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Nucleosomes

par douarche - publié le , mis à jour le

 

 

NUCLEOSOMES


In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. The stability of this complex is ensured by electrostatic interactions between the negatively charged DNA molecule and the proteins (histones), which are mainly positively charged. The global charge of the nucleosome is negative (around 150 e-), and the charge distribution is quite heterogeneous : the DNA molecule (negatively charged) is located at the periphery while the histone tails (positively charged) lie around the particle (A).
Inside the living cell, these tails are subject to various reversible chemical modifications that regulate the transcriptional activity as well as the degree of condensation of chromatin.
Atomic structures of nucleosome core particles have been obtained from crystallography (B) and single particle cryo electron microscopy of identical engineered complexes. But native nucleosomes have with diverse DNA sequence and histone content ; they are also dynamical entities showing conformational transitions.

 

• A tail bridging effect :
Using Small Angle X-ray Scattering (coll. D. Durand) we followed changes in the conformation and interactions of nucleosome core particles as a function of the monovalent salt concentration. We pointed out some complex behaviour : repulsive electrostatic interactions are progressively screened with an increase of the salt concentration, but attractive interactions are observed above a critical salt concentration, for which histone tails extend around the particle.
To take this attraction into account, we propose a model of histone tail bridging between adjacent nucleosomes. This model is confirmed by the fact that attractive interactions disappear after digestion of the histone tails with a protease.

To get insight into the specific role of H3 and H4 histone tails, perfectly monodisperse recombinant nucleosome core particles were reconstituted, either intact or deprived of both H3 and H4 histone tails. The main result is that H3 and H4 histone tails are necessary to induce attractive interactions between NCPs.

The important role played by the protein extension (histone tails) in the interactions between particles is also revealed by the diversity of the dense phases.

 
 

Evidence for native nucleosome conformations less compact than canonical crystallographic structure
Using cryo electron microscopy of vitreous sections we analyse native nucleosomes, both in vitro, using purified particles solubilised at physiologically relevant concentrations (25 to 50%), and in situ, within interphase nuclei. We visualise individual nucleosomes at a level of detail that allows us to measure the distance between the DNA gyres wrapped around. In concentrated solutions, we demonstrate a salt-dependent transition, with a high salt compact conformation resembling the canonical nucleosome, and an open low salt one, closer to nuclear nucleosomes.


Salt-dependant opening of the nucleosome (A) CEMOVIS imaging of the lamello-columnar phase formed by nucleosome core particles in concentrated solution (low salt environment, 15 mM). Bilayers of columns of stacked nucleosomes are seen in transverse section are separated by particle-free layers of solvent (white stars). Columns of nucleosomes are seen in top (arrowheads), side (arrows) or oblique views. Top and side views are compared to the corresponding projections of the crystallographic structure of the NCP (from PDB 1EQZ) in the inserts. We measure the distance P between DNA gyres. (B) Distribution of P-distances for different added salt concentration and comparison with the canonical crystallographic structure (PDB ID 1EQZ).

 
 

REFERENCES


 

ELTSOV M., GREWE D., LEMERCIER N., FRANGAKIS A., LIVOLANT F., LEFORESTIER A. (2018) Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections. Nucleic Acid Research, 46, 9189-9200. doi : 10.1093/nar/gky670.

BERTIN A., RENOUARD M., PEDERSEN J.S., LIVOLANT F., DURAND D. (2007) H3 and H4 histone tails play a central role in the interactions of recombinant NCPs. Biophys. J., 92, 2633-2645.

BERTIN A., MANGENOT S., RENOUARD M., DURAND D., LIVOLANT F. (2007) Structure and phase diagram of nucleosome core particles aggregated by multivalent cations. Biophysical Journal. 93:3652-63.

BERTIN A., DURAND D., RENOUARD M., LIVOLANT F. MANGENOT S. (2007) H2A and H2B tails are essential to properly reconstitute nucleosome core particles. Eur Biophys J. 36, 1083-94.

BERTIN A., LEFORESTIER A., DURAND D., LIVOLANT F. (2004) Role of histone tails in the conformation and interactions of nucleosome core particles. Biochemistry, 43, 4773-4780.

S. MANGENOT, A. LEFORESTIER, P. VACHETTE, D. DURAND, F. LIVOLANT (2002) Salt-induced conformation and interaction changes of Nucleosome Core Particles. Biophysical Journal, 82, 345-356.