DNA G-quadruplex structures: more than simple roadblocks to transcription?

G-Quadruplex Structures Colocalize with Transcription Factories and Nuclear Speckles Surrounded by Acetylated and Dimethylated Histones H3

(2021) Denisa Komůrková et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Parallel G-quadruplexes recruit the HSV-1 transcription factor ICP4 to promote viral transcription in herpes virus-infected human cells

(2021) Ilaria Frasson et al.   Communications Biology

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

(2021) Sara Lago et al.   Nature Communications

Resolution of ROS‐induced G‐quadruplexes and R‐loops at transcriptionally active sites is dependent on BLM helicase

(2020) Jun Tan et al.   FEBS LETTERS

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Evaluating Enhancer Function and Transcription

(2020) Andrew Field et al.   Annual Review of Biochemistry

Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures

(2020) Iulia I. Pavlova et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Enhancer–promoter interactions and transcription

(2020) Douglas R. Higgs   NATURE GENETICS

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

(2020) Jonathan A. Beagan et al.   NATURE NEUROSCIENCE

Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop ‘G4 Kissing’ interaction

(2020) Jonathan D Williams et al.   NUCLEIC ACIDS RESEARCH

Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome

(2020) Shrabasti Roychoudhury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Marco Di Antonio et al.   Nature Chemistry

Landscape of G-quadruplex DNA structural regions in breast cancer

(2020) Robert Hänsel-Hertsch et al.   NATURE GENETICS

R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation

(2020) Chun-Ying Lee et al.   Nature Communications

Liquid–Liquid Phase Separation in Crowded Environments

(2020) Alain A. M. André et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Detection of genomic G-quadruplexes in living cells using a small artificial protein

(2020) Ke-wei Zheng et al.   NUCLEIC ACIDS RESEARCH

G‐quadruplex‐forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression

(2020) Kyoko Matsumoto et al.   GENES TO CELLS

YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression

(2020) Lin Li et al.   Nature Chemical Biology

G-Quadruplex loops regulate PARP-1 enzymatic activation

(2020) Andrea D Edwards et al.   NUCLEIC ACIDS RESEARCH

Oxidative Modification of the Potential G-Quadruplex Sequence in the PCNA Gene Promoter Can Turn on Transcription

(2019) Samuel C. J. Redstone et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress

(2019) Aaron M Fleming et al.   NUCLEIC ACIDS RESEARCH

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure

(2019) Yue Hou et al.   Epigenetics

Human NEIL3 Gene Expression Regulated by Epigenetic-Like Oxidative DNA Modification

(2019) Aaron M. Fleming et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stress granules and neurodegeneration

(2019) Benjamin Wolozin et al.   NATURE REVIEWS NEUROSCIENCE

Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters

(2019) Aaron M. Fleming et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies

(2018) Briana Van Treeck et al.   CELL

R-loop generation during transcription: Formation, processing and cellular outcomes

(2018) Boris P. Belotserkovskii et al.   DNA REPAIR

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

(2018) Ann Boija et al.   CELL

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

Non-duplex G-Quadruplex Structures Emerge as Mediators of Epigenetic Modifications

(2018) Ananda Kishore Mukherjee et al.   TRENDS IN GENETICS

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

(2017) Gang Ren et al.   MOLECULAR CELL

The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription

(2017) Susanna Cogoi et al.   NUCLEIC ACIDS RESEARCH

Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

(2017) Aaron M. Fleming et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G-Quadruplexes: Prediction, Characterization, and Biological Application

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

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours

(2017) Hong Xu et al.   Nature Communications

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

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

The Interplay between G-quadruplex and Transcription

(2017) Nayun Kim   CURRENT MEDICINAL CHEMISTRY

Enhancer deregulation in cancer and other diseases

(2016) Hans-Martin Herz   BIOESSAYS

Nucleolar organizer regions: genomic ‘dark matter’ requiring illumination

(2016) Brian McStay   GENES & DEVELOPMENT

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

(2016) Alicia K. Byrd et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

G-quadruplex structures mark human regulatory chromatin

(2016) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Disruption of PARP1 function inhibits base excision repair of a sub-set of DNA lesions

(2015) Pamela Reynolds et al.   NUCLEIC ACIDS RESEARCH

Enhancer-promoter interaction facilitated by transiently forming G-quadruplexes

(2015) Hedi Hegyi   Scientific Reports

Effects of cytosine methylation on transcription factor binding sites

(2014) Yulia A Medvedeva et al.   BMC GENOMICS

Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells

(2014) D. Schiavone et al.   EMBO JOURNAL

Quantification of Topological Coupling between DNA Superhelicity and G-quadruplex Formation

(2014) Sangeetha Selvam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Human AP endonuclease inefficiently removes abasic sites within G4 structures compared to duplex DNA

(2014) Christopher Broxson et al.   NUCLEIC ACIDS RESEARCH

One-electron oxidation reactions of purine and pyrimidine bases in cellular DNA

(2013) Jean Cadet et al.   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control

(2013) Ke-wei Zheng et al.   NUCLEIC ACIDS RESEARCH

Anticancer Activity and Cellular Repression of c-MYC by the G-Quadruplex-Stabilizing 11-Piperazinylquindoline Is Not Dependent on Direct Targeting of the G-Quadruplex in the c-MYC Promoter

(2012) Peda V. L. Boddupally et al.   JOURNAL OF MEDICINAL CHEMISTRY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

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

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Cohesin Mediates Chromatin Interactions That Regulate Mammalian β-globin Expression

(2011) Richard Chien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

(2011) Shankar Balasubramanian et al.   NATURE REVIEWS DRUG DISCOVERY

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

Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes

(2011) J. M. Lamonica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TheKRASPromoter Responds to Myc-associated Zinc Finger and Poly(ADP-ribose) Polymerase 1 Proteins, Which Recognize a Critical Quadruplex-formingGA-element

(2010) Susanna Cogoi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic Instability due to Defective Replication of Structured DNA

(2010) Peter Sarkies et al.   MOLECULAR CELL

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

(2009) Kangkan Halder et al.   Molecular BioSystems

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA

(2009) Ke-wei Zheng et al.   NUCLEIC ACIDS RESEARCH

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

(2009) Zhuo Du et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Regulatory Functions of Mammalian AP-Endonuclease (APE1/Ref-1), an Essential Multifunctional Protein

(2008) Kishor K. Bhakat et al.   ANTIOXIDANTS & REDOX SIGNALING

Thermodynamic prediction of RNA–DNA duplex-forming regions in the human genome

(2008) Julian L. Huppert   Molecular BioSystems

Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins

(2008) Susanna Cogoi et al.   NUCLEIC ACIDS RESEARCH

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes

(2008) Johanna Eddy et al.   NUCLEIC ACIDS RESEARCH