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

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening

(2013) Verena Pfeiffer et al.   EMBO JOURNAL

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

The Rs of Biology: R-Loops and the Regulation of Regulators

(2013) Lamia Wahba et al.   MOLECULAR CELL

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

(2013) Manuele Castelnuovo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence

(2013) Bettina Balk et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation

(2013) Jessica Marinello et al.   NUCLEIC ACIDS RESEARCH

R-Loop Mediated Transcription-Associated Recombination in trf4Δ Mutants Reveals New Links between RNA Surveillance and Genome Integrity

(2013) Sandra Gavaldá 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

R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

(2013) Q. Sun et al.   SCIENCE

Plenary Sessions

(2013)   YEAST

High-Throughput Genetic and Gene Expression Analysis of the RNAPII-CTD Reveals Unexpected Connections to SRB10/CDK8

(2013) Maria J. Aristizabal et al.   PLoS Genetics

The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

(2013) Lamia Wahba et al.   eLife

CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures

(2012) T. Hentrich et al.   BIOINFORMATICS

Deficiency in Mammalian Histone H2B Ubiquitin Ligase Bre1 (Rnf20/Rnf40) Leads to Replication Stress and Chromosomal Instability

(2012) S. B. Chernikova et al.   CANCER RESEARCH

Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

(2012) Amaya Alzu et al.   CELL

Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae

(2012) Mercedes E. Arana et al.   DNA REPAIR

R-loops cause replication impairment and genome instability during meiosis

(2012) Maikel Castellano-Pozo et al.   EMBO REPORTS

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

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

DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation

(2012) Mina Nakama et al.   GENES TO CELLS

RNA Polymerase II Collision Interrupts Convergent Transcription

(2012) David J. Hobson 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

Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress

(2012) Géraldine Servant et al.   NUCLEIC ACIDS RESEARCH

Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli

(2012) J. Krishna Leela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

(2012) Thanasis Margaritis et al.   PLoS Genetics

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

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

R-loop-mediated genomic instability is caused by impairment of replication fork progression

(2011) W. Gan et al.   GENES & DEVELOPMENT

Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes

(2011) Anne Helmrich et al.   MOLECULAR CELL

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

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Antisense expression increases gene expression variability and locus interdependency

(2011) Z. Xu et al.   Molecular Systems Biology

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

SomaticSF3B1Mutation in Myelodysplasia with Ring Sideroblasts

(2011) E. Papaemmanuil et al.   NEW ENGLAND JOURNAL OF MEDICINE

SF3B1and Other Novel Cancer Genes in Chronic Lymphocytic Leukemia

(2011) Lili Wang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Genome Instability and Transcription Elongation Impairment in Human Cells Depleted of THO/TREX

(2011) María S. Domínguez-Sánchez et al.   PLoS Genetics

The Complete Spectrum of Yeast Chromosome Instability Genes Identifies Candidate CIN Cancer Genes and Functional Roles for ASTRA Complex Components

(2011) Peter C. Stirling et al.   PLoS Genetics

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

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

Functional Genomics Analysis of the Saccharomyces cerevisiae Iron Responsive Transcription Factor Aft1 Reveals Iron-Independent Functions

(2010) S. Berthelet et al.   GENETICS

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

(2009) J. Camblong et al.   GENES & DEVELOPMENT

Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation

(2009) Amila Suraweera et al.   HUMAN MOLECULAR GENETICS

Linking Cell Cycle to Histone Modifications: SBF and H2B Monoubiquitination Machinery and Cell-Cycle Regulation of H3K79 Dimethylation

(2009) Julia M. Schulze et al.   MOLECULAR CELL

Fail-Safe Transcriptional Termination for Protein-Coding Genes in S. cerevisiae

(2009) Ana G. Rondón et al.   MOLECULAR CELL

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

(2009) E. Matsuda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination

(2008) J. Kawauchi et al.   GENES & DEVELOPMENT

The THP1-SAC3-SUS1-CDC31 Complex Works in Transcription Elongation-mRNA Export Preventing RNA-mediated Genome Instability

(2008) Cristina González-Aguilera et al.   MOLECULAR BIOLOGY OF THE CELL

The Rat1p 5′ to 3′ Exonuclease Degrades Telomeric Repeat-Containing RNA and Promotes Telomere Elongation in Saccharomyces cerevisiae

(2008) Brian Luke et al.   MOLECULAR CELL

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification

(2008) Harm van Bakel et al.   NUCLEIC ACIDS RESEARCH

Spt2p Defines a New Transcription-Dependent Gross Chromosomal Rearrangement Pathway

(2008) Nilabja Sikdar et al.   PLoS Genetics