Evolution of diverse strategies for promoter regulation
DNA is fundamentally important for all cellular organisms due to its role as a store of
hereditary genetic information. The precise and accurate regulation of gene transcription …
hereditary genetic information. The precise and accurate regulation of gene transcription …
Spatial and temporal organization of chromatin at small and large scales
H Schiessel - Annual Review of Condensed Matter Physics, 2023 - annualreviews.org
DNA molecules with a total length of two meters contain the genetic information in every cell
in our body. To control access to the genes, to organize its spatial structure in the nucleus …
in our body. To control access to the genes, to organize its spatial structure in the nucleus …
Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone
core. Although not directly reading out the DNA sequence, some chromatin remodelers …
core. Although not directly reading out the DNA sequence, some chromatin remodelers …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
Exploring the free energy landscape of nucleosomes
The nucleosome is the fundamental unit for packaging the genome. A detailed molecular
picture for its conformational dynamics is crucial for understanding transcription and gene …
picture for its conformational dynamics is crucial for understanding transcription and gene …
[HTML][HTML] Coarse-grained modeling of DNA curvature
The interaction of DNA with proteins occurs over a wide range of length scales, and
depends critically on its local structure. In particular, recent experimental work suggests that …
depends critically on its local structure. In particular, recent experimental work suggests that …
DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
While nucleosomes are highly stable structures as fundamental units of chromatin, they also
slide along the DNA, either spontaneously or by active remodelers. Here, we investigate the …
slide along the DNA, either spontaneously or by active remodelers. Here, we investigate the …
In silico evidence for sequence-dependent nucleosome sliding
J Lequieu, DC Schwartz… - Proceedings of the …, 2017 - National Acad Sciences
Nucleosomes represent the basic building block of chromatin and provide an important
mechanism by which cellular processes are controlled. The locations of nucleosomes …
mechanism by which cellular processes are controlled. The locations of nucleosomes …
DNA methylation cues in nucleosome geometry, stability, and unwrapping
2532-Pos A study on alterations in membrane physiology of human erythrocytes due to
extracellular tonicity through dielectrophoresis Jogu Sumathi, Mohd Abdul Saleem, Adeel …
extracellular tonicity through dielectrophoresis Jogu Sumathi, Mohd Abdul Saleem, Adeel …
Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects
A recently published coarse-grained DNA model [DM Hinckley, GS Freeman, JK Whitmer,
and JJ de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization …
and JJ de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization …