G-Quadruplexes in RNA Biology: Recent Advances and Future Directions

Poly(ADP-ribose): A Dynamic Trigger for Biomolecular Condensate Formation

(2020) Anthony K.L. Leung   TRENDS IN CELL BIOLOGY

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations

(2020) David S. M. Lee et al.   Nature Communications

Potential G-Quadruplex Forming Sequences and N6-Methyladenosine Colocalize at Human Pre-mRNA Intron Splice Sites

(2020) Manuel Jara-Espejo et al.   ACS Chemical Biology

Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

(2020) David W. Sanders et al.   CELL

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

RNA G-quadruplex regulates microRNA-26a biogenesis and function

(2020) Geng Liu et al.   JOURNAL OF HEPATOLOGY

The regulation and functions of DNA and RNA G-quadruplexes

(2020) Dhaval Varshney et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Hsp27 chaperones FUS phase separation under the modulation of stress-induced phosphorylation

(2020) Zhenying Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms and Regulation of RNA Condensation in RNP Granule Formation

(2020) Devin Tauber et al.   TRENDS IN BIOCHEMICAL SCIENCES

hnRNP H/F drive RNA G-quadruplex-mediated translation linked to genomic instability and therapy resistance in glioblastoma

(2020) Pauline Herviou et al.   Nature Communications

Single-molecule visualization of DNA G-quadruplex formation in live cells

(2020) Marco Di Antonio et al.   Nature Chemistry

RNA contributions to the form and function of biomolecular condensates

(2020) Christine Roden et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences

(2020) Raeann Goering et al.   eLife

The Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA) binds to the G-quadruplex of the BAG-1 5′UTR

(2020) François Bolduc et al.   BIOCHIMIE

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

Colocalization of m6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N6-Methylation

(2019) Aaron M. Fleming et al.   ACS Central Science

Purification of cross-linked RNA-protein complexes by phenol-toluol extraction

(2019) Erika C. Urdaneta et al.   Nature Communications

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

A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos

(2019) Andrea Putnam et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TEFM regulates both transcription elongation and RNA processing in mitochondria

(2019) Shan Jiang et al.   EMBO REPORTS

METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

(2019) Luca Pandolfini et al.   MOLECULAR CELL

Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions

(2019) Julia K. Nussbacher et al.   NEURON

RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36

(2019) Ramreddy Tippana et al.   Nature Communications

m6A enhances the phase separation potential of mRNA

(2019) Ryan J. Ries et al.   NATURE

DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions

(2019) Markus Sauer et al.   Nature Communications

G-quadruplex dynamics contribute to regulation of mitochondrial gene expression

(2019) M. Falabella et al.   Scientific Reports

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

Phospho-dependent phase separation of FMRP and CAPRIN1 recapitulates regulation of translation and deadenylation

(2019) Tae Hun Kim et al.   SCIENCE

The role of RNA G‐quadruplexes in human diseases and therapeutic strategies

(2019) Prakash Kharel et al.   Wiley Interdisciplinary Reviews-RNA

PhaSepDB: a database of liquid–liquid phase separation related proteins

(2019) Kaiqiang You et al.   NUCLEIC ACIDS RESEARCH

Tracking the Dynamic Folding and Unfolding of RNA G-Quadruplexes in Live Cells

(2018) Xiu-Cai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5′ UTR of tumor-associated mRNAs

(2018) Tatsuo Serikawa et al.   BIOCHIMIE

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation

(2018) Mario Hofweber et al.   CELL

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

(2018) Nicola Guzzi et al.   CELL

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

Capturing the interactome of newly transcribed RNA

(2018) Xichen Bao et al.   NATURE METHODS

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

mRNA structure determines specificity of a polyQ-driven phase separation

(2018) Erin M. Langdon et al.   SCIENCE

Protein Phase Separation: A New Phase in Cell Biology

(2018) Steven Boeynaems et al.   TRENDS IN CELL BIOLOGY

Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome

(2018) Chun Kit Kwok et al.   Cold Spring Harbor Perspectives in Biology

Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria

(2018) Zbigniew Pietras et al.   Nature Communications

Structural analysis reveals the formation and role of RNA G-quadruplex structures in human mature microRNAs

(2018) Ka Lung Chan et al.   CHEMICAL COMMUNICATIONS

Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts

(2018) Barbara Herdy et al.   NUCLEIC ACIDS RESEARCH

G-Quadruplexes: More Than Just a Kink in Microbial Genomes

(2018) Nandhini Saranathan et al.   TRENDS IN MICROBIOLOGY

Controllable protein phase separation and modular recruitment to form responsive membraneless organelles

