40 research outputs found
Dynamical DNA accessibility induced by chromatin remodeling and protein binding
International audienceChromatin remodeling factors are enzymes being able to alter locally chromatin structure at the nucleosomal level and they actively participate in the regulation of gene expression. Using simple rules for individual nucleosome motion induced by a remodeling factor, we designed simulations of the remodeling of oligomeric chromatin, in order to address quantitatively collective effects in DNA accessibility upon nucleosome mobilization. Our results suggest that accessibility profiles are inhomogeneous thanks to borders effects like protein binding. Remarkably, we show that the accessibility lifetime of DNA sequence is roughly doubled in the vicinity of borders as compared to its value in bulk regions far from the borders. These results are quantitatively interpreted as resulting from the confined diffusion of a large nucleosome depleted region
Entropic control of particle sizes during viral self-assembly
Morphologic diversity is observed across all families of viruses. Yet these supra-molecular assemblies are produced most of the time in a spontaneous way through complex molecular self-assembly scenarios. The modeling of these phenomena remains a challenging problem within the emerging field of Physical Virology. We present in this work a theoretical analysis aiming at highlighting the particular role of configuration entropy in the control of viral particle size distribution. Specializing this model to retroviruses like HIV-1, we predict a new mechanism of entropic control of both RNA uptake into the viral particle, and of the particle's size distribution. Evidence of this peculiar behavior has been recently reported experimentally
RSC remodeling of oligo-nucleosomes: an atomic force microscopy study
RSC is an essential chromatin remodeling factor that is required for the
control of several processes including transcription, repair and replication.
The ability of RSC to relocate centrally positioned mononucleosomes at the end
of nucleosomal DNA is firmly established, but the data on RSC action on
oligo-nucleosomal templates remains still scarce. By using Atomic Force
Microscopy (AFM) imaging, we have quantitatively studied the RSC- induced
mobilization of positioned di- and trinucleosomes as well as the directionality
of mobilization on mononucleosomal template labeled at one end with
streptavidin. AFM imaging showed only a limited set of distinct configurational
states for the remodeling products. No stepwise or preferred directionality of
the nucleosome motion was observed. Analysis of the corresponding reaction
pathways allows deciphering the mechanistic features of RSC-induced nucleosome
relocation. The final outcome of RSC remodeling of oligosome templates is the
packing of the nucleosomes at the edge of the template, providing large
stretches of DNA depleted of nucleosomes. This feature of RSC may be used by
the cell to overcome the barrier imposed by the presence of nucleosomes
RNA Control of HIV-1 Particle Size Polydispersity
HIV-1, an enveloped RNA virus, produces viral particles that are known to be
much more heterogeneous in size than is typical of non-enveloped viruses. We
present here a novel strategy to study HIV-1 Viral Like Particles (VLP)
assembly by measuring the size distribution of these purified VLPs and
subsequent viral cores thanks to Atomic Force Microscopy imaging and
statistical analysis. This strategy allowed us to identify whether the presence
of viral RNA acts as a modulator for VLPs and cores size heterogeneity in a
large population of particles. These results are analyzed in the light of a
recently proposed statistical physics model for the self-assembly process. In
particular, our results reveal that the modulation of size distribution by the
presence of viral RNA is qualitatively reproduced, suggesting therefore an
entropic origin for the modulation of RNA uptake by the nascent VLP
The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct AFM visualization of variant chromatin
Chromatin organization and dynamics is studied in this work at scales ranging
from single nucleosome to nucleosomal array by using a unique combination of
biochemical assays, single molecule imaging technique and numerical modeling.
We demonstrate that a subtle modification in the nucleosome structure induced
by the histone variant H2A.Bbd drastically modifies the higher order
organization of the nucleosomal arrays. Importantly, as directly visualized by
AFM, conventional H2A nucleosomal arrays exhibit specific local organization,
in contrast to H2A.Bbd arrays, which show "beads on a string" structure. The
combination of systematic image analysis and theoretical modeling allows a
quantitative description relating the observed gross structural changes of the
arrays to their local organization. Our results strongly suggest that
higher-order organization of H1-free nucleosomal arrays is mainly determined by
the fluctuation properties of individual nucleosomes. Moreover, numerical
simulations suggest the existence of attractive interactions between
nucleosomes to provide the degree of compaction observed for conventional
chromatin fibers.Comment: Biophys J. in pres
The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome
In this work we have studied the properties of the novel mouse histone variant H2AL2. H2AL2 was used to reconstitute nucleosomes and the structural and functional properties of these particles were studied by a combination of biochemical approaches, atomic force microscopy (AFM) and electron cryo-microscopy. DNase I and hydroxyl radical footprinting as well as micrococcal and exonuclease III digestion demonstrated an altered structure of the H2AL2 nucleosomes all over the nucleosomal DNA length. Restriction nuclease accessibility experiments revealed that the interactions of the H2AL2 histone octamer with the ends of the nucleosomal DNA are highly perturbed. AFM imaging showed that the H2AL2 histone octamer was complexed with only ∼130 bp of DNA. H2AL2 reconstituted trinucleosomes exhibited a type of a ‘beads on a string’ structure, which was quite different from the equilateral triangle 3D organization of conventional H2A trinucleosomes. The presence of H2AL2 affected both the RSC and SWI/SNF remodeling and mobilization of the variant particles. These unusual properties of the H2AL2 nucleosomes suggest a specific role of H2AL2 during mouse spermiogenesis
The N-terminal domains of TRF1 and TRF2 regulate their ability to condense telomeric DNA
TRF1 and TRF2 are key proteins in human telomeres, which, despite their similarities, have different behaviors upon DNA binding. Previous work has shown that unlike TRF1, TRF2 condenses telomeric, thus creating consequential negative torsion on the adjacent DNA, a property that is thought to lead to the stimulation of single-strand invasion and was proposed to favor telomeric DNA looping. In this report, we show that these activities, originating from the central TRFH domain of TRF2, are also displayed by the TRFH domain of TRF1 but are repressed in the full-length protein by the presence of an acidic domain at the N-terminus. Strikingly, a similar repression is observed on TRF2 through the binding of a TERRA-like RNA molecule to the N-terminus of TRF2. Phylogenetic and biochemical studies suggest that the N-terminal domains of TRF proteins originate from a gradual extension of the coding sequences of a duplicated ancestral gene with a consequential progressive alteration of the biochemical properties of these proteins. Overall, these data suggest that the N-termini of TRF1 and TRF2 have evolved to finely regulate their ability to condense DNA
The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling
Histone variants within the H2A family show high divergences in their C-terminal regions. In this work, we have studied how these divergences and in particular, how a part of the H2A COOH-terminus, the docking domain, is implicated in both structural and functional properties of the nucleosome. Using biochemical methods in combination with Atomic Force Microscopy and Electron Cryo-Microscopy, we show that the H2A-docking domain is a key structural feature within the nucleosome. Deletion of this domain or replacement with the incomplete docking domain from the variant H2A.Bbd results in significant structural alterations in the nucleosome, including an increase in overall accessibility to nucleases, un-wrapping of ∼10 bp of DNA from each end of the nucleosome and associated changes in the entry/exit angle of DNA ends. These structural alterations are associated with a reduced ability of the chromatin remodeler RSC to both remodel and mobilize the nucleosomes. Linker histone H1 binding is also abrogated in nucleosomes containing the incomplete docking domain of H2A.Bbd. Our data illustrate the unique role of the H2A-docking domain in coordinating the structural-functional aspects of the nucleosome properties. Moreover, our data suggest that incorporation of a ‘defective’ docking domain may be a primary structural role of H2A.Bbd in chromatin
AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding
We propose a combined experimental (Atomic Force Microscopy) and theoretical
study of the structural and dynamical properties of nucleosomes. In contrast to
biochemical approaches, this method allows to determine simultaneously the DNA
complexed length distribution and nucleosome position in various contexts.
First, we show that differences in the nucleo-proteic structure observed
between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative
changes in the in the length distribution of DNA complexed with histones. Then,
the sliding action of remodeling complex SWI/SNF is characterized through the
evolution of the nucleosome position and wrapped DNA length mapping. Using a
linear energetic model for the distribution of DNA complexed length, we extract
the net wrapping energy of DNA onto the histone octamer, and compare it to
previous studies.Comment: 25 pages,5 figures, to appear in Biophysical Journa
Understanding the molecular stability of viral capsids from a physics perspective
International audienceDuring its replication cycle, viral capsids undergo various transformations going from protein selfassembly to disassembly. The micro-environment is thought to play a major role in triggering these transformations. In this work, we review the current understanding of the correlation of viral capsid molecular stability with its physical and chemical environment. In particular, by analyzing the forces that act on capsid proteins and the ways in which they are held together, one can gain insight into how capsids maintain their structural integrity under different conditions and how they may be affected by external perturbations such as mutations, drug treatments, or mechanical triggers