A Tale of Loops and Tails: The Role of Intrinsically Disordered Protein Regions in R-Loop Recognition and Phase Separation

Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

(2021) Martin Bartas et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation

(2021) Erik W Martin et al.   NUCLEIC ACIDS RESEARCH

From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork

(2020) Antonio Maffia et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Molecular dissection of ALS‐linked TDP‐43 – involvement of the Gly‐rich domain in interaction with G‐quadruplex mRNA

(2020) Akira Ishiguro et al.   FEBS LETTERS

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible states tunes cap-dependent translation inhibition

(2020) Jennifer E. Dawson et al.   Nature Communications

Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome

(2020) Arijita Chakraborty et al.   Cell Reports

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination

(2019) Zhuobin Liang et al.   Cell Reports

Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation

(2019) Brian Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

DSB structure impacts DNA recombination leading to class switching and chromosomal translocations in human B cells

(2019) Clare C. So et al.   PLoS Genetics

ALBA protein complex reads genic R-loops to maintain genome stability in Arabidopsis

(2019) Wei Yuan et al.   Science Advances

Drugging the R-loop interactome: RNA-DNA hybrid binding proteins as targets for cancer therapy

(2019) Beáta Boros-Oláh et al.   DNA REPAIR

Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids

(2019) Sofiane Y Mersaoui et al.   EMBO JOURNAL

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

(2019) Qian Li et al.   NUCLEIC ACIDS RESEARCH

Dual Processing of R-Loops and Topoisomerase I Induces Transcription-Dependent DNA Double-Strand Breaks

(2019) Agnese Cristini et al.   Cell Reports

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

G-quadruplex structures trigger RNA phase separation

(2019) Yueying Zhang et al.   NUCLEIC ACIDS RESEARCH

The balancing act of R-loop biology: The good, the bad, and the ugly

(2019) Youssef A. Hegazy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional Implications of Intracellular Phase Transitions

(2018) Alex S. Holehouse et al.   BIOCHEMISTRY

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

(2018) Claudia Ribeiro de Almeida et al.   MOLECULAR CELL

Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers

(2018) Vladimir A Kuznetsov et al.   NUCLEIC ACIDS RESEARCH

G-quadruplex binding ability of TLS/FUS depends on the β-spiral structure of the RGG domain

(2018) Ryota Yagi et al.   NUCLEIC ACIDS RESEARCH

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair

(2018) Wei-Ting Lu et al.   Nature Communications

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

(2018) Sarah Cohen et al.   Nature Communications

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

(2018) Agnese Cristini et al.   Cell Reports

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

Human proteins that interact with RNA/DNA hybrids

(2018) Isabel X. Wang et al.   GENOME RESEARCH

Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

(2018) Lorenzo Costantino et al.   MOLECULAR CELL

R-Loops in Motor Neuron Diseases

(2018) Martina G. L. Perego et al.   MOLECULAR NEUROBIOLOGY

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Identification of G-Quadruplex-Binding Protein from the Exploration of RGG Motif/G-Quadruplex Interactions

(2018) Zhou-Li Huang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

GADD45A binds R-loops and recruits TET1 to CpG island promoters

(2018) Khelifa Arab et al.   NATURE GENETICS

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

(2018) Alessio De Magis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

(2017) Robert Hänsel-Hertsch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors

(2017) et al.   Genes

Aquarius is required for proper CtIP expression and homologous recombination repair

(2017) Ryo Sakasai et al.   Scientific Reports

Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

(2016) Corina Ohle et al.   CELL

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

(2016) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

(2016) Julio C. Morales et al.   PLoS Genetics

Distinct stages in stress granule assembly and disassembly

(2016) Joshua R Wheeler et al.   eLife

Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters

(2016) Jessica Marinello et al.   PLoS One

Structural Biology Turned on Its Head

(2015) Guillaume Bouvignies et al.   CHEMBIOCHEM

Nuclear bodies: the emerging biophysics of nucleoplasmic phases

(2015) Lian Zhu et al.   CURRENT OPINION IN CELL BIOLOGY

Targeting intrinsically disordered proteins in rational drug discovery

(2015) Susmitha Ambadipudi et al.   Expert Opinion on Drug Discovery

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

(2015) Inessa De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

(2015) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

(2015) Raquel Boque-Sastre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

(2015) Nikita Vasilyev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breaking bad: R-loops and genome integrity

(2015) Julie Sollier et al.   TRENDS IN CELL BIOLOGY

The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

(2015) Inessa De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

R-loops highlight the nucleus in ALS

(2015) Jayesh S Salvi et al.   Nucleus

R-loops highlight the nucleus in ALS

(2015) Jayesh S Salvi et al.   Nucleus

A Chromatin-Dependent Role of the Fragile X Mental Retardation Protein FMRP in the DNA Damage Response

(2014) Roman Alpatov et al.   CELL

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts

(2014) E. Herrera-Moyano et al.   GENES & 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

Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain

(2014) Leila K. Myrick et al.   HUMAN MOLECULAR GENETICS

DNA and RNA Quadruplex-Binding Proteins

(2014) Václav Brázda et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2014) Julie Sollier et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch

(2014) Alaji Bah et al.   NATURE

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

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

(2014) Matthias Groh 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

Specific Binding of Modified RGG Domain in TLS/FUS to G-Quadruplex RNA: Tyrosines in RGG Domain Recognize 2′-OH of the Riboses of Loops in G-Quadruplex

(2013) Kentaro Takahama et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

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

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

R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli

(2013) Hallie Wimberly et al.   Nature Communications

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

(2012) Amaya Alzu et al.   CELL

Intrinsically disordered proteins and novel strategies for drug discovery

(2012) Vladimir N. Uversky   Expert Opinion on Drug Discovery

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

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Versatility from Protein Disorder

(2012) M. M. Babu et al.   SCIENCE

Molecular Mechanisms of Fragile X Syndrome: A Twenty-Year Perspective

(2011) Michael R. Santoro et al.   Annual Review of Pathology-Mechanisms of Disease

Cruciform structures are a common DNA feature important for regulating biological processes

(2011) Václav Brázda et al.   BMC MOLECULAR BIOLOGY

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

(2011) Roberto Chiarle et al.   CELL

Intrinsically disordered proteins: regulation and disease

(2011) M Madan Babu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2011) Prasun Chakraborty et al.   DNA REPAIR

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

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

Novel Strategies for Drug Discovery Based on Intrinsically Disordered Proteins (IDPs)

(2011) Jihua Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2011) Lamia Wahba 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

Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity

(2011) T. Wongsurawat et al.   NUCLEIC ACIDS RESEARCH

Dynamic protein–DNA recognition: beyond what can be seen

(2011) Monika Fuxreiter et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Arginines of the RGG box regulate FMRP association with polyribosomes and mRNA

(2010) E. Blackwell et al.   HUMAN MOLECULAR GENETICS

Mammalian Mitochondrial DNA Replication Intermediates Are Essentially Duplex but Contain Extensive Tracts of RNA/DNA Hybrid

(2010) Jaakko L.O. Pohjoismäki et al.   JOURNAL OF MOLECULAR BIOLOGY

Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives

(2010) Kenneth N Kreuzer et al.   Virology Journal

Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment

(2009) Eric L. Peterson et al.   BIOINFORMATICS

Ribonuclease H: the enzymes in eukaryotes

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

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

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

A Novel Function for Fragile X Mental Retardation Protein in Translational Activation

(2009) Elias G Bechara et al.   PLOS BIOLOGY

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept

(2008) Vladimir N. Uversky et al.   Annual Review of Biophysics

Fragile X syndrome

(2008) Kathryn B Garber et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Structure and function of KH domains

(2008) Roberto Valverde et al.   FEBS Journal