Search

In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome–nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. In this review, we provide a summary of recent progress on the structure of chromatin fibers in vitro and in the nucleus, highlight studies on the dynamic regulation of chromatin fibers, and discuss their related biological functions and abnormal organization in diseases. [ABSTRACT FROM AUTHOR]

Advanced track structure codes excel as state-of-the-art tools to low-scale dosimetric models: the rational evolution for a cell-like scenario is detailed within a microsecond of an ion collision, that is the standard timescale for critical DNA modifications. The in vitro DNA double-strand breaks (DSB) yield is matched indirectly by nanodosimetric track structure assessments; however, the score to specific DSB motifs (i.e., the yield associated to each DSB distance between DNA cuts) is mostly overlooked. In this work, we extend the PDB4DNA example of the Geant4-DNA toolkit, to briefly assess the hit and DSB scores over a nucleosome tetramer framework (Protein Data Bank entry: 1zbb). We describe a critical scenario that biases the statistical significance for an event-by-event track structure assessment at the nanometric scale, based on a Shannon's entropy estimate of the volumetric hit score; finally, we draw a tentative correlation between the mean DSB quality and a proton track, and conclude that short-distanced DSBs by direct effect are favored within a Bragg peak-relevant energy range.

Genomic DNA is hierarchically packaged into chromatin in eukaryotes. As a central-level chromatin structure between nucleosomal arrays and higher order organizations, 30 nm chromatin fiber, and its dynamics play a crucial role in regulating DNA accessibility for gene transcription. However, despite extensive efforts over three decades, the higher-order structure of the 30 nm chromatin fiber remains unresolved and controversial. We have recently reconstituted the 30 nm chromatin fibers from 12 nucleosomal arrays in vitro in the presence of linker histone H1, and determined their cryo-EM structures at resolution of 11 Å (Song et al., Science 344, 376-380). Here, we briefly reviewed the higher-order structure studies of chromatin fibers, mainly focusing on the insights from the cryo-EM structures we recently solved. © 2016 IUBMB Life, 68(11):873-878, 2016 [ABSTRACT FROM AUTHOR]