Negative supercoil at gene boundaries modulates gene topology

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions

(2017) Xingwang Li et al.   Nature Protocols

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

(2017) Fedor Kouzine et al.   Cell Systems

Transcription–replication conflicts: how they occur and how they are resolved

(2016) Tatiana García-Muse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin remodeller SMARCA4 recruits topoisomerase 1 and suppresses transcription-associated genomic instability

(2016) Afzal Husain et al.   Nature Communications

Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

(2015) Silvia Emma Rossi et al.   Cell Reports

Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability

(2014) Fei-Long Meng et al.   CELL

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

(2014) Stephan Hamperl et al.   DNA REPAIR

Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils

(2014) X. Fernandez et al.   EMBO JOURNAL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin

(2014) Divakaran Murugesapillai et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Profiling of Yeast DNA:RNA Hybrid Prone Sites with DRIP-Chip

(2014) Yujia A. Chan et al.   PLoS Genetics

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton 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

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Preventing Replication Stress to Maintain Genome Stability: Resolving Conflicts between Replication and Transcription

(2012) Rodrigo Bermejo et al.   MOLECULAR CELL

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

(2012) Dane Z. Hazelbaker et al.   MOLECULAR CELL

Rates of Gyrase Supercoiling and Transcription Elongation Control Supercoil Density in a Bacterial Chromosome

(2012) Nikolay Rovinskiy et al.   PLoS Genetics

DNA Topoisomerases Maintain Promoters in a State Competent for Transcriptional Activation in Saccharomyces cerevisiae

(2012) Jakob Madsen Pedersen et al.   PLoS Genetics

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast

(2011) A. S. Sperling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments

(2010) Arnaud Droit et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Replication Termination at Eukaryotic Chromosomes Is Mediated by Top2 and Occurs at Genomic Loci Containing Pausing Elements

(2010) Daniele Fachinetti et al.   MOLECULAR CELL

A method for genome-wide analysis of DNA helical tension by means of psoralen–DNA photobinding

(2010) Ignacio Bermúdez et al.   NUCLEIC ACIDS RESEARCH

Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription

(2009) Rodrigo Bermejo et al.   CELL

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

(2009) Sue Mei Tan-Wong et al.   GENES & DEVELOPMENT

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

(2009) Roberto Perales et al.   MOLECULAR CELL

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY