Literature DB >> 25938907

The Yin and Yang of R-loop biology.

Lorenzo Costantino1, Douglas Koshland2.   

Abstract

RNA performs diverse functions in cells, directing translation, modulating transcription and catalyzing enzymatic reactions. Remarkably RNA can also anneal to its genomic template co- or post-transcriptionally to generate an RNA-DNA hybrid and a displaced single-stranded DNA. These unusual nucleic acid structures are called R-loops. Studies in the last decades concentrated on the detrimental effects of R-loop formation, particularly on genome stability. In fact, R-loops are thought to play a role in several human diseases like cancer and neurodegenerative syndromes. But recent data has revealed that R-loops can also have a positive impact on cell processes, like regulating gene expression, chromosome structure and DNA repair. Here we summarize our current understanding of the formation and dissolution of R-loops, and discuss their negative and positive impact on genome structure and function.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 25938907      PMCID: PMC4522345          DOI: 10.1016/j.ceb.2015.04.008

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  59 in total

1.  Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination.

Authors:  Pablo Huertas; Andrés Aguilera
Journal:  Mol Cell       Date:  2003-09       Impact factor: 17.970

2.  Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli.

Authors:  A Beletskii; A S Bhagwat
Journal:  Proc Natl Acad Sci U S A       Date:  1996-11-26       Impact factor: 11.205

3.  Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome.

Authors:  Dilek Colak; Nikica Zaninovic; Michael S Cohen; Zev Rosenwaks; Wang-Yong Yang; Jeannine Gerhardt; Matthew D Disney; Samie R Jaffrey
Journal:  Science       Date:  2014-02-28       Impact factor: 47.728

4.  The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction.

Authors:  Nadine M Shaban; Scott Harvey; Fred W Perrino; Thomas Hollis
Journal:  J Biol Chem       Date:  2009-11-18       Impact factor: 5.157

5.  Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2.

Authors:  Maria-Céu Moreira; Sandra Klur; Mitsunori Watanabe; Andrea H Németh; Isabelle Le Ber; José-Carlos Moniz; Christine Tranchant; Patrick Aubourg; Meriem Tazir; Lüdger Schöls; Massimo Pandolfo; Jörg B Schulz; Jean Pouget; Patrick Calvas; Masami Shizuka-Ikeda; Mikio Shoji; Makoto Tanaka; Louise Izatt; Christopher E Shaw; Abderrahim M'Zahem; Eimear Dunne; Pascale Bomont; Traki Benhassine; Naïma Bouslam; Giovanni Stevanin; Alexis Brice; João Guimarães; Pedro Mendonça; Clara Barbot; Paula Coutinho; Jorge Sequeiros; Alexandra Dürr; Jean-Marie Warter; Michel Koenig
Journal:  Nat Genet       Date:  2004-02-08       Impact factor: 38.330

6.  Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity.

Authors:  Bjoern Hiller; Martin Achleitner; Silke Glage; Ronald Naumann; Rayk Behrendt; Axel Roers
Journal:  J Exp Med       Date:  2012-07-16       Impact factor: 14.307

7.  R-loops induce repressive chromatin marks over mammalian gene terminators.

Authors:  Konstantina Skourti-Stathaki; Kinga Kamieniarz-Gdula; Nicholas J Proudfoot
Journal:  Nature       Date:  2014-10-05       Impact factor: 49.962

8.  Transcription-associated R-loop formation across the human FMR1 CGG-repeat region.

Authors:  Erick W Loomis; Lionel A Sanz; Frédéric Chédin; Paul J Hagerman
Journal:  PLoS Genet       Date:  2014-04-17       Impact factor: 5.917

9.  Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip.

Authors:  Yujia A Chan; Maria J Aristizabal; Phoebe Y T Lu; Zongli Luo; Akil Hamza; Michael S Kobor; Peter C Stirling; Philip Hieter
Journal:  PLoS Genet       Date:  2014-04-17       Impact factor: 5.917

10.  C9orf72 nucleotide repeat structures initiate molecular cascades of disease.

Authors:  Aaron R Haeusler; Christopher J Donnelly; Goran Periz; Eric A J Simko; Patrick G Shaw; Min-Sik Kim; Nicholas J Maragakis; Juan C Troncoso; Akhilesh Pandey; Rita Sattler; Jeffrey D Rothstein; Jiou Wang
Journal:  Nature       Date:  2014-03-05       Impact factor: 49.962

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  61 in total

1.  TERRA and the state of the telomere.

Authors:  Karsten Rippe; Brian Luke
Journal:  Nat Struct Mol Biol       Date:  2015-11       Impact factor: 15.369

2.  The MYC mRNA 3'-UTR couples RNA polymerase II function to glutamine and ribonucleotide levels.

Authors:  Francesca R Dejure; Nadine Royla; Steffi Herold; Jacqueline Kalb; Susanne Walz; Carsten P Ade; Guido Mastrobuoni; Jens T Vanselow; Andreas Schlosser; Elmar Wolf; Stefan Kempa; Martin Eilers
Journal:  EMBO J       Date:  2017-04-13       Impact factor: 11.598

3.  Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis.

Authors:  Kevin S Lang; Ashley N Hall; Christopher N Merrikh; Mark Ragheb; Hannah Tabakh; Alex J Pollock; Joshua J Woodward; Julia E Dreifus; Houra Merrikh
Journal:  Cell       Date:  2017-08-10       Impact factor: 41.582

4.  An ATR-dependent function for the Ddx19 RNA helicase in nuclear R-loop metabolism.

Authors:  Dana Hodroj; Bénédicte Recolin; Kamar Serhal; Susan Martinez; Nikolay Tsanov; Raghida Abou Merhi; Domenico Maiorano
Journal:  EMBO J       Date:  2017-03-17       Impact factor: 11.598

Review 5.  Transcription-replication conflicts at chromosomal fragile sites-consequences in M phase and beyond.

Authors:  Vibe H Oestergaard; Michael Lisby
Journal:  Chromosoma       Date:  2016-10-28       Impact factor: 4.316

6.  The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers.

Authors:  Chen Zhang; Hang Fu; Yajun Yang; Erchi Zhou; Zhijie Tan; Huijuan You; Xinghua Zhang
Journal:  Biophys J       Date:  2018-12-13       Impact factor: 4.033

Review 7.  R-loop generation during transcription: Formation, processing and cellular outcomes.

Authors:  Boris P Belotserkovskii; Silvia Tornaletti; Alicia D D'Souza; Philip C Hanawalt
Journal:  DNA Repair (Amst)       Date:  2018-08-25

Review 8.  When DNA Topology Turns Deadly - RNA Polymerases Dig in Their R-Loops to Stand Their Ground: New Positive and Negative (Super)Twists in the Replication-Transcription Conflict.

Authors:  Andrei Kuzminov
Journal:  Trends Genet       Date:  2017-11-25       Impact factor: 11.639

Review 9.  R-Loops as Cellular Regulators and Genomic Threats.

Authors:  Madzia P Crossley; Michael Bocek; Karlene A Cimprich
Journal:  Mol Cell       Date:  2019-02-07       Impact factor: 17.970

10.  Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability.

Authors:  Lorenzo Costantino; Douglas Koshland
Journal:  Mol Cell       Date:  2018-08-02       Impact factor: 17.970

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