Literature DB >> 27252122

R-loop: an emerging regulator of chromatin dynamics.

Qais Al-Hadid1, Yanzhong Yang2.   

Abstract

The dynamic structure of chromatin, which exists in two conformational states: heterochromatin and euchromatin, alters the accessibility of the DNA to regulatory factors during transcription, replication, recombination, and DNA damage repair. Chemical modifications of histones and DNA, as well as adenosine triphospahate-dependent nucleosome remodeling, have been the major focus of research on chromatin dynamics over the past two decades. However, recent studies using a DNA-RNA hybrid-specific antibody and next-generation sequencing approaches have revealed that the formation of R-loops, one of the most common non-canonical DNA structures, is an emerging regulator of chromatin states. This review focuses on recent insights into the interplay between R-loop formation and the epigenetic modifications of chromatin in normal and disease states.
© The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Keywords:  DNA–RNA hybrid; R-loop; epigenetic modification; transcription

Mesh:

Substances:

Year:  2016        PMID: 27252122      PMCID: PMC6259673          DOI: 10.1093/abbs/gmw052

Source DB:  PubMed          Journal:  Acta Biochim Biophys Sin (Shanghai)        ISSN: 1672-9145            Impact factor:   3.848


  103 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.  DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation.

Authors:  Mina Nakama; Kei Kawakami; Takuya Kajitani; Takeshi Urano; Yota Murakami
Journal:  Genes Cells       Date:  2012-01-27       Impact factor: 1.891

3.  Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids.

Authors:  S J Boguslawski; D E Smith; M A Michalak; K E Mickelson; C O Yehle; W L Patterson; R J Carrico
Journal:  J Immunol Methods       Date:  1986-05-01       Impact factor: 2.303

4.  Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes.

Authors:  H Bierhoff; K Schmitz; F Maass; J Ye; I Grummt
Journal:  Cold Spring Harb Symp Quant Biol       Date:  2011-04-18

Review 5.  Transcription-replication encounters, consequences and genomic instability.

Authors:  Anne Helmrich; Monica Ballarino; Evgeny Nudler; Laszlo Tora
Journal:  Nat Struct Mol Biol       Date:  2013-04       Impact factor: 15.369

6.  A high-resolution atlas of nucleosome occupancy in yeast.

Authors:  William Lee; Desiree Tillo; Nicolas Bray; Randall H Morse; Ronald W Davis; Timothy R Hughes; Corey Nislow
Journal:  Nat Genet       Date:  2007-09-16       Impact factor: 38.330

7.  The C-terminal domain of RNA polymerase II is modified by site-specific methylation.

Authors:  Robert J Sims; Luis Alejandro Rojas; David B Beck; Roberto Bonasio; Roland Schüller; William J Drury; Dirk Eick; Danny Reinberg
Journal:  Science       Date:  2011-04-01       Impact factor: 47.728

8.  The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability.

Authors:  Lamia Wahba; Steven K Gore; Douglas Koshland
Journal:  Elife       Date:  2013-06-11       Impact factor: 8.140

9.  RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships.

Authors:  Julie Nadel; Rodoniki Athanasiadou; Christophe Lemetre; N Ari Wijetunga; Pilib Ó Broin; Hanae Sato; Zhengdong Zhang; Jeffrey Jeddeloh; Cristina Montagna; Aaron Golden; Cathal Seoighe; John M Greally
Journal:  Epigenetics Chromatin       Date:  2015-11-16       Impact factor: 4.954

Review 10.  Out of balance: R-loops in human disease.

Authors:  Matthias Groh; Natalia Gromak
Journal:  PLoS Genet       Date:  2014-09-18       Impact factor: 5.917

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  9 in total

1.  The R-Loop Atlas of Arabidopsis Development and Responses to Environmental Stimuli.

Authors:  Wei Xu; Kuan Li; Shuai Li; Quancan Hou; Yushun Zhang; Kunpeng Liu; Qianwen Sun
Journal:  Plant Cell       Date:  2020-02-19       Impact factor: 11.277

2.  RNA metabolism is the primary target of formamide in vivo.

Authors:  Rafael Hoyos-Manchado; Félix Reyes-Martín; Charalampos Rallis; Enrique Gamero-Estévez; Pablo Rodríguez-Gómez; Juan Quintero-Blanco; Jürg Bähler; Juan Jiménez; Víctor A Tallada
Journal:  Sci Rep       Date:  2017-11-21       Impact factor: 4.379

3.  Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice.

Authors:  Yuan Fang; Lifen Chen; Kande Lin; Yilong Feng; Pengyue Zhang; Xiucai Pan; Jennifer Sanders; Yufeng Wu; Xiu-E Wang; Zhen Su; Caiyan Chen; Hairong Wei; Wenli Zhang
Journal:  Genome Res       Date:  2019-07-01       Impact factor: 9.043

4.  Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors.

Authors:  Emily M Schleicher; Ashna Dhoonmoon; Lindsey M Jackson; Kristen E Clements; Coryn L Stump; Claudia M Nicolae; George-Lucian Moldovan
Journal:  PLoS Genet       Date:  2020-11-02       Impact factor: 5.917

Review 5.  Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability.

Authors:  Carlo Rinaldi; Paolo Pizzul; Maria Pia Longhese; Diego Bonetti
Journal:  Front Cell Dev Biol       Date:  2021-01-11

Review 6.  The Dynamic Regulation of G-Quadruplex DNA Structures by Cytosine Methylation.

Authors:  Aaron John Stevens; Lucy de Jong; Martin Alexander Kennedy
Journal:  Int J Mol Sci       Date:  2022-02-22       Impact factor: 5.923

Review 7.  Recent advances in the chromatin-based mechanism of FLOWERING LOCUS C repression through autonomous pathway genes.

Authors:  Jinseul Kyung; Myeongjune Jeon; Ilha Lee
Journal:  Front Plant Sci       Date:  2022-08-12       Impact factor: 6.627

8.  Interplay of DNA and RNA N 6 -methyladenine with R-loops in regulating gene transcription in Arabidopsis.

Authors:  Pengyue Zhang; Jingjing Gao; Xinxu Li; Yilong Feng; Manli Shi; Yining Shi; Wenli Zhang
Journal:  Physiol Mol Biol Plants       Date:  2021-05-23

9.  Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome.

Authors:  Emma Briggs; Graham Hamilton; Kathryn Crouch; Craig Lapsley; Richard McCulloch
Journal:  Nucleic Acids Res       Date:  2018-12-14       Impact factor: 16.971

  9 in total

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