When force met fluorescence: single-molecule manipulation and visualization of protein–DNA interactions

GNL Chua, S Liu - Annual Review of Biophysics, 2024 - annualreviews.org
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational
changes while on DNA or alter the physical configuration of the DNA substrate to control its …

Molecular dynamics simulations of nucleosomes are coming of age

AS Fedulova, GA Armeev… - Wiley …, 2024 - Wiley Online Library
Understanding the function of eukaryotic genomes, including the human genome, is
undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of …

[HTML][HTML] The impact of chromatin on double-strand break repair: Imaging tools and discoveries

MAE van Bueren, A Janssen - DNA repair, 2024 - Elsevier
Eukaryotic nuclei are constantly being exposed to factors that break or chemically modify the
DNA. Accurate repair of this DNA damage is crucial to prevent DNA mutations and maintain …

Real-time multistep asymmetrical disassembly of nucleosomes and chromatosomes visualized by high-speed atomic force microscopy

B Onoa, C Díaz-Celis, C Cañari-Chumpitaz… - ACS Central …, 2023 - ACS Publications
During replication, expression, and repair of the eukaryotic genome, cellular machinery must
access the DNA wrapped around histone proteins forming nucleosomes. These octameric …

A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint

H Sánchez, Z Liu, E van Veen, T van Laar… - Nature …, 2023 - nature.com
Chromatin replication involves the assembly and activity of the replisome within the
nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which …

Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers

P Shrestha, D Yang, A Ward, WM Shih… - Journal of the …, 2023 - ACS Publications
The ability to accurately map the 3D geometry of single-molecule complexes in trace
samples is a challenging goal that would lead to new insights into molecular mechanics and …

Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

M Zhang, C Díaz-Celis, J Liu, J Tao, PD Ashby… - Nature …, 2024 - nature.com
The conformational dynamics of nucleosome arrays generate a diverse spectrum of
microscopic states, posing challenges to their structural determination. Leveraging …

The Histone Chaperones SET/TAF‐1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c‐Dependent …

P Buzón, A Velázquez‐Cruz… - Advanced …, 2023 - Wiley Online Library
Chromatin homeostasis mediates essential processes in eukaryotes, where histone
chaperones have emerged as major regulatory factors during DNA replication, repair, and …

Testis-specific H2B. W1 disrupts nucleosome integrity by reducing DNA–histone interactions

D Ding, MYH Pang, M Deng, TT Nguyen… - Nucleic Acids …, 2024 - academic.oup.com
Multiple testis-specific histone variants are involved in the dynamic chromatin transitions
during spermatogenesis. H2B. W1 (previously called H2BFWT) is an H2B variant specific to …

Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly

H Nozawa, F Nagae, S Ogihara, R Hirano… - Communications …, 2024 - nature.com
The nucleosome including H2A. B, a mammalian-specific H2A variant, plays pivotal roles in
spermatogenesis, embryogenesis, and oncogenesis, indicating unique involvement in …