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

RNA Polymerase III Regulates Cytosolic RNA:DNA Hybrids and Intracellular MicroRNA Expression

(2015) Christine Xing'er Koo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

RNA helicase A activity is inhibited by oncogenic transcription factor EWS-FLI1

(2015) Hayriye Verda Erkizan et al.   NUCLEIC ACIDS RESEARCH

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unusual Characteristics of the DNA Binding Domain of Epigenetic Regulatory Protein MeCP2 Determine Its Binding Specificity

(2014) Sergei Khrapunov et al.   BIOCHEMISTRY

Effects of cytosine methylation on transcription factor binding sites

(2014) Yulia A Medvedeva et al.   BMC GENOMICS

EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma

(2014) Nicolò Riggi et al.   CANCER CELL

Existence and consequences of G-quadruplex structures in DNA

(2014) Pierre Murat et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

(2014) Maxim Pimkin et al.   GENOME RESEARCH

Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

(2014) Claudia Günther et al.   JOURNAL OF CLINICAL INVESTIGATION

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

(2014) Aaron R. Haeusler et al.   NATURE

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

(2014) Vaibhav Bhatia et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

The ets transcription factor Fli-1 in development, cancer and disease

(2014) Y Li et al.   ONCOGENE

R-Loops in Proliferating Cells but Not in the Brain: Implications for AOA2 and Other Autosomal Recessive Ataxias

(2014) Abrey J. Yeo et al.   PLoS One

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

(2014) Mark D. Szczelkun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome

(2014) D. Colak et al.   SCIENCE

Out of Balance: R-loops in Human Disease

(2014) Matthias Groh et al.   PLoS Genetics

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

Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

(2014) Erick W. Loomis et al.   PLoS Genetics

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

(2013) Verena Pfeiffer et al.   EMBO JOURNAL

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

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

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

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

(2013) Q. Sun et al.   SCIENCE

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

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

(2013) Lamia Wahba et al.   eLife

DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation

(2012) Mina Nakama et al.   GENES TO CELLS

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

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

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

A hybrid G-quadruplex structure formed between RNA and DNA explains the extraordinary stability of the mitochondrial R-loop

(2012) P. H. Wanrooij et al.   NUCLEIC ACIDS RESEARCH

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

(2012) Aaron Diaz et al.   GENOME BIOLOGY

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

(2012) Christoffer Nellåker et al.   GENOME BIOLOGY

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes

(2011) Prasun Chakraborty et al.   DNA REPAIR

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

Integrative genomic analysis of human ribosomal DNA

(2011) Gabriel E. Zentner et al.   NUCLEIC ACIDS RESEARCH

A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro

(2011) Eun-Ang Raiber et al.   NUCLEIC ACIDS RESEARCH

Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells

(2010) R. Zheng et al.   JOURNAL OF CELL SCIENCE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

(2010) B. P. Belotserkovskii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

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

Competition between the RNA Transcript and the Nontemplate DNA Strand during R-Loop Formation In Vitro: a Nick Can Serve as a Strong R-Loop Initiation Site

(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

A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma

(2009) Hayriye V Erkizan et al.   NATURE MEDICINE

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

R loops stimulate genetic instability of CTG{middle dot}CAG repeats

(2009) Y. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native R-loops Persist throughout the Mouse Mitochondrial DNA Genome

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

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY