hybrids Associated with R-Loops at the IgH Switch Sequence in Activated B Cells
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    Chapter 6 Locus-Specific Analysis of Replication Dynamics and Detection of DNA–RNA Hybrids by Immuno Electron Microscopy
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    Chapter 7 RNase H1, the Gold Standard for R-Loop Detection
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    Chapter 8 RNase H1 Hybrid-Binding Domain-Based Tools for Cellular Biology Studies of DNA–RNA Hybrids in Mammalian Cells
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    Chapter 9 Detection and Quantification of RNA Modifications on RNA-DNA Hybrids Using SID-UPLC-MS/MS.
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    Chapter 10 DNA-RNA Hybrids at Telomeres in Budding Yeast.
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    Chapter 11 Detection of TERRA R-Loops at Human Telomeres
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    Chapter 12 R-Loops and Mitochondrial DNA Metabolism
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    Chapter 13 Highly Purified Top1-Bound DNA Fragments
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    Chapter 14 R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors
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    Chapter 15 Studies on Protein–RNA:DNA Hybrid Interactions by Microscale Thermophoresis (MST)
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    Chapter 16 Studying R-Loop Recognizing Proteins Using Single-Molecule DNA Curtain Technique and Electrophoretic Mobility Shift Assay
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    Chapter 17 Immunostaining and Protein Pull-Down of Methyl-5-Cytosine-Marked RNA:DNA Hybrids
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    Chapter 18 In Vitro Binding of GADD45A to RNA:DNA Hybrids
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    Chapter 19 Proximity Ligation Assay for Detection of R-Loop Complexes upon DNA Damage
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    Chapter 20 Biochemical Analysis of RNA–DNA Hybrid and R-Loop Unwinding Via Motor Proteins
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    Chapter 21 Topology of RNA:DNA Hybrids and R-Loops in Yeast
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    Chapter 22 Detecting and Mapping N6-Methyladenosine on RNA/DNA Hybrids
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    Chapter 23 Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag)
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    Chapter 24 Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP)
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    Chapter 25 Targeted Nuclease Approaches for Mapping Native R-Loops
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    Chapter 26 Quantitative DNA–RNA Immunoprecipitation Sequencing with Spike-Ins
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    Chapter 27 DNA:RNA Immunoprecipitation from S. pombe Cells for qPCR and Genome-Wide Sequencing
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    Chapter 28 Genome-Wide Analysis of DNA–RNA Hybrids in Yeast by DRIPc-Seq and DRIP-Seq
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    Chapter 29 Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms
Attention for Chapter 9: Detection and Quantification of RNA Modifications on RNA-DNA Hybrids Using SID-UPLC-MS/MS.
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (63rd percentile)
  • High Attention Score compared to outputs of the same age and source (85th percentile)

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Chapter title
Detection and Quantification of RNA Modifications on RNA-DNA Hybrids Using SID-UPLC-MS/MS.
Chapter number 9
Book title
R-Loops
Published in
Methods in molecular biology, January 2022
DOI 10.1007/978-1-0716-2477-7_9
Pubmed ID
35704189
Book ISBNs
978-1-07-162476-0, 978-1-07-162477-7
Authors

Starczak, Marta, Abakir, Abdulkadir, Ruzov, Alexey, Gackowski, Daniel

Abstract

R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and an unpaired strand of nontemplate DNA that represent a major source of genomic instability and are involved in regulation of several important biological processes in eukaryotic cells. A growing body of experimental evidence suggests that RNA moieties of RNA-DNA hybrids may convey RNA modifications influencing various aspects of R-loop biology. Here we present a protocol for quantitative analysis of RNA modifications on RNA-DNA hybrids using stable-isotope dilution ultraperformance liquid chromatography coupled with tandem mass spectrometry (SID-UPLC-MS/MS). Supplemented by other techniques, this method can be instrumental in deciphering the roles of RNA modifications in R-loop metabolism.

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 Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 29 June 2022.
All research outputs
#7,655,010
of 23,305,591 outputs
Outputs from Methods in molecular biology
#2,380
of 13,332 outputs
Outputs of similar age
#172,116
of 507,805 outputs
Outputs of similar age from Methods in molecular biology
#86
of 595 outputs
Altmetric has tracked 23,305,591 research outputs across all sources so far. This one is in the 44th percentile – i.e., 44% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,332 research outputs from this source. They receive a mean Attention Score of 3.4. This one has done well, scoring higher than 75% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 507,805 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 63% of its contemporaries.
We're also able to compare this research output to 595 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 85% of its contemporaries.

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