Energy-driven genome regulation by ATP-dependent chromatin remodellers

S Eustermann, AB Patel, KP Hopfner, Y He… - … Reviews Molecular Cell …, 2024 - nature.com
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA
replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re) arrange …

[HTML][HTML] Reading the chromatinized genome

AK Michael, NH Thomä - Cell, 2021 - cell.com
Eukaryotic DNA-binding proteins operate in the context of chromatin, where nucleosomes
are the elementary building blocks. Nucleosomal DNA is wrapped around a histone core …

Contributions of histone variants in nucleosome structure and function

H Kurumizaka, T Kujirai, Y Takizawa - Journal of molecular biology, 2021 - Elsevier
Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the
nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and …

Single-molecule analysis and engineering of DNA motors

S Mohapatra, CT Lin, XA Feng, A Basu, T Ha - Chemical reviews, 2019 - ACS Publications
Molecular motors are diverse enzymes that transduce chemical energy into mechanical
work and, in doing so, perform critical cellular functions such as DNA replication and …

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 …

Unravelling the role of epigenetics in reproductive adaptations to early-life environment

B Bar-Sadeh, S Rudnizky, L Pnueli… - Nature Reviews …, 2020 - nature.com
Reproductive function adjusts in response to environmental conditions in order to optimize
success. In humans, this plasticity includes age of pubertal onset, hormone levels and age at …

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 …

The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics

BT Donovan, Y Luo, Z Meng… - Nucleic Acids Research, 2023 - academic.oup.com
Transcription factors (TF) require access to target sites within nucleosomes to initiate
transcription. The target site position within the nucleosome significantly influences TF …

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

J Yoo, S Park, C Maffeo, T Ha… - Nucleic acids …, 2021 - academic.oup.com
Eukaryotic genome and methylome encode DNA fragments' propensity to form nucleosome
particles. Although the mechanical properties of DNA possibly orchestrate such encoding …

Single-Macromolecule Studies of Eukaryotic Genomic Maintenance

S Rudnizky, PJ Murray, CH Wolfe… - Annual Review of …, 2024 - annualreviews.org
Genomes are self-organized and self-maintained as long, complex macromolecules of
chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin …