Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops

R-loops are evolutionarily conserved three-stranded structures that result from the formation of stable DNA:RNA hybrids in the genome. R-loops have attracted increasing interest in recent years as potent regulators of gene expression and genome stability. In particular, their strong association with...

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Main Author: Vincent Vanoosthuyse
Format: Article
Language:English
Published: MDPI AG 2018-03-01
Series:Non-Coding RNA
Subjects:
Online Access:http://www.mdpi.com/2311-553X/4/2/9
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spelling doaj-d3f570f00baa47c3ac06d92bb36196522020-11-25T01:21:12ZengMDPI AGNon-Coding RNA2311-553X2018-03-0142910.3390/ncrna4020009ncrna4020009Strengths and Weaknesses of the Current Strategies to Map and Characterize R-LoopsVincent Vanoosthuyse0UMR5239 CNRS, Université de Lyon, ENS-Lyon, 46 allée d’Italie, 69007 Lyon, FranceR-loops are evolutionarily conserved three-stranded structures that result from the formation of stable DNA:RNA hybrids in the genome. R-loops have attracted increasing interest in recent years as potent regulators of gene expression and genome stability. In particular, their strong association with severe replication stress makes them potential oncogenic structures. Despite their importance, the rules that govern their formation and their dynamics are still controversial and an in-depth description of their direct impact on chromatin organization and DNA transactions is still lacking. To better understand the diversity of R-loop functions, reliable, accurate, and quantitative mapping techniques, as well as functional assays are required. Here, I review the different approaches that are currently used to do so and to highlight their individual strengths and weaknesses. In particular, I review the advantages and disadvantages of using the S9.6 antibody to map R-loops in vivo in an attempt to propose guidelines for best practices.http://www.mdpi.com/2311-553X/4/2/9R-loopsS9.6RNase H1DRIPR-ChIP
collection DOAJ
language English
format Article
sources DOAJ
author Vincent Vanoosthuyse
spellingShingle Vincent Vanoosthuyse
Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
Non-Coding RNA
R-loops
S9.6
RNase H1
DRIP
R-ChIP
author_facet Vincent Vanoosthuyse
author_sort Vincent Vanoosthuyse
title Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
title_short Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
title_full Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
title_fullStr Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
title_full_unstemmed Strengths and Weaknesses of the Current Strategies to Map and Characterize R-Loops
title_sort strengths and weaknesses of the current strategies to map and characterize r-loops
publisher MDPI AG
series Non-Coding RNA
issn 2311-553X
publishDate 2018-03-01
description R-loops are evolutionarily conserved three-stranded structures that result from the formation of stable DNA:RNA hybrids in the genome. R-loops have attracted increasing interest in recent years as potent regulators of gene expression and genome stability. In particular, their strong association with severe replication stress makes them potential oncogenic structures. Despite their importance, the rules that govern their formation and their dynamics are still controversial and an in-depth description of their direct impact on chromatin organization and DNA transactions is still lacking. To better understand the diversity of R-loop functions, reliable, accurate, and quantitative mapping techniques, as well as functional assays are required. Here, I review the different approaches that are currently used to do so and to highlight their individual strengths and weaknesses. In particular, I review the advantages and disadvantages of using the S9.6 antibody to map R-loops in vivo in an attempt to propose guidelines for best practices.
topic R-loops
S9.6
RNase H1
DRIP
R-ChIP
url http://www.mdpi.com/2311-553X/4/2/9
work_keys_str_mv AT vincentvanoosthuyse strengthsandweaknessesofthecurrentstrategiestomapandcharacterizerloops
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