Carrivain, P. | Search bioRxiv

bioRxiv2022

Cryo-electron tomography and deep learning-based denoising reveal native chromatin landscapes of interphase nuclei

The chromatin machinery, with DNA-histone assembly and further folding of nucleosome chains, influences DNA availability for functional interactions necessary to the regulation of transcription, DNA replication and repair. Despite models based on in vitro studies, the nucleosome chain geometry within the crowded cell nucleus remains elusive. Using cryo-electron tomography of thin vitreous sections, we directly observed the path of nucleosomal and linker DNA in situ in intact flash-frozen organism - Drosophila embryo. We quantified linker length and curvature characterizing an irregular zig-zag chromatin folding motif, with a low degree of linker bending. Additionally, nucleosome conformational variability with non-canonical structures and non-octameric particles were observed as individual objects, without structure averaging, highlighting the high structural heterogeneity of native chromatin.

cell biology↗

bioRxiv2017

In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction

Chromosome mechanical properties determine DNA folding and dynamics, and underlie all major nuclear functions. Here we combine modeling and real-time motion tracking experiments to infer the physical parameters describing chromatin fibers. In vitro, motion of nucleosome arrays can be accurately modeled by assuming a Kuhn length of 35-55 nm. In vivo, the amplitude of chromosome fluctuations is drastically reduced, and depends on transcription. Transcription activation increases chromatin dynamics only if it involves gene relocalization, while global transcriptional inhibition augments the fluctuations, yet without relocalization. Chromatin fiber motion is accounted for by a model of equilibrium fluctuations of a polymer chain, in which random contacts along the chromosome contour induce an excess of internal friction. Simulations that reproduce chromosome conformation capture and imaging data corroborate this hypothesis. This model unravels the transient nature of chromosome contacts, characterized by a life time of [~]2 seconds and a free energy of formation of [~]1 kBT.

genetics↗