(2018) Benjamin S. Schuster et al.   Nature Communications

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

(2018) Jakob Trendel 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

Translational control of tumor immune escape via the eIF4F–STAT1–PD-L1 axis in melanoma

(2018) Michaël Cerezo et al.   NATURE MEDICINE

Binding of cellular nucleolin with the viral core RNA G-quadruplex structure suppresses HCV replication

(2018) Wen-Xiu Bian et al.   NUCLEIC ACIDS RESEARCH

Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture

(2018) Joel I. Perez-Perri et al.   Nature Communications

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

(2018) Sunny Y. Yang et al.   Nature Communications

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms

(2017) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein–RNA Interactome

(2017) A. Emilia Arguello et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics

(2017) Steven Boeynaems et al.   MOLECULAR CELL

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human DDX21 binds and unwinds RNA guanine quadruplexes

(2017) Ewan K.S. McRae et al.   NUCLEIC ACIDS RESEARCH

Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding

(2017) Bagdeser A. Ozdilek et al.   NUCLEIC ACIDS RESEARCH

Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances

(2017) Sarah F. Pearce et al.   TRENDS IN BIOCHEMICAL SCIENCES

G-Quadruplexes: Prediction, Characterization, and Biological Application

(2017) Chun Kit Kwok et al.   TRENDS IN BIOTECHNOLOGY

Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs

(2017) Shawn M. Lyons et al.   Nature Communications

Nucleolin directly mediates Epstein-Barr virus immune evasion through binding to G-quadruplexes of EBNA1 mRNA

(2017) María José Lista et al.   Nature Communications

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ALS/FTD-Associated C9ORF72 Repeat RNA Promotes Phase Transitions In Vitro and in Cells

(2017) Marta M. Fay et al.   Cell Reports

The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation

(2017) Daniel Benhalevy et al.   Cell Reports

Structural Analysis using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA

(2016) Chun Kit Kwok et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Visualization of NRAS RNA G-Quadruplex Structures in Cells with an Engineered Fluorogenic Hybridization Probe

(2016) Shuo-Bin Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Comprehensive Identification of RNA-Binding Domains in Human Cells

(2016) Alfredo Castello et al.   MOLECULAR CELL

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

(2016) Chun Kit Kwok et al.   NATURE METHODS

Re-evaluation of G-quadruplex propensity with G4Hunter

(2016) Amina Bedrat et al.   NUCLEIC ACIDS RESEARCH

RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

(2016) J. U. Guo et al.   SCIENCE

The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains

(2016) Erin G Conlon et al.   eLife

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

(2015) Guramrit Singh et al.   Annual Review of Biochemistry

G4-associated human diseases

(2015) N. Maizels   EMBO REPORTS

Visualization of RNA-Quadruplexes in Live Cells

(2015) Aurélien Laguerre et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Post-transcriptional Regulation of Nkx2-5 by RHAU in Heart Development

(2015) Junwei Nie et al.   Cell Reports

Aven recognition of RNA G-quadruplexes regulates translation of the mixed lineage leukemia protooncogenes

(2015) Palaniraja Thandapani et al.   eLife

A second layer of information in RNA

(2014) Silvia B. V. Ramos et al.   NATURE

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer

(2014) Andrew L. Wolfe et al.   NATURE

C9orf72 nucleotide repeat structures initiate molecular cascades of disease

(2014) Aaron R. Haeusler et al.   NATURE

G-quadruplexes regulate Epstein-Barr virus–encoded nuclear antigen 1 mRNA translation

(2014) Pierre Murat et al.   Nature Chemical Biology

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

Identification and characterization of RNA guanine-quadruplex binding proteins

(2014) Annekathrin von Hacht et al.   NUCLEIC ACIDS RESEARCH

GRSF1 Regulates RNA Processing in Mitochondrial RNA Granules

(2013) Alexis A. Jourdain et al.   Cell Metabolism

Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs

(2010) Cyril Dominguez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Role for G-Quadruplex RNA Binding by Epstein-Barr Virus Nuclear Antigen 1 in DNA Replication and Metaphase Chromosome Attachment

(2009) J. Norseen et al.   JOURNAL OF VIROLOGY

The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes

(2009) Jinzhi Tan et al.   PLoS Pathogens

G-quadruplexes: the beginning and end of UTRs

(2008) Julian Leon Huppert et al.   NUCLEIC ACIDS RESEARCH