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

Understanding the Role of the Transcription Factor Sp1 in Ovarian Cancer: from Theory to Practice

(2020) Vellingiri et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A guide to computational methods for G-quadruplex prediction

(2020) Emilia Puig Lombardi et al.   NUCLEIC ACIDS RESEARCH

Mgs1 protein supports genome stability via recognition of G-quadruplex DNA structures

(2020) Theresa Zacheja et al.   FASEB JOURNAL

Landscape of G-quadruplex DNA structural regions in breast cancer

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

The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma

(2020) Sara Lago et al.   NUCLEIC ACIDS RESEARCH

Maintaining mitochondria in beige adipose tissue

(2019) Xiaodan Lu   Adipocyte

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

(2019) Giovanni Marsico et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Yue Hou et al.   Epigenetics

The diverse structural landscape of quadruplexes

(2019) Helen L. Lightfoot et al.   FEBS LETTERS

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

(2019) Anna Varizhuk et al.   BIOESSAYS

DNA G‐quadruplex stability, position and chromatin accessibility are associated with CpG island methylation

(2019) Manuel Jara‐Espejo et al.   FEBS Journal

DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation

(2019) Guanhui Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Oncogenic Signaling Pathways in BRAF-Mutant Melanoma Cells are Modulated by Naphthalene Diimide-Like G-Quadruplex Ligands

(2019) Recagni et al.   Cells

Hijacking of the AP-1 Signaling Pathway during Development of ATL

(2018) Hélène Gazon et al.   Frontiers in Microbiology

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

(2018) Ilias Georgakopoulos-Soares et al.   GENOME RESEARCH

Down-Regulation of the Androgen Receptor by G-Quadruplex Ligands Sensitizes Castration-Resistant Prostate Cancer Cells to Enzalutamide

(2018) Martina Tassinari et al.   JOURNAL OF MEDICINAL CHEMISTRY

DNA G-quadruplex structures mold the DNA methylome

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

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer

(2017) Gemma Macchia et al.   GENETICS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks

(2017) Mathieu Lavallée-Adam et al.   NUCLEIC ACIDS RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

A core extended naphtalene diimide G-quadruplex ligand potently inhibits herpes simplex virus 1 replication

(2017) Sara Callegaro et al.   Scientific Reports

The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer

(2017) Gemma Macchia et al.   GENETICS

The Interplay between G-quadruplex and Transcription

(2017) Nayun Kim   CURRENT MEDICINAL CHEMISTRY

Quadruplex Nucleic Acids as Novel Therapeutic Targets

(2016) Stephen Neidle   JOURNAL OF MEDICINAL CHEMISTRY

Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA

(2016) Carika Weldon et al.   Nature Chemical Biology

G-quadruplex structures mark human regulatory chromatin

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

G-quadruplexes as novel cis-elements controlling transcription during embryonic development

(2016) Aldana P. David et al.   NUCLEIC ACIDS RESEARCH

Re-evaluation of G-quadruplex propensity with G4Hunter

(2016) Amina Bedrat et al.   NUCLEIC ACIDS RESEARCH

Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends

(2016) Julia H. Chariker et al.   PLoS One

GNG Motifs Can Replace a GGG Stretch during G-Quadruplex Formation in a Context Dependent Manner

(2016) Kohal Das et al.   PLoS One

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

Direct visualization of both DNA and RNA quadruplexes in human cells via an uncommon spectroscopic method

(2016) Aurélien Laguerre et al.   Scientific Reports

The Herpes Simplex Virus-1 genome contains multiple clusters of repeated G-quadruplex: Implications for the antiviral activity of a G-quadruplex ligand

(2015) Sara Artusi et al.   ANTIVIRAL RESEARCH

Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

(2015) John A. Smestad et al.   BMC Medical Genetics

Visualization of RNA-Quadruplexes in Live Cells

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

High-throughput sequencing of DNA G-quadruplex structures in the human genome

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

Sp1 transcription factor: A long-standing target in cancer chemotherapy

(2015) Carolina Vizcaíno et al.   PHARMACOLOGY & THERAPEUTICS

Telomeric G-quadruplexes are a substrate and site of localization for human telomerase

(2015) Aaron L. Moye et al.   Nature Communications

The interactions between a small molecule and G-quadruplexes are visualized by fluorescence lifetime imaging microscopy

(2015) Arun Shivalingam et al.   Nature Communications

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues

(2014) Giulia Biffi et al.   PLoS One

Toll-Like Receptor 9 in Breast Cancer

(2014) Jouko Sandholm et al.   Frontiers in Immunology

Quantitative visualization of DNA G-quadruplex structures in human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Detection of G-quadruplex DNA in mammalian cells

(2013) A. Henderson et al.   NUCLEIC ACIDS RESEARCH

Formation of a Unique Cluster of G-Quadruplex Structures in the HIV-1 nef Coding Region: Implications for Antiviral Activity

(2013) Rosalba Perrone et al.   PLoS One

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

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

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

Heterogeneous Nuclear Ribonucleoprotein K and Nucleolin as Transcriptional Activators of the Vascular Endothelial Growth Factor Promoter through Interaction with Secondary DNA Structures

(2011) Diana J. Uribe et al.   BIOCHEMISTRY

DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase

(2011) Katrin Paeschke et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

Characteristic increase in nucleocytoplasmic protein glycosylation by O -GlcNAc in 3T3-L1 adipocyte differentiation

(2010) Katsunori Ishihara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification and Characterization of Nucleolin as a c-mycG-quadruplex-binding Protein

(2009) Verónica González et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evaluation of cytochrome P450 1 (CYP1) and N-acetyltransferase 1 (NAT1) activities in HaCaT cells: Implications for the development of in vitro techniques for predictive testing of contact sensitizers

(2009) Jutta Bonifas et al.   TOXICOLOGY IN VITRO

TLR7 and TLR8 as targets in cancer therapy

(2008) M P Schön et al.   ONCOGENE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Genome-wide analysis reveals regulatory role of G4 DNA in gene transcription

(2007) Z. Du et al.   GENOME RESEARCH