MYC assembles and stimulates topoisomerases 1 and 2 in a “topoisome”

Targeting MYCN in Pediatric and Adult Cancers

(2021) Zhihui Liu et al.   Frontiers in Oncology

Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing

(2021) Andrés Herrero-Ruiz et al.   Cell Reports

Transcription-mediated supercoiling regulates genome folding and loop formation

(2021) Maria Victoria Neguembor et al.   MOLECULAR CELL

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1

(2021) Anika Wiegard et al.   MOLECULAR CELL

Target gene-independent functions of MYC oncoproteins

(2020) Apoorva Baluapuri et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Suppressing proteasome mediated processing of Topoisomerase II DNA-protein complexes preserves genome integrity

(2020) Nicholas Sciascia et al.   eLife

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Topoisomerase IIα is essential for maintenance of mitotic chromosome structure

(2020) Christian F. Nielsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissecting transcriptional amplification by MYC

(2020) Zuqin Nie et al.   eLife

Discovery and Mechanistic Study of Tailor-Made Quinoline Derivatives as Topoisomerase 1 Poisons with Potent Anticancer Activity

(2019) Biswajit Kundu et al.   JOURNAL OF MEDICINAL CHEMISTRY

epic2 efficiently finds diffuse domains in ChIP-seq data

(2019) Endre Bakken Stovner et al.   BIOINFORMATICS

Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole

(2019) Aisha Yesbolatova et al.   METHODS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity

(2019) Tung T. Le et al.   CELL

Multiple direct interactions of TBP with the MYC oncoprotein

(2019) Yong Wei et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome

(2019) William H. Gittens et al.   Nature Communications

Neutral Porphyrin Derivative Exerts Anticancer Activity by Targeting Cellular Topoisomerase I (Top1) and Promotes Apoptotic Cell Death without Stabilizing Top1-DNA Cleavage Complexes

(2018) Subhendu K. Das et al.   JOURNAL OF MEDICINAL CHEMISTRY

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

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

(2018) Benjamin R. Sabari et al.   SCIENCE

The Expanding World of N-MYC–Driven Tumors

(2018) David S. Rickman et al.   Cancer Discovery

Post-translational modifications in DNA topoisomerase 2α highlight the role of a eukaryote-specific residue in the ATPase domain

(2018) Claire Bedez et al.   Scientific Reports

MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis

(2018) Manpreet Kalkat et al.   MOLECULAR CELL

Resveratrol: A novel type of topoisomerase II inhibitor

(2017) Joyce H. Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PAF1 complex component Leo1 helps recruitDrosophilaMyc to promoters

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

Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle

(2017) Gabriele Büchel et al.   Cell Reports

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

(2017) Fedor Kouzine et al.   Cell Systems

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Nucleoporin-mediated regulation of cell identity genes

(2016) Arkaitz Ibarra et al.   GENES & DEVELOPMENT

Poly(ADP-ribose) polymers regulate DNA topoisomerase I (Top1) nuclear dynamics and camptothecin sensitivity in living cells

(2016) Subhendu K. Das et al.   NUCLEIC ACIDS RESEARCH

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

(2016) Toyoaki Natsume et al.   Cell Reports

Different promoter affinities account for specificity in MYC-dependent gene regulation

(2016) Francesca Lorenzin et al.   eLife

Emerging therapies in systemic lupus erythematous: from clinical trial to the real life

(2016) Huza Zhang et al.   Expert Review of Clinical Pharmacology

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

(2015) Janusz Puc et al.   CELL

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

(2015) Ram Madabhushi et al.   CELL

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability

(2015) Stephanie A. Schalbetter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A rapid and sensitive assay for DNA–protein covalent complexes in living cells

(2013) Kostantin Kiianitsa et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Gene regulation and priming by topoisomerase IIα in embryonic stem cells

(2013) Sudhir Thakurela et al.   Nature Communications

Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation

(2013) Swagat Ray et al.   Nature Communications

Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss

(2013) Maxim Y. Sheinin et al.   Nature Communications

Drugging Topoisomerases: Lessons and Challenges

(2012) Yves Pommier   ACS Chemical Biology

The importance of being supercoiled: How DNA mechanics regulate dynamic processes

(2012) Laura Baranello et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Topoisomerase II is required for the production of long Pol II gene transcripts in yeast

(2012) Ricky S. Joshi et al.   NUCLEIC ACIDS RESEARCH

Target genes of Topoisomerase II  regulate neuronal survival and are defined by their chromatin state

(2012) V. K. Tiwari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Myc’s secret life without Max

(2011) Peter Gallant et al.   CELL CYCLE

Chromosome length influences replication-induced topological stress

(2011) Andreas Kegel et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

The functional response of upstream DNA to dynamic supercoiling in vivo

(2008) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY