Solution Scattering and FRET Studies on Nucleosomes Reveal DNA Unwrapping Effects of H3 and H4 Tail Removal

Abstract

Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.

The human telomeric nucleosome displays distinct structural and dynamic properties

“…This conclusion was also supported by dynamic light scattering investigations, which displayed a larger hydrodynamic diameter for Telo-NCP in comparison with 601-NCP (data not shown). Earlier works have shown that the depth of the dip in the NCP SAXS spectrum at 0.14 Å -1 is sensitive to DNA unwrapping (71)(72)(73)(74). The NCP at low concentration (1-2.5 mg/mL) in low salt buffer (10 mM KCl) exhibit minimal inter-particle interactions, thereby facilitating the study of the form factor of the NCP SAXS spectrum (52).…”

Approach to the Investigation of Nucleosome Structure by Using the Highly Emissive Nucleobase thdG–tC FRET Pair

“…Although fluorescence of DNA and nucleosome with acceptor (A 41st or A 27th) is similar (Figure S12, Supporting Information), nucleosome containing donor (D 40th) increased fluorescence intensity 1.89‐fold compared with duplex DNA. We estimated R DA based on a minimized structure using the software BIOVIA discovery studio version 17.1 . After minimization of th dG and tC‐containing nucleosome structure, the R DA of nucleosome with D 40th+A 41st (47.2±0.06 Å) and D 40th+A 27th (26.5±0.05 Å) was observed (Figure S9, Supporting Information).…”

“…We estimated R DA based on am inimized structure using the softwareB IOVIA discoverys tudio version 17.1. [25][26][27][28][29][30][31] After minimizationo f th dG and tC-containing nucleosome structure, the In the B-form structure,t he angle between the helicala xis and the fluorescent nucleobase is almost 908 in the cylinder model of the DNA duplex because of the fixed parallel plan of the fluorescent nucleobase caused by hydrogen bonding with the counterbase and stacking interaction between neighboring bases, indicating that k 2 can be assumed to between 0a nd 1. [20,41,42] On the other hand, the base pair of the DNA duplex in the nucleosome undergoes geometrical changes such as roll, tilt, and twist unlike typical B-form DNA.…”

Monte Carlo simulation algorithm for B‐DNA

“…We chose these examples because they correspond to two areas of active investigation, DNA breathing and unwrapping from a NCP, and the configuration of a short array of nucleosomes. [10– For the NCP, we designated 30 bp on each end to be flexible (in Figs.…”

“…While much has been learned by studying NCPs and nucleosome arrays in these biologically artificial environments, understanding the structure–function relationship of chromatin in vivo requires experiments in solution. To date, efforts to identify model structures from solution studies of nucleosomes and nucleosome arrays have been limited to qualitative comparisons, or structure models generated from dummy spheres, manual modifications of atomic structures, or by replacing nucleosome‐bound DNA with linear DNA fragments . Robust structure models of these and other nucleosome complexes require efficient simulation tools to complement the experimental methods used; in this context, a robust structure model refers to an atomic representation of a physically realistic molecular structure.…”