Beads on a string—nucleosome array arrangements and folding of the chromatin fiber

S Baldi, P Korber, PB Becker - Nature structural & molecular biology, 2020 - nature.com
Understanding how the genome is structurally organized as chromatin is essential for
understanding its function. Here, we review recent developments that allowed the …

Mechanistic modeling of chromatin folding to understand function

CA Brackey, D Marenduzzo, N Gilbert - Nature Methods, 2020 - nature.com
Experimental approaches have been applied to address questions in understanding three-
dimensional chromatin organization and function. As datasets increase in size and …

[HTML][HTML] In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization

E Oberbeckmann, K Quililan, P Cramer… - Nature Genetics, 2024 - nature.com
Eukaryotic genomes are organized into chromatin domains. The molecular mechanisms
driving the formation of these domains are difficult to dissect in vivo and remain poorly …

[HTML][HTML] Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions

SE Farr, EJ Woods, JA Joseph, A Garaizar… - Nature …, 2021 - nature.com
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …

Genome modeling: from chromatin fibers to genes

S Portillo-Ledesma, Z Li, T Schlick - Current opinion in structural biology, 2023 - Elsevier
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …

[HTML][HTML] Current understanding of molecular phase separation in chromosomes

JK Ryu, DE Hwang, JM Choi - International Journal of Molecular Sciences, 2021 - mdpi.com
Biomolecular phase separation denotes the demixing of a specific set of intracellular
components without membrane encapsulation. Recent studies have found that biomolecular …

Nucleosome clutches are regulated by chromatin internal parameters

S Portillo-Ledesma, LH Tsao, M Wagley… - Journal of Molecular …, 2021 - Elsevier
Nucleosomes cluster together when chromatin folds in the cell to form heterogeneous
groups termed “clutches”. These structural units add another level of chromatin regulation …

Nucleosome positioning and chromatin organization

JJ Parmar, R Padinhateeri - Current Opinion in Structural Biology, 2020 - Elsevier
In our cells, DNA is folded and packed with the help of many proteins into chromatin whose
basic unit is a nucleosome—DNA wrapped around octamer of histone proteins. The chain of …

[HTML][HTML] Multiscale modelling of chromatin organisation: resolving nucleosomes at near-atomistic resolution inside genes

J Huertas, EJ Woods, R Collepardo-Guevara - Current Opinion in Cell …, 2022 - Elsevier
The three-dimensional organisation of the genome modulates biological processes and is,
in turn, transformed by the activity in the nucleus. Not surprisingly, understanding how the …

[HTML][HTML] Bottom-up meets top-down: the crossroads of multiscale chromatin modeling

J Moller, JJ de Pablo - Biophysical Journal, 2020 - cell.com
Chromatin can be viewed as a hierarchically structured fiber that regulates gene expression.
It consists of a complex network of DNA and proteins whose characteristic dynamical modes …