[HTML][HTML] DNA methylation: Precise modulation of chromatin structure and dynamics

S Li, Y Peng, AR Panchenko - Current opinion in structural biology, 2022 - Elsevier
DNA methylation plays a vital role in epigenetic regulation in both plants and animals, and
typically occurs at the 5-carbon position of the cytosine pyrimidine ring within the CpG …

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

J Yoo, A Aksimentiev - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …

[HTML][HTML] Transcription shapes genome-wide histone acetylation patterns

BJE Martin, J Brind'Amour, A Kuzmin… - Nature …, 2021 - nature.com
Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between
histone acetylation and transcription is causal or consequential has not been addressed …

[HTML][HTML] Histone dynamics mediate DNA unwrapping and sliding in nucleosomes

GA Armeev, AS Kniazeva, GA Komarova… - Nature …, 2021 - nature.com
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …

[HTML][HTML] Histone tail conformations: a fuzzy affair with DNA

M Ghoneim, HA Fuchs, CA Musselman - Trends in biochemical sciences, 2021 - cell.com
The core histone tails are critical in chromatin structure and signaling. Studies over the past
several decades have provided a wealth of information on the histone tails and their …

Copper: an intracellular achilles' heel allowing the targeting of epigenetics, kinase pathways, and cell metabolism in cancer therapeutics

F Michniewicz, F Saletta, JRC Rouaen… - …, 2021 - Wiley Online Library
Copper is an essential transition metal frequently increased in cancer known to strongly
influence essential cellular processes. Targeted therapy protocols utilizing both novel and …

HistoneDB 2.0: a histone database with variants—an integrated resource to explore histones and their variants

EJ Draizen, AK Shaytan, L Mariño-Ramírez… - Database, 2016 - academic.oup.com
Compaction of DNA into chromatin is a characteristic feature of eukaryotic organisms. The
core (H2A, H2B, H3, H4) and linker (H1) histone proteins are responsible for this compaction …

[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization

X Lin, Y Qi, AP Latham, B Zhang - The Journal of chemical physics, 2021 - pubs.aip.org
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …

[HTML][HTML] The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

EA Morrison, S Bowerman, KL Sylvers… - Elife, 2018 - elifesciences.org
Histone tails harbor a plethora of post-translational modifications that direct the function of
chromatin regulators, which recognize them through effector domains. Effector …

Exploring the free energy landscape of nucleosomes

B Zhang, W Zheng, GA Papoian… - Journal of the American …, 2016 - ACS Publications
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 …