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

C Naughton, N Avlonitis, S Corless… - Nature structural & …, 2013 - nature.com
DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating
gene expression and DNA replication. However, DNA supercoiling at a genomic scale in …

[HTML][HTML] Supercoiling in DNA and chromatin

N Gilbert, J Allan - Current opinion in genetics & development, 2014 - Elsevier
Supercoiling is a fundamental property of DNA and chromatin. It is modulated by
polymerase and topoisomerase activities and, through regulated constraint, by …

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

F Kouzine, A Gupta, L Baranello, D Wojtowicz… - Nature structural & …, 2013 - nature.com
Transcription has the capacity to mechanically modify DNA topology, DNA structure and
nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn …

Effects of DNA supercoiling on chromatin architecture

S Corless, N Gilbert - Biophysical reviews, 2016 - Springer
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes,
from remodelling of nucleosomes at the base pair level through to large-scale chromatin …

Enhancer hubs and loop collisions identified from single-allele topologies

A Allahyar, C Vermeulen, BAM Bouwman, PHL Krijger… - Nature …, 2018 - nature.com
Chromatin folding contributes to the regulation of genomic processes such as gene activity.
Existing conformation capture methods characterize genome topology through analysis of …

Chromatin higher order folding--wrapping up transcription

PJ Horn, CL Peterson - Science, 2002 - science.org
Eukaryotic genomes are organized into condensed, heterogeneous chromatin fibers
throughout much of the cell cycle. Here we describe recent studies indicating that even …

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective

DA Koster, A Crut, S Shuman, MA Bjornsti, NH Dekker - Cell, 2010 - cell.com
Entangling and twisting of cellular DNA (ie, supercoiling) are problems inherent to the
helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication …

Three-dimensional genome architecture: players and mechanisms

A Pombo, N Dillon - Nature reviews Molecular cell biology, 2015 - nature.com
The different cell types of an organism share the same DNA, but during cell differentiation
their genomes undergo diverse structural and organizational changes that affect gene …

Transcription-mediated supercoiling regulates genome folding and loop formation

MV Neguembor, L Martin, Á Castells-García… - Molecular cell, 2021 - cell.com
The chromatin fiber folds into loops, but the mechanisms controlling loop extrusion are still
poorly understood. Using super-resolution microscopy, we visualize that loops in intact …

The hierarchy of the 3D genome

JH Gibcus, J Dekker - Molecular cell, 2013 - cell.com
Mammalian genomes encode genetic information in their linear sequence, but appropriate
expression of their genes requires chromosomes to fold into complex three-dimensional …