Genome-wide mapping of G-quadruplex structures with CUT&Tag

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor

(2021) Kang Wang et al.   Science Advances

Essential histone chaperones collaborate to regulate transcription and chromatin integrity

(2021) Olga Viktorovskaya et al.   GENES & DEVELOPMENT

Ligand-induced native G-quadruplex stabilization impairs transcription initiation

(2021) Conghui Li et al.   GENOME RESEARCH

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

(2021) Jenna Robinson et al.   NUCLEIC ACIDS RESEARCH

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

(2021) Sara Lago et al.   Nature Communications

Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ

(2020) Tong Wu et al.   NATURE METHODS

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

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

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

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

An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility

(2020) Carmen Navarro et al.   Nature Communications

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions

(2020) Panagiotis Kotsantis et al.   Cell Reports

Replication of G Quadruplex DNA

(2019) Leticia Koch Lerner et al.   Genes

G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma

(2019) Yuxiang Wang et al.   Nature Communications

Whole genome experimental maps of DNA G-quadruplexes in multiple species

(2019) Giovanni Marsico et al.   NUCLEIC ACIDS RESEARCH

Open Chromatin, Epigenetic Plasticity, and Nuclear Organization in Pluripotency

(2019) Sharon Schlesinger et al.   DEVELOPMENTAL CELL

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

G-quadruplex in animal development: Contribution to gene expression and genomic heterogeneity

(2018) Pablo Armas et al.   MECHANISMS OF DEVELOPMENT

Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

(2018) Robert Hänsel-Hertsch et al.   Nature Protocols

DNA G-quadruplex structures mold the DNA methylome

(2018) Shi-Qing Mao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design

(2017) S. Harikrishna et al.   Molecular BioSystems

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

Local epigenetic reprogramming induced by G-quadruplex ligands

(2017) Guillaume Guilbaud et al.   Nature Chemistry

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

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

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

(2017) Hong Xu et al.   Nature Communications

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome

(2017) Boris Simovski et al.   GigaScience

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

(2017) Fedor Kouzine et al.   Cell Systems

S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

(2016) Lamia Wahba et al.   GENES & DEVELOPMENT

G-quadruplex structures mark human regulatory chromatin

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

G-Quadruplexes Involving Both Strands of Genomic DNA Are Highly Abundant and Colocalize with Functional Sites in the Human Genome

(2016) Andrzej S Kudlicki   PLoS One

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

Enhancer-promoter interaction facilitated by transiently forming G-quadruplexes

(2015) Hedi Hegyi   Scientific Reports

Nucleotide Pool Depletion Induces G-Quadruplex-Dependent Perturbation of Gene Expression

(2015) Charikleia Papadopoulou et al.   Cell Reports

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

(2014) Heeyoun Bunch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions

(2014) Caiyan Jia et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

Quantitative visualization of DNA G-quadruplex structures in human cells

(2013) Giulia Biffi et al.   Nature Chemistry

TherMos: Estimating protein–DNA binding energies from in vivo binding profiles

(2013) Wenjie Sun et al.   NUCLEIC ACIDS RESEARCH

The G4 Genome

(2013) Nancy Maizels et al.   PLoS Genetics

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

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

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pyridostatin analogues promote telomere dysfunction and long-term growth inhibition in human cancer cells

(2012) Sebastian Müller et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Discovery of CX-5461, the First Direct and Selective Inhibitor of RNA Polymerase I, for Cancer Therapeutics

(2012) Mustapha Haddach et al.   ACS Medicinal Chemistry Letters

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Targeting RNA Polymerase I with an Oral Small Molecule CX-5461 Inhibits Ribosomal RNA Synthesis and Solid Tumor Growth

(2010) Denis Drygin et al.   CANCER RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis

(2009) D. Drygin et al.   CANCER RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

341 POSTER CX-5461, a novel, orally bioavailable selective small molecule inhibitor of RNA polymerase I transcription, induces autophagy and shows potent antitumor activity

(2008) D. Drygin et al.   EJC SUPPLEMENTS

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

Antitumor activity of G-quadruplex–interactive agent TMPyP4 in K562 leukemic cells

(2007) Yoko Mikami-Terao et al.   CANCER LETTERS