Literature DB >> 26045257

Breaking bad: R-loops and genome integrity.

Julie Sollier1, Karlene A Cimprich2.   

Abstract

R-loops, nucleic acid structures consisting of an RNA-DNA hybrid and displaced single-stranded (ss) DNA, are ubiquitous in organisms from bacteria to mammals. First described in bacteria where they initiate DNA replication, it now appears that R-loops regulate diverse cellular processes such as gene expression, immunoglobulin (Ig) class switching, and DNA repair. Changes in R-loop regulation induce DNA damage and genome instability, and recently it was shown that R-loops are associated with neurodegenerative disorders. We discuss recent developments in the field; in particular, the regulation and effects of R-loops in cells, their effect on genomic and epigenomic stability, and their potential contribution to the origin of diseases including cancer and neurodegenerative disorders.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  R-loop; epigenomic stability; gene expression; genomic instability

Mesh：

Substances：

Year:  2015        PMID： 26045257      PMCID： PMC4554970          DOI： 10.1016/j.tcb.2015.05.003

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN： 0962-8924            Impact factor:   20.808


  69 in total

1.  Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA.

Authors:  Michelle L Duquette; Priya Handa; Jack A Vincent; Andrew F Taylor; Nancy Maizels
Journal:  Genes Dev       Date:  2004-07-01       Impact factor: 11.361

2.  R loops are linked to histone H3 S10 phosphorylation and chromatin condensation.

Authors:  Maikel Castellano-Pozo; José M Santos-Pereira; Ana G Rondón; Sonia Barroso; Eloisa Andújar; Mónica Pérez-Alegre; Tatiana García-Muse; Andrés Aguilera
Journal:  Mol Cell       Date:  2013-11-07       Impact factor: 17.970

3.  Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation.

Authors:  Yanzhong Yang; Kevin M McBride; Sean Hensley; Yue Lu; Frederic Chedin; Mark T Bedford
Journal:  Mol Cell       Date:  2014-02-06       Impact factor: 17.970

4.  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

5.  DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4).

Authors:  Ying-Zhang Chen; Craig L Bennett; Huy M Huynh; Ian P Blair; Imke Puls; Joy Irobi; Ines Dierick; Annette Abel; Marina L Kennerson; Bruce A Rabin; Garth A Nicholson; Michaela Auer-Grumbach; Klaus Wagner; Peter De Jonghe; John W Griffin; Kenneth H Fischbeck; Vincent Timmerman; David R Cornblath; Phillip F Chance
Journal:  Am J Hum Genet       Date:  2004-04-21       Impact factor: 11.025

6.  Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy.

Authors:  Xiao Zhu; George C Schatz
Journal:  J Phys Chem B       Date:  2012-11-14       Impact factor: 2.991

7.  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

8.  Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes.

Authors:  Amaya Alzu; Rodrigo Bermejo; Martina Begnis; Chiara Lucca; Daniele Piccini; Walter Carotenuto; Marco Saponaro; Alessandra Brambati; Andrea Cocito; Marco Foiani; Giordano Liberi
Journal:  Cell       Date:  2012-11-09       Impact factor: 41.582

9.  GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination.

Authors:  Paul A Ginno; Yoong Wearn Lim; Paul L Lott; Ian Korf; Frédéric Chédin
Journal:  Genome Res       Date:  2013-07-18       Impact factor: 9.043

10.  Signatures of mutational processes in human cancer.

Authors:  Ludmil B Alexandrov; Serena Nik-Zainal; David C Wedge; Samuel A J R Aparicio; Sam Behjati; Andrew V Biankin; Graham R Bignell; Niccolò Bolli; Ake Borg; Anne-Lise Børresen-Dale; Sandrine Boyault; Birgit Burkhardt; Adam P Butler; Carlos Caldas; Helen R Davies; Christine Desmedt; Roland Eils; Jórunn Erla Eyfjörd; John A Foekens; Mel Greaves; Fumie Hosoda; Barbara Hutter; Tomislav Ilicic; Sandrine Imbeaud; Marcin Imielinski; Marcin Imielinsk; Natalie Jäger; David T W Jones; David Jones; Stian Knappskog; Marcel Kool; Sunil R Lakhani; Carlos López-Otín; Sancha Martin; Nikhil C Munshi; Hiromi Nakamura; Paul A Northcott; Marina Pajic; Elli Papaemmanuil; Angelo Paradiso; John V Pearson; Xose S Puente; Keiran Raine; Manasa Ramakrishna; Andrea L Richardson; Julia Richter; Philip Rosenstiel; Matthias Schlesner; Ton N Schumacher; Paul N Span; Jon W Teague; Yasushi Totoki; Andrew N J Tutt; Rafael Valdés-Mas; Marit M van Buuren; Laura van 't Veer; Anne Vincent-Salomon; Nicola Waddell; Lucy R Yates; Jessica Zucman-Rossi; P Andrew Futreal; Ultan McDermott; Peter Lichter; Matthew Meyerson; Sean M Grimmond; Reiner Siebert; Elías Campo; Tatsuhiro Shibata; Stefan M Pfister; Peter J Campbell; Michael R Stratton
Journal:  Nature       Date:  2013-08-14       Impact factor: 49.962
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  150 in total

Review 1.  The regulation and functions of the nuclear RNA exosome complex.

Authors:  Cornelia Kilchert; Sina Wittmann; Lidia Vasiljeva
Journal:  Nat Rev Mol Cell Biol       Date:  2016-01-04       Impact factor: 94.444

Review 2.  The role of fork stalling and DNA structures in causing chromosome fragility.

Authors:  Simran Kaushal; Catherine H Freudenreich
Journal:  Genes Chromosomes Cancer       Date:  2019-01-29       Impact factor: 5.006

Review 3.  The impact of replication stress on replication dynamics and DNA damage in vertebrate cells.

Authors:  Hervé Técher; Stéphane Koundrioukoff; Alain Nicolas; Michelle Debatisse
Journal:  Nat Rev Genet       Date:  2017-07-17       Impact factor: 53.242

Review 4.  Replication Stress: An Achilles' Heel of Glioma Cancer Stem-like Cells.

Authors:  Meredith A Morgan; Christine E Canman
Journal:  Cancer Res       Date:  2018-11-29       Impact factor: 12.701

5.  DNA damage and genome instability by G-quadruplex ligands are mediated by R loops in human cancer cells.

Authors:  Alessio De Magis; Stefano G Manzo; Marco Russo; Jessica Marinello; Rita Morigi; Olivier Sordet; Giovanni Capranico
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-27       Impact factor: 11.205

6.  ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop.

Authors:  Dominick A Matos; Jia-Min Zhang; Jian Ouyang; Hai Dang Nguyen; Marie-Michelle Genois; Lee Zou
Journal:  Mol Cell       Date:  2019-11-07       Impact factor: 17.970

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

8.  The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations.

Authors:  Liang Chen; Jia-Yu Chen; Yi-Jou Huang; Ying Gu; Jinsong Qiu; Hao Qian; Changwei Shao; Xuan Zhang; Jing Hu; Hairi Li; Shunmin He; Yu Zhou; Omar Abdel-Wahab; Dong-Er Zhang; Xiang-Dong Fu
Journal:  Mol Cell       Date:  2018-01-27       Impact factor: 17.970

9.  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

Review 10.  Impact of Replication Stress in Human Papillomavirus Pathogenesis.

Authors:  Cary A Moody
Journal:  J Virol       Date:  2019-01-04       Impact factor: 5.103
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