Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Roles of eukaryotic topoisomerases in transcription, replication and genomic stability

(2016) Yves Pommier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation

(2016) Eric J. Rawdon et al.   NUCLEIC ACIDS RESEARCH

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Stochastic Model of Supercoiling-Dependent Transcription

(2016) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Mechanisms of backtrack recovery by RNA polymerases I and II

(2016) Ana Lisica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Afzal Husain et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

(2015) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

(2015) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

Driving knots on DNA with AC/DC electric fields: topological friction and memory effects

(2014) Marco Di Stefano et al.   Soft Matter

BAF complexes facilitate decatenation of DNA by topoisomerase IIα

(2013) Emily C. Dykhuizen et al.   NATURE

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

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength

(2012) A. Tempestini et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Ignacio Bermúdez et al.   NUCLEIC ACIDS RESEARCH

Topological origins of chromosomal territories

(2009) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

DNA relaxation dynamics as a probe for the intracellular environment

(2009) J. K. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of chiral discrimination by topoisomerase IV

(2009) K. C. Neuman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Single-Molecule Studies of RNA Polymerase: Motoring Along

(2008) Kristina M. Herbert et al.   Annual Review of Biochemistry

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

The functional response of upstream DNA to dynamic supercoiling in vivo

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

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology