Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome

Abstract

Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.

Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy

“…Previous studies on dense phases of nucleosomes demonstrated formation of highly ordered structures consisting of columns of stacked nucleosomes ( Allahverdi et al, 2011 ; Berezhnoy et al, 2016 ; Bertin et al, 2007b ; Eltsov et al, 2018 ; Korolev et al, 2012 ; Leforestier and Livolant, 1997 ; Livolant et al, 2006 ; Mangenot et al, 2003a , b ). For the isotropic columnar phase, SAXS scattering curves showed three broad scattering peaks corresponding to (i) the average intercolumnar distance, typically at q * =~ 0.065, with q * decreasing as the linker DNA increases ( Mangenot et al, 2003b ; Wang et al, 2021 ), (ii) the stacking distance between nucleosomes in a column (typically at q * =~ 0.11), and (iii) the form factor of the column ( Livolant et al, 2006 ). In a highly ordered columnar phase, such as obtained from Mg 2+ -induced precipitation of nucleosome core particles, these peaks appear sharp and well-resolved ( Berezhnoy et al, 2016 ).…”

MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes

“…It is generally accepted that linker histones bind to the nucleosome and protect an extra 20 bp of linker DNA. Many explanations have been proposed to describe the location of the linker histones, or linker histone globular domains, within the nucleosome, their interaction and chromatosome protection through biochemical analysis, structural studies or computing simulations [ 9 , 36 , 37 , 38 , 39 , 40 , 57 , 62 , 63 , 64 , 65 , 66 , 67 ]. The current study is the first in vitro analysis of chromatosomal DNA extensions protected by linker histones or linker histone globular domains, in the context of a long-range nucleosome array formed on a natural genomic DNA sequence.…”

The Role of MeCP2 in Regulating Synaptic Plasticity in the Context of Stress and Depression

“…They form a repetitive structure (beads on a string) that results in chromatin fiber [ 4 ]. The winged-helix domain (WHD) of histone H1 [ 5 ] also binds close to the entry and exit sites of DNA in the nucleosome [ 6 , 7 , 8 ], and this binding plays a critical role in the modulation of the chromatin fiber folding [ 9 ]. Both ‘core histones’ and ‘linker histones’ consist of a bipartite/tripartite protein organization in which an N-terminal intrinsically disordered domain (IDD) [ 10 ] flanks a structured domain WHD [ 11 ] for linker histones or a histone fold domain (HFD) [ 12 ] for core histones.…”