The physics of epigenetics

R Cortini, M Barbi, BR Caré, C Lavelle, A Lesne… - Reviews of Modern …, 2016 - APS
In higher organisms, all cells share the same genome, but every cell expresses only a
limited and specific set of genes that defines the cell type. During cell division, not only the …

Predicting genome architecture: challenges and solutions

P Belokopytova, V Fishman - Frontiers in genetics, 2021 - frontiersin.org
Genome architecture plays a pivotal role in gene regulation. The use of high-throughput
methods for chromatin profiling and 3-D interaction mapping provide rich experimental data …

Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin

K Hiragami-Hamada, S Soeroes, M Nikolov… - Nature …, 2016 - nature.com
Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein
1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for …

Nonequilibrium theory of epigenomic microphase separation in the cell nucleus

D Michieletto, D Colì, D Marenduzzo, E Orlandini - Physical Review Letters, 2019 - APS
Understanding the spatial organization of the genome in the cell nucleus is one of the
current grand challenges in biophysics. Certain biochemical—or epigenetic—marks that are …

[HTML][HTML] Beyond the nucleosome: nucleosome-protein interactions and higher order chromatin structure

VR Lobbia, MCT Sanchez, H van Ingen - Journal of molecular biology, 2021 - Elsevier
The regulation of chromatin biology ultimately depends on the manipulation of its smallest
subunit, the nucleosome. The proteins that bind and operate on the nucleosome do so …

Changing chromatin fiber conformation by nucleosome repositioning

O Müller, N Kepper, R Schöpflin, R Ettig, K Rippe… - Biophysical journal, 2014 - cell.com
Chromatin conformation is dynamic and heterogeneous with respect to nucleosome
positions, which can be changed by chromatin remodeling complexes in the cell. These …

DNA sequence-dependent formation of heterochromatin nanodomains

GJ Thorn, CT Clarkson, A Rademacher… - Nature …, 2022 - nature.com
The mammalian epigenome contains thousands of heterochromatin nanodomains (HNDs)
marked by di-and trimethylation of histone H3 at lysine 9 (H3K9me2/3), which have a typical …

Heterochromatin assembly by interrupted Sir3 bridges across neighboring nucleosomes

R Behrouzi, C Lu, MA Currie, G Jih, N Iglesias… - Elife, 2016 - elifesciences.org
Heterochromatin is a conserved feature of eukaryotic chromosomes with central roles in
regulation of gene expression and maintenance of genome stability. Heterochromatin …

Nucleosome-free DNA regions differentially affect distant communication in chromatin

EV Nizovtseva, N Clauvelin, S Todolli… - Nucleic acids …, 2017 - academic.oup.com
Communication between distantly spaced genomic regions is one of the key features of
gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter …

Biology and Physics of Heterochromatin-Like Domains/Complexes

PB Singh, SN Belyakin, PP Laktionov - Cells, 2020 - mdpi.com
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble
heterochromatin-like domains/complexes outside canonical constitutively heterochromatic …