Beads on a string—nucleosome array arrangements and folding of the chromatin fiber
Understanding how the genome is structurally organized as chromatin is essential for
understanding its function. Here, we review recent developments that allowed the …
understanding its function. Here, we review recent developments that allowed the …
Mechanistic modeling of chromatin folding to understand function
Experimental approaches have been applied to address questions in understanding three-
dimensional chromatin organization and function. As datasets increase in size and …
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 …
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
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
Genome modeling: from chromatin fibers to genes
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …
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 …
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 …
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 …
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
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 …
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 …
It consists of a complex network of DNA and proteins whose characteristic dynamical modes …