DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops

Proximity labeling identifies a repertoire of site-specific R-loop modulators

(2022) Qingqing Yan et al.   Nature Communications

Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops

(2022) João C Sabino et al.   eLife

Sources, resolution and physiological relevance of R-loops and RNA–DNA hybrids

(2022) Eva Petermann et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation

(2022) Agnese Cristini et al.   Nature Communications

MeCP2: The Genetic Driver of Rett Syndrome Epigenetics

(2021) Katrina V. Good et al.   Frontiers in Genetics

BRCA2 promotes R‐loop resolution by DDX5 helicase at DNA breaks to facilitate their repair by homologous recombination

(2021) Gaetana Sessa et al.   EMBO JOURNAL

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

(2021) Aleix Bayona-Feliu et al.   NATURE GENETICS

ARID1A regulates R-loop associated DNA replication stress

(2021) Shuhe Tsai et al.   PLoS Genetics

UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair

(2021) Greg H. P. Ngo et al.   Nature Communications

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

(2020) Carmen Pérez-Calero et al.   GENES & DEVELOPMENT

MeCP2 links heterochromatin condensates and neurodevelopmental disease

(2020) Charles H. Li et al.   NATURE

Nucleolar RNA polymerase II drives ribosome biogenesis

(2020) Karan J. Abraham et al.   NATURE

TDP-43 dysfunction results in R-loop accumulation and DNA replication defects

(2020) Matthew Wood et al.   JOURNAL OF CELL SCIENCE

Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability

(2020) Lisa Prendergast et al.   Nature Communications

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage

(2020) Marta Giannini et al.   PLoS Genetics

R-Loops as Cellular Regulators and Genomic Threats

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

Transcription-mediated replication hindrance: a major driver of genome instability

(2019) Belén Gómez-González et al.   GENES & DEVELOPMENT

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

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

(2019) Sonia Barroso et al.   EMBO REPORTS

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability

(2019) Jessica L. Feldman et al.   Cell Reports

Genetic interactions of G-quadruplexes in humans

(2019) Katherine G Zyner et al.   eLife

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

MeCP2 Represses the Rate of Transcriptional Initiation of Highly Methylated Long Genes

(2019) Lisa D. Boxer et al.   MOLECULAR CELL

DNA methylation directs microRNA biogenesis in mammalian cells

(2019) Ohad Glaich et al.   Nature Communications

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

Rett syndrome: insights into genetic, molecular and circuit mechanisms

(2018) Jacque P. K. Ip et al.   NATURE REVIEWS NEUROSCIENCE

Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis

(2018) Mikael S. Lindström et al.   ONCOGENE

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

Human proteins that interact with RNA/DNA hybrids

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

FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress

(2018) Yusuke Okamoto et al.   FEBS Journal

SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability

(2017) Chenlin Song et al.   GENES & DEVELOPMENT

R Loops and Links to Human Disease

(2017) Patricia Richard et al.   JOURNAL OF MOLECULAR BIOLOGY

Histone Mutants Separate R Loop Formation from Genome Instability Induction

(2017) Desiré García-Pichardo et al.   MOLECULAR CELL

PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes

(2017) Phong Lan Thao Tran et al.   Nature Communications

Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation

(2017) Sreerama Chaitanya Sridhara et al.   Cell Reports

DEAD Box 1 Facilitates Removal of RNA and Homologous Recombination at DNA Double-Strand Breaks

(2016) Lei Li et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription

(2015) Rebekka A. Schwab et al.   MOLECULAR CELL

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

(2015) Elodie Hatchi et al.   MOLECULAR CELL

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

(2015) Julie Nadel et al.   Epigenetics & Chromatin

The Fanconi Anemia Pathway Protects Genome Integrity from R-loops

(2015) María L. García-Rubio et al.   PLoS Genetics

MeCP2 Suppresses Nuclear MicroRNA Processing and Dendritic Growth by Regulating the DGCR8/Drosha Complex

(2014) Tian-Lin Cheng et al.   DEVELOPMENTAL CELL

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

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

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

RNA helicase DDX21 coordinates transcription and ribosomal RNA processing

(2014) Eliezer Calo et al.   NATURE

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

(2014) Vaibhav Bhatia et al.   NATURE

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

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

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

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

Ubiquitin and Proteasomes in Transcription

(2012) Fuqiang Geng et al.   Annual Review of Biochemistry

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

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

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

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

From unwinding to clamping — the DEAD box RNA helicase family

(2011) Patrick Linder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo

(2010) Alicia Subtil-Rodríguez et al.   EMBO REPORTS

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

(2010) Peter J. Skene et al.   MOLECULAR CELL

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL