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 …

Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function

R Singh, E Bassett, A Chakravarti… - Nucleic acids …, 2018 - academic.oup.com
Replication-dependent histones are expressed in a cell cycle regulated manner and supply
the histones necessary to support DNA replication. In mammals, the replication-dependent …

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 …

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

AT Fenley, R Anandakrishnan, YH Kidane… - Epigenetics & …, 2018 - Springer
Background Controlled modulation of nucleosomal DNA accessibility via post-translational
modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs …

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

GB Brandani, T Niina, C Tan, S Takada - Nucleic acids research, 2018 - academic.oup.com
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 …

Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility

A Osakabe, ZJ Lorković, W Kobayashi… - Nucleic Acids …, 2018 - academic.oup.com
In eukaryotes, variants of core histone H2A are selectively incorporated in distinct functional
domains of chromatin and are distinguished by conserved sequences of their C-terminal tail …

Structural rearrangements of the histone octamer translocate DNA

S Bilokapic, M Strauss, M Halic - Nature communications, 2018 - nature.com
Nucleosomes, the basic unit of chromatin, package and regulate expression of eukaryotic
genomes. Nucleosomes are highly dynamic and are remodeled with the help of ATP …

Nucleosome positions establish an extended mutation signature in melanoma

AJ Brown, P Mao, MJ Smerdon, JJ Wyrick… - PLoS …, 2018 - journals.plos.org
Ultraviolet (UV) light-induced mutations are unevenly distributed across skin cancer
genomes, but the molecular mechanisms responsible for this heterogeneity are not fully …

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

GB Brandani, S Takada - PLoS computational biology, 2018 - journals.plos.org
ATP-dependent chromatin remodelers are molecular machines that control genome
organization by repositioning, ejecting, or editing nucleosomes, activities that confer them …

Molecular mechanism for the role of the H2A and H2B histone tails in nucleosome repositioning

K Chakraborty, M Kang… - The Journal of Physical …, 2018 - ACS Publications
The nucleosome core particle (NCP) is the basic packaging unit of DNA. Recently reported
structures of the NCP suggest that the histone octamer undergoes conformational changes …