Chromatin compaction under mixed salt conditions: Opposite effects of sodium and potassium ions on nucleosome array folding

Abstract

It is well known that chromatin structure is highly sensitive to the ionic environment. However, the combined effects of a physiologically relevant mixed ionic environment of K+, Mg2+ and Na+, which are the main cations of the cell cytoplasm, has not been systematically investigated. We studied folding and self-association (aggregation) of recombinant 12-mer nucleosome arrays with 177 bp DNA repeat length in solutions of mixtures of K+ and Mg2+ or Na+ and Mg2+. In the presence of Mg2+, the addition of sodium ions promotes folding of array into 30-nm fibres, whereas in mixtures of K+ and Mg2+, potassium ions abrogate folding. We found that self-association of nucleosome arrays in mixed salt solutions is synergistically promoted by Mg2+ and monovalent ions, with sodium being slightly more efficient than potassium in amplifying the self-association. The results highlight the importance of a mixed ionic environment for the compaction of chromatin under physiological conditions and demonstrate the complicated nature of the various factors that determine and regulate chromatin compaction in vivo.

Chromatin fibers stabilize nucleosomes under torsional stress

“…Our force-spectroscopy data obtained on 197-NRL chromatin are most compatible with this interpretation. We note, that chromatin structure critically depends on other factors e.g., specific buffer conditions or the presence of linker histones (H1/ H5) 11,57 , which could induce alternative fiber topologies.…”

Chromatin plates in the interphase nucleus

“…In these studies, the extrusion of chromatin fibers was observed when nuclei were swollen with water. Taking into account that significant concentrations of K + , Na + , and Mg 2+ are present in the cell nucleus and that these cations are relevant for chromatin folding , we tried to obtain chromatin emanation from nuclei suspended in buffers containing these cations.…”

Frozen‐hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure

“…To circumvent this problem, we analyzed the structure of thin chromatin plates emanated from soft-denatured metaphase chromosomes using cryo-ET (see the preceding sections), and we applied synchrotron SAXS to investigate the chromatin structure within whole intact chromosomes ( Fig 5). The scattering study was performed using different divalent and trivalent cations that produce chromosome condensation (Strick et al, 2001;Caravaca et al, 2005;Daban, 2011;Allahverdi et al, 2015;Maeshima et al, 2018). The peaks at~3.7 and~2.7 nm corresponding to the internal nucleosome structure (Widom & Klug, 1985) were observed in all samples with different intensities.…”