Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core

Abstract

The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during saltinduced disassembly of canonical NCPs. We find that H2A-H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.G enome access is highly regulated through the hierarchical organization of proteins and nucleic acids within the cell nucleus. The nucleosome core particle (NCP) is the first level of this hierarchy (1) and contains two dimers of H2A-H2B histones and an (H3-H4) 2 tetramer that is assembled as a dimer of dimers. Around this symmetric octamer core, ∼146 base pairs of dsDNA are wrapped in ∼1.7 superhelical turns (1, 2). The NCP structure physically impedes access to DNA, but is dynamically modulated by numerous mechanisms: posttranslational modification (PTM) of histones, incorporation of histone variants, DNA sequence-dependent effects, and the actions of extrinsic protein factors (e.g., histone chaperones, ATP-dependent remodeling complexes, and histone PTM binding proteins) (3, 4).Studies of the intrinsic properties and dynamics of NCPs are critical for understanding how nuclear machinery gains DNA access in vivo (3,5,6). Insight into the nature of partially unfolded NCP structures has been gleaned from in vitro studies of NCP assembly and disassembly. Intermediate species with partially unwrapped DNA (5, 7), disrupted histone-histone interfaces (8, 9), and dissociation of one (hexasomes) or two (tetrasomes) H2A-H2B dimers have been reported (10-12). Some of these NCP intermediates have been directly connected to chromatin function in vivo. For example, the hexasome is formed by the action of RNA Pol II (13) and the essential histone chaperone FACT (14).In addition to equilibrium studies, the kinetics of nucleosome assembly and disassembly have been characterized by bulk and single-molecule methods, including Förster resonance energy transfer (FRET) (7,8,(15)(16)(17), atomic force microscopy (AFM) (9, 18), force spectroscopy (19-21), and small-angle X-ray scattering (SAXS) (10,22). Many studies focused primarily on specific DNA-histon...

The human telomeric nucleosome displays distinct structural and dynamic properties

“…The asymmetric DNA unwrapping on the nucleosome core observed in the Figure S13 and Supplementary Table S4 for more details of the fitting procedure. solution SAXS experiment is dependent on local DNA sequence (75,76) and has been observed previously (73,76,77). We also observed lower salt-dependent stability and lower affinity for Telo-NCP compared to the other DNA sequences investigated.…”

Effects of H2A.B incorporation on nucleosome structures and dynamics

“…In both systems we note that nucleosome stability is enhanced by strong DNA-dimer interactions, which are roughly equal in strength in H2A and H2A.B containing systems. This is in line with experiments which have shown that DNA is required for nucleosome stability at physiological salt concentrations, and that the histone core will only assemble at high salt concentrations without DNA (61)(62)(63). We note that the MM/GBSA analysis presented here is relatively crude and does not include important thermodynamic terms such as conformational entropy and explicit solvation, therefore although the trends are of qualitative value, care should be taken in quantitative interpretation of the energetic values (64-68).…”

Insight into the unwrapping of the dinucleosome

“…This phenomenon and the observed asymmetric unwrapping in the dinucleosome, occur in a way that reduces the energy cost of the bent DNA. In experiments, different features of the unwinding such as the asymmetric and symmetric openings have been observed with different probabilities [22,[30][31][32]. The different patterns of the unwinding of the dinucleosome can be understood from the energy landscape, (see Fig.…”