Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

Ribonucleotides in DNA: Origins, repair and consequences

(2014) Jessica S. Williams et al.   DNA REPAIR

RNA:DNA hybrids are a novel molecular pattern sensed by TLR9

(2014) R. E. Rigby et al.   EMBO JOURNAL

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

The molecular topography of silenced chromatin in Saccharomyces cerevisiae

(2014) D. M. Thurtle et al.   GENES & DEVELOPMENT

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

The Strength of an Ig Switch Region Is Determined by Its Ability to Drive R Loop Formation and Its Number of WGCW Sites

(2014) Zheng Z. Zhang et al.   Cell Reports

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

(2014) Yujia A. Chan et al.   PLoS Genetics

R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome

(2014) Matthias Groh et al.   PLoS Genetics

Chromatin states at ribosomal DNA loci

(2013) Stephan Hamperl et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A unique nucleosome arrangement, maintained actively by chromatin remodelers facilitates transcription of yeast tRNA genes

(2013) Yatendra Kumar et al.   BMC GENOMICS

DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability

(2013) Boris P. Belotserkovskii et al.   CHEMICAL REVIEWS

RNA polymerase and the ribosome: the close relationship

(2013) Katelyn McGary et al.   CURRENT OPINION IN MICROBIOLOGY

The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability

(2013) J. M. Santos-Pereira et al.   GENES & DEVELOPMENT

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

(2013) P. A. Ginno et al.   GENOME RESEARCH

Competition between Pre-mRNAs for the Splicing Machinery Drives Global Regulation of Splicing

(2013) Elizabeth M. Munding et al.   MOLECULAR CELL

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-replication encounters, consequences and genomic instability

(2013) Anne Helmrich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global ‘bootprinting’ reveals the elastic architecture of the yeast TFIIIB–TFIIIC transcription complex in vivo

(2013) V. Nagarajavel et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial DNA replication proceeds via a ‘bootlace’ mechanism involving the incorporation of processed transcripts

(2013) Aurelio Reyes et al.   NUCLEIC ACIDS RESEARCH

RNase H2 roles in genome integrity revealed by unlinking its activities

(2013) Hyongi Chon et al.   NUCLEIC ACIDS RESEARCH

The Mitochondrial RNA Landscape of Saccharomyces cerevisiae

(2013) Edward M. Turk et al.   PLoS One

R-loop formation atSnord116mediates topotecan inhibition ofUbe3a-antisenseand allele-specific chromatin decondensation

(2013) Weston T. Powell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron–exon recognition

(2013) Marina N. Nedelcheva-Veleva et al.   Nature Communications

Transcription reinitiation by RNA polymerase III

(2012) Giorgio Dieci et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development

(2012) Martin A.M. Reijns et al.   CELL

R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants

(2012) P. C. Stirling et al.   GENES & DEVELOPMENT

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

(2012) L. Mularoni et al.   GENOME RESEARCH

A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon

(2012) J. A. Baller et al.   GENOME RESEARCH

Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity

(2012) Bjoern Hiller et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptome-wide Analysis of Exosome Targets

(2012) Claudia Schneider et al.   MOLECULAR CELL

Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells

(2012) Rajani Kanth Gudipati et al.   MOLECULAR CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface

(2012) Antoine Bridier-Nahmias et al.   Mobile DNA

Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells

(2011) Heini Ruhanen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The RNA Exosome Targets the AID Cytidine Deaminase to Both Strands of Transcribed Duplex DNA Substrates

(2011) Uttiya Basu et al.   CELL

Selective Autophagy Regulates Insertional Mutagenesis by the Ty1 Retrotransposon in Saccharomyces cerevisiae

(2011) Kuninori Suzuki et al.   DEVELOPMENTAL CELL

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

(2011) Belén Gómez-González et al.   EMBO JOURNAL

RNA polymerase I activity is regulated at multiple steps in the transcription cycle: Recent insights into factors that influence transcription elongation

(2011) David Alan Schneider   GENE

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability

(2011) Lamia Wahba et al.   MOLECULAR CELL

Yeast Sen1 Helicase Protects the Genome from Transcription-Associated Instability

(2011) Hannah E. Mischo et al.   MOLECULAR CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

All tangled up: how cells direct, manage and exploit topoisomerase function

(2011) Seychelle M. Vos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

(2010) A. El Hage et al.   GENES & DEVELOPMENT

An Upstream Open Reading Frame and the Context of the Two AUG Codons Affect the Abundance of Mitochondrial and Nuclear RNase H1

(2010) Y. Suzuki et al.   MOLECULAR AND CELLULAR BIOLOGY

Distinguishing the Roles of Topoisomerases I and II in Relief of Transcription-Induced Torsional Stress in Yeast rRNA Genes

(2010) S. L. French et al.   MOLECULAR AND CELLULAR BIOLOGY

Strand Invasion Structures in the Inverted Repeat of Candida albicans Mitochondrial DNA Reveal a Role for Homologous Recombination in Replication

(2010) Joachim M. Gerhold et al.   MOLECULAR CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

(2009) Melissa J. Moore et al.   CELL

Connections between antiviral defense and autoimmunity

(2009) Daniel B Stetson   CURRENT OPINION IN IMMUNOLOGY

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

G Clustering Is Important for the Initiation of Transcription-Induced R-Loops In Vitro, whereas High G Density without Clustering Is Sufficient Thereafter

(2009) D. Roy et al.   MOLECULAR AND CELLULAR BIOLOGY

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

The Take and Give Between Retrotransposable Elements and their Hosts

(2008) Arthur Beauregard et al.   Annual Review of Genetics

Chromatin-Associated Genes Protect the Yeast Genome From Ty1 Insertional Mutagenesis

(2008) Katherine M. Nyswaner et al.   GENETICS

Native R-loops Persist throughout the Mouse Mitochondrial DNA Genome

(2008) Timothy A. Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY