Non-canonical DNA structures in the human ribosomal DNA

Structure and Formation of Z-DNA and Z-RNA

(2023) Jeffrey B. Krall et al.   MOLECULES

Noncanonical DNA structures are drivers of genome evolution

(2023) Kateryna D. Makova et al.   TRENDS IN GENETICS

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

(2023) Radost Waszkiewicz et al.   NUCLEIC ACIDS RESEARCH

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

(2023) Esther Marchena-Cruz et al.   Cell Reports

Structural insights and shedding light on preferential interactions of dietary flavonoids with G-quadruplex DNA structures: A new horizon

(2023) Sagar Bag et al.   Heliyon

Non-B DNA structures as a booster of genome instability

(2023) Renée C. Duardo et al.   BIOCHIMIE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Dynamic alternative DNA structures in biology and disease

(2022) Guliang Wang et al.   NATURE REVIEWS GENETICS

Variability of Human rDNA and Transcription Activity of the Ribosomal Genes

(2022) Nikola Chmúrčiaková et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Variability of Human rDNA

(2021) Evgeny Smirnov et al.   Cells

Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell Integrity

(2021) Yu Yamamoto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

R‐loops mediate transcription‐associated formation of human rDNA secondary constrictions

(2021) Hong Zhou et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Regulatory roles of nucleolus organizer region-derived long non-coding RNAs

(2021) Qinyu Hao et al.   MAMMALIAN GENOME

Supercoiling and looping promote DNA base accessibility and coordination among distant sites

(2021) Jonathan M. Fogg et al.   Nature Communications

Human rDNA and Cancer

(2021) Evgeny Smirnov et al.   Cells

Ultra-Deep Coverage Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

(2020) Maika Malig et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Non-coding RNAs at the eukaryotic rDNA locus: RNA-DNA hybrids and beyond

(2020) Olga Vydzhak et al.   JOURNAL OF MOLECULAR BIOLOGY

The regulation and functions of DNA and RNA G-quadruplexes

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

A genome-wide and cotranscriptional suppressor of R loops

(2020) Jacob P. Matson et al.   GENES & DEVELOPMENT

Global analysis of inverted repeat sequences in human gene promoters reveals their non-random distribution and association with specific biological pathways

(2020) Václav Brázda et al.   GENOMICS

Nucleolar RNA polymerase II drives ribosome biogenesis

(2020) Karan J. Abraham et al.   NATURE

The Molecular Tête‐à‐tête between G‐Quadruplex and I‐motif in Human Genome

(2020) Pallabi Sengupta et al.   CHEMBIOCHEM

Interplay between DNA sequence and negative superhelicity drives R-loop structures

(2019) Robert Stolz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations

(2019) Roman Matyášek et al.   DNA RESEARCH

Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates?

(2019) Nadine Puget et al.   DNA REPAIR

Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

(2019) Xiao-Ou Zhang et al.   GENOME RESEARCH

Nucleolar Sequestration: Remodeling Nucleoli Into Amyloid Bodies

(2019) Miling Wang et al.   Frontiers in Genetics

Structural Characterization of i-Motif Structure in the Human Acetyl-CoA Carboxylase 1 Gene Promoters and Their Role in the Regulation of Gene Expression

(2018) Mangesh H. Kaulage et al.   CHEMBIOCHEM

lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures

(2018) Zhongliang Zhao et al.   GENES & DEVELOPMENT

I-motif DNA structures are formed in the nuclei of human cells

(2018) Mahdi Zeraati et al.   Nature Chemistry

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

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

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

(2018) Jung-Hyun Kim et al.   NUCLEIC ACIDS RESEARCH

RNA–DNA hybrids promote the expansion of Friedreich's ataxia (GAA)n repeats via break-induced replication

(2018) Alexander J Neil et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Map of R-Loop-Induced Damage Reveals How a Subset of R-Loops Contributes to Genomic Instability

(2018) Lorenzo Costantino et al.   MOLECULAR CELL

i-Motif DNA: structural features and significance to cell biology

(2018) Hala Abou Assi et al.   NUCLEIC ACIDS RESEARCH

Chemical-induced formation of BZ-junction with base extrusion

(2018) Vinod Kumar Subramani et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment

(2018) Giuseppina D’Alessandro et al.   Nature Communications

DNA sequence encodes the position of DNA supercoils

(2018) Sung Hyun Kim et al.   eLife

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH

(2017) Bartomeu Mir et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

4n–1 Is a “Sweet Spot” in DNA i-Motif Folding of 2′-Deoxycytidine Homopolymers

(2017) Aaron M. Fleming et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH

(2017) Elisé P. Wright et al.   NUCLEIC ACIDS RESEARCH

Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase

(2017) Shuntaro Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition

(2017) Mandar Kulkarni et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Purine– and pyrimidine–triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus

(2017) Rodrigo Maldonado et al.   RNA

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

(2017) Hong Xu et al.   Nature Communications

Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes

(2017) Amanda C. Hall et al.   Nucleus

Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes

(2017) Amanda C. Hall et al.   Nucleus

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

(2017) Fedor Kouzine et al.   Cell Systems

Mutually Exclusive Formation of G-Quadruplex and i-Motif Is a General Phenomenon Governed by Steric Hindrance in Duplex DNA

(2016) Yunxi Cui et al.   BIOCHEMISTRY

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

A Mechanosensor Mechanism Controls the G-Quadruplex/i-Motif Molecular Switch in the MYC Promoter NHE III1

(2016) Caleb Sutherland et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNase H enables efficient repair of R-loop induced DNA damage

(2016) Jeremy D Amon et al.   eLife

Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters

(2016) Jessica Marinello et al.   PLoS One

Alu element-containing RNAs maintain nucleolar structure and function

(2015) M. Caudron-Herger et al.   EMBO JOURNAL

BLM helicase facilitates telomere replication during leading strand synthesis of telomeres

(2015) William C. Drosopoulos et al.   JOURNAL OF CELL BIOLOGY

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

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

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

(2015) Julie Nadel et al.   Epigenetics & Chromatin

Analysis of histone modifications at human ribosomal DNA in liver cancer cell

(2015) Feng Yu et al.   Scientific Reports

Epigenetic Modification, Dehydration, and Molecular Crowding Effects on the Thermodynamics of i-Motif Structure Formation from C-Rich DNA

(2014) Yogini P. Bhavsar-Jog et al.   BIOCHEMISTRY

APTE: identification of indirect read-out A-DNA promoter elements in genomes

(2014) David C Whitley et al.   BMC BIOINFORMATICS

lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs

(2014) Nataša Savić et al.   Cell Stem Cell

Roles for Pbp1 and Caloric Restriction in Genome and Lifespan Maintenance via Suppression of RNA-DNA Hybrids

(2014) Jayesh S. Salvi et al.   DEVELOPMENTAL CELL

Ribosomal RNA gene repeats, their stability and cellular senescence

(2014) Takehiko KOBAYASHI   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Out of Balance: R-loops in Human Disease

(2014) Matthias Groh et al.   PLoS Genetics

50 years of DNA ‘Breathing’: Reflections on old and new approaches [For special issue of biopolymers on 50 years of nucleic acids research]

(2013) Peter H. von Hippel et al.   BIOPOLYMERS

DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability

(2013) Boris P. Belotserkovskii et al.   CHEMICAL REVIEWS

Noisy silence

(2013) Holger Bierhoff et al.   Epigenetics

Human Origin Recognition Complex Binds Preferentially to G-quadruplex-preferable RNA and Single-stranded DNA

(2013) Shoko Hoshina et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences

(2013) Vineeth Thachappilly Mukundan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Effect of Molecular Crowding on the Stability of Human c-MYC Promoter Sequence I-Motif at Neutral pH

(2013) Jingjing Cui et al.   MOLECULES

Nucleophosmin mutations alter its nucleolar localization by impairing G-quadruplex binding at ribosomal DNA

(2013) Sara Chiarella et al.   NUCLEIC ACIDS RESEARCH

Watching DNA breath one molecule at a time

(2013) J. Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

(2013) Lamia Wahba et al.   eLife

The nucleolar detention pathway

(2012) Timothy E. Audas et al.   CELL CYCLE

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells

(2012) B. S. Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Nucleophosmin is essential for c-Myc nucleolar localization and c-Myc-mediated rDNA transcription

(2012) Z Li et al.   ONCOGENE

Nucleolin Inhibits G4 Oligonucleotide Unwinding by Werner Helicase

(2012) Fred E. Indig et al.   PLoS One

Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork

(2012) D. Jose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bullied no more: when and how DNA shoves proteins around

(2012) Jonathan M. Fogg et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Cruciform structures are a common DNA feature important for regulating biological processes

(2011) Václav Brázda et al.   BMC MOLECULAR BIOLOGY

Conformational changes of non-B DNA

(2011) Jungkweon Choi et al.   CHEMICAL SOCIETY REVIEWS

A model for the topology of active ribosomal RNA genes

(2011) Serguei Denissov et al.   EMBO REPORTS

RNA polymerase I–specific subunits promote polymerase clustering to enhance the rRNA gene transcription cycle

(2011) Benjamin Albert et al.   JOURNAL OF CELL BIOLOGY

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

Integrative genomic analysis of human ribosomal DNA

(2011) Gabriel E. Zentner et al.   NUCLEIC ACIDS RESEARCH

Zalpha-domains: At the intersection between RNA editing and innate immunity

(2011) Alekos Athanasiadis   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Genome organization in and around the nucleolus

(2011) Attila Németh et al.   TRENDS IN GENETICS

Making sense of G-quadruplex and i-motif functions in oncogene promoters

(2010) Tracy A. Brooks et al.   FEBS Journal

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

(2010) R. Z. Cer et al.   NUCLEIC ACIDS RESEARCH

Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

(2010) M. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structure of the Eukaryotic Ribosome

(2010) A. Ben-Shem et al.   SCIENCE

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

(2009) D. Drygin et al.   CANCER RESEARCH

The folding and unfolding of eukaryotic chromatin

(2009) Andrew Bassett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin

(2009) Aurélien Bancaud et al.   EMBO JOURNAL

Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans

(2009) Raffaella Santoro et al.   EMBO REPORTS

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

Nonlinear Analysis of the Dynamics of DNA Breathing

(2009) M. Peyrard et al.   JOURNAL OF BIOLOGICAL PHYSICS

The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i-Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression

(2009) Daekyu Sun et al.   JOURNAL OF MEDICINAL CHEMISTRY

The i-Motif in thebcl-2P1 Promoter Forms an Unexpectedly Stable Structure with a Unique 8:5:7 Loop Folding Pattern

(2009) Samantha Kendrick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Formation of a Unique End-to-End Stacked Pair of G-Quadruplexes in the hTERT Core Promoter with Implications for Inhibition of Telomerase by G-Quadruplex-Interactive Ligands

(2009) SunMi L. Palumbo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

(2009) Boian S. Alexandrov et al.   NUCLEIC ACIDS RESEARCH

DNA triple helices: Biological consequences and therapeutic potential

(2008) Aklank Jain et al.   BIOCHIMIE

The structure of NoRC-associated RNA is crucial for targeting the chromatin remodelling complex NoRC to the nucleolus

(2008) Christine Mayer et al.   EMBO REPORTS

Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species

(2008) K. S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA