Alterations in the chromatin packaging, driven by transcriptional activity, revealed by AFM

BACKGROUND

The gene expression differs in the nuclei of normal and malignant mammalian cells, and transcription is a critical initial step, which defines the difference. The mechanical properties of transcriptionally active chromatin are still poorly understood. Recently we have probed transcriptionally active chromatin of the nuclei subjected to mechanical stress, by Atomic Force Microscopy (AFM) [1]. Nonetheless, a systematic study of the phenomenon is needed.

METHODS

Nuclei were deformed and studied by AFM. Non-deformed nuclei were studied by fluorescence confocal microscopy. Their transcriptional activity was studied by RNA electrophoresis.

RESULTS

The malignant nuclei under the study were stable to deformation and assembled of 100-300 nm beads-like units, while normal cell nuclei were prone to deformation. The difference in stability to deformation of the nuclei correlated with DNA supercoiling, and transcription-depended units were responsive to supercoils breakage. The inhibitors of the topoisomerases I and II disrupted supercoiling and made the malignant nucleus prone to deformation. Cell nuclei treatment with histone deacetylase inhibitors (HDACIs) preserved the mechanical stability of deformed malignant nuclei and, at the same time, made it possible to observe chromatin decondensation up to 20-60 nm units. The AFM results were supplemented with confocal microscopy and RNA electrophoresis data.

CONCLUSIONS

Self-assembly of transcriptionally active chromatin and its decondensation, driven by DNA supercoiling-dependent rigidity, was visualized by AFM in the mechanically deformed nuclei.

GENERAL SIGNIFICANCE

We demonstrated that supercoiled DNA defines the transcription mechanics, and hypothesized the nuclear mechanics in vivo should depend on the chromatin architecture.

Experimental evidence for logarithmic fractal structure of botanical trees

The area-preserving rule for botanical trees by Leonardo da Vinci is discussed in terms of a very specific fractal structure, a logarithmic fractal. We use a method of the numerical Fourier analysis to distinguish the logarithmic fractal properties of the two-dimensional objects and apply it to study the branching system of real trees through its projection on the two-dimensional space, i.e., using their photographs. For different species of trees (birch and oak) we observe the Q^{-2} decay of the spectral intensity characterizing the branching structure that is associated with the logarithmic fractal structure in two-dimensional space. The experiments dealing with the side view of the tree should complement the area preserving Leonardo's rule with one applying to the product of diameter d and length l of the k branches: d_{i}l_{i}=kd_{i+1}l_{i+1}. If both rules are valid, then the branch's length of the next generation is sqrt[k] times shorter than previous one: l_{i}=sqrt[k]l_{i+1}. Moreover, the volume (mass) of all branches of the next generation is a factor of d_{i}/d_{i+1} smaller than previous one. We conclude that a tree as a three-dimensional object is not a logarithmic fractal, although its projection onto a two-dimensional plane is. Consequently, the life of a tree flows according to the laws of conservation of area in two-dimensional space, as if the tree were a two-dimensional object.

Bifractal structure of chromatin in rat lymphocyte nuclei

The small-angle neutron scattering (SANS) on the rat lymphocyte nuclei demonstrates the bifractal nature of the chromatin structural organization. The scattering intensity from rat lymphocyte nuclei is described by power law Q^{-D} with fractal dimension approximately 2.3 on smaller scales and 3 on larger scales. The crossover between two fractal structures is detected at momentum transfer near 10^{-1}nm^{-1}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the structural organizations of nucleic acids (NA) and proteins. Both chromatin components show bifractal behavior with logarithmic fractal structure on the large scale and volume fractal with slightly smaller than 2.5 structure on the small scale. Scattering intensities from chromatin, protein component, and NA component demonstrate an extremely extensive range of logarithmic fractal behavior (from 10^{-3} to approximately 10^{-1}nm^{-1}). We compare the fractal arrangement of rat lymphocyte nuclei with that of chicken erythrocytes and the immortal HeLa cell line. We conclude that the bifractal nature of the chromatin arrangement is inherent in the nuclei of all these cells. The details of the fractal arrangement-its range and correlation/interaction between nuclear acids and proteins are specific for different cells and is related to their functionality.

Observation of nucleic acid and protein correlation in chromatin of HeLa nuclei using small-angle neutron scattering with D_{2}O-H_{2}O contrast variation

The small-angle neutron scattering (SANS) on HeLa nuclei demonstrates the bifractal nature of the chromatin structural organization. The border line between two fractal structures is detected as a crossover point at Q_{c}≈4×10^{-2}nm^{-1} in the momentum transfer dependence Q^{-D}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the large scale structural organizations of nucleic acids (NA) and proteins. Both NA and protein structures have a mass fractal arrangement with the fractal dimension of D≈2.5 at scales smaller than 150 nm down to 20 nm. Both NA and proteins show a logarithmic fractal behavior with D≈3 at scales larger than 150 nm up to 6000 nm. The combined analysis of the SANS and atomic force microscopy data allows one to conclude that chromatin and its constitutes (DNA and proteins) are characterized as soft, densely packed, logarithmic fractals on the large scale and as rigid, loosely packed, mass fractals on the smaller scale. The comparison of the partial cross sections from NA and proteins with one from chromatin as a whole demonstrates spatial correlation of two chromatin's components in the range up to 900 nm. Thus chromatin in HeLa nuclei is built as the unified structure of the NA and proteins entwined through each other. Correlation between two components is lost upon scale increases toward 6000 nm. The structural features at the large scale, probably, provide nuclei with the flexibility and chromatin-free space to build supercorrelations on the distance of 10^{3} nm resembling cycle cell activity, such as an appearance of nucleoli and a DNA replication.

Instrument Base of the Reactor PIK

Abstract

The program of developing the instrument base of reactor complex PIK is reviewed. This program is carried out in correspondence with the Decree of the President of the Russian Federation No. 356 on July 25, 2019 and the Federal Scientific and Technical Program for the Development of Synchrotron and Neutron Research and Research Infrastructure on the 2019–2027s. The general concept and plans of formation of the instrument base are reported in the four-volume manuscript PIK Reactor Complex (editors V.L. Aksenov and M.V. Kovalchuk), published in 2015.

Switch of fractal properties of DNA in chicken erythrocytes nuclei by mechanical stress

The small-angle neutron scattering (SANS) on the chicken erythrocyte nuclei demonstrates the bifractal nature of the chromatin structural organization. Use of the contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals the differences in the DNA and protein arrangements inside the chromatin substance. It is the DNA that serves as a framework that constitutes the bifractal behavior showing the mass fractal properties with D=2.22 at a smaller scale and the logarithmic fractal behavior with D≈3 at a larger scale. The protein spatial organization shows the mass fractal properties with D≈2.34 throughout the whole nucleus. The borderline between two fractal levels can be significantly shifted toward smaller scales by centrifugation of the nuclei disposed on the dry substrate, since nuclei suffer from mechanical stress transforming them to a disklike shape. The height of this disk measured by atomic force microscopy (AFM) coincides closely with the fractal borderline, thus characterizing two types of the chromatin with the soft (at larger scale) and rigid (at smaller scale) properties. The combined SANS and AFM measurements demonstrate the stress induced switch of the DNA fractal properties from the rigid, but loosely packed, mass fractal to the soft, but densely packed, logarithmic fractal.

Lattice dynamics in FeSi measured by inelastic x-ray scattering

The phonon dispersion of FeSi was measured by inelastic x-ray scattering. The study of its temperature evolution in the range of 100 K-300 K showed that the phonon modes soften to a different extent. The phonons exhibiting specifically strong softening were revealed to belong to the weakly dispersive optical branch. At the same time, the calculations of the lattice dynamics of FeSi suggest that this branch corresponds mainly to the atomic displacements that change the Fe-Fe nearest neighbor distance. It points to the role of the Fe-Fe interaction in the phonon softening.

Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei

Small-angle neutron scattering (SANS) on nuclei of chicken erythrocytes demonstrates the cubic dependence of the scattering intensity Q^{-3} in the range of momentum transfer Q∈10^{-3}-10^{-2}nm^{-1}. Independent spin-echo SANS measurements give the spin-echo function, which is well described by the exponential law in a range of sizes (3×10^{2})-(3×10^{4}) nm. Both experimental dependences reflect the nature of the structural organization of chromatin in the nucleus of a living cell, which corresponds to the correlation function γ(r)=ln(ξ/r) for r<ξ, where ξ=(3.69±0.07)×10^{3} nm, the size of the nucleus. It has the specific scaling property of the logarithmic fractal γ(r/a)=γ(r)+ln(a), i.e., the scaling down by a gives an additive constant to the correlation function, which distinguishes it from the mass fractal, which is characterized by multiplicative constant.

High-pressure single-crystal synchrotron diffraction study of MnGe and related compounds

Single crystal synchrotron diffraction for pressures up to 50 GPa has revealed an essential difference in structural properties and compressibility of MnGe compared with Mn1-x Co x Ge and Mn1-x Fe x Ge solid solutions. A negative thermal expansion has been observed for MnGe at low-temperatures and high-pressures. The single crystal refinement has shown a discontinuous change of the atomic coordinates and Mn-Ge interatomic distances of MnGe in contrast to Mn0.1Co0.9Ge. These peculiarities of MnGe are likely to be associated with high-spin-low-spin transition. The relation between anisotropy of the coordination of Mn-atom and its magnetic moment is discussed.

Thermal expansion of monogermanides of 3d-metals

Temperature dependent powder and single-crystal synchrotron diffraction, specific heat, magnetic susceptibility and small-angle neutron scattering experiments have revealed an anomalous response of MnGe. The anomaly becomes smeared out with decreasing Mn content in Mn1-x Co x Ge and Mn1-x Fe x Ge solid solutions. Mn spin state instability is discussed as a possible candidate for the observed effects.

Scrutinizing Hall Effect in Mn_{1-x}Fe_{x}Si: Fermi Surface Evolution and Hidden Quantum Criticality

Separating between the ordinary Hall effect and anomalous Hall effect in the paramagnetic phase of Mn_{1-x}Fe_{x}Si reveals an ordinary Hall effect sign inversion associated with the hidden quantum critical (QC) point x^{*}∼0.11. The effective hole doping at intermediate Fe content leads to verifiable predictions in the field of fermiology, magnetic interactions, and QC phenomena in Mn_{1-x}Fe_{x}Si. The change of electron and hole concentrations is considered as a "driving force" for tuning the QC regime in Mn_{1-x}Fe_{x}Si via modifying the Ruderman-Kittel-Kasuya-Yosida exchange interaction within the Heisenberg model of magnetism.

Spin chirality is flipped in transition-metal monogermanides

Using high pressure method polycrystalline powder samples of Mn1-xFexGe and Fe1-yCoyGe have been synthesized with x/y running from 0.0 to 1.0. The crystallite size for these compounds is in the order of 10 microns. SQUID magnetization and small angle neutron scattering (using SANS-1 at the MLZ, Garching) have revealed the helical magnetic ordering of the samples within the concentration range of x = [0.0 – 1.0] and y = [0.0 – 0.8]. The values of the helical wavevector k have been taken from the SANS pattern. As it could be seen in Fig.1 a) for Mn1-xFexGe the wavevector k remains roughly constant around 2 nm^-1 for x ≤ 0.4, while going down to a minimum for (|k| -> 0) at xc ≍ 0.75 and increases again to a value of 0.09 nm^-1 for pure FeGe. For Fe1-yCoyGe the k value smoothly decreases from 0.09 nm-1 for pure FeGe to its minimum at yc ≍ 0.6 and increase again for y = 0.8 to its maximum of 0.14 nm^-1 (Fig.1 b). For x/y -> xc/yc we observe a transformation of the helical magnetic structure to a ferromagnetic-like one at the critical concentrations. The change of the magnetic structure from helimagnetic to ferromagnetic-like goes along with a different sign of the magnetic chirality for x/y < xc/yc and x/y > xc/yc [1,2].

Chiral properties of structure and magnetism in Mn(1-x)Fe(x)Ge compounds: when the left and the right are fighting, who wins?

Magnetic susceptibility measurements have shown that the compounds Mn(1-x)Fe(x)Ge are magnetically ordered through the whole range of concentrations x = [0.0,1.0]. Small-angle neutron scattering reveals the helical nature of the spin structure with a wave vector, which changes from its maximum (|k| = 2.3 nm(-1)) for pure MnGe, through its minimum (|k| → 0) at x(c) ≈ 0.75, to the value of |k| = 0.09 nm(-1) for pure FeGe. The macroscopic magnetic measurements confirm the ferromagnetic nature of the compound with x = x(c). The observed transformation of the helix structure to the ferromagnet at x = x(c) is explained by different signs of chirality for the compounds with x > x(c) and x<x(c). We used x-ray diffraction and polarized neutron scattering to evaluate the crystallographic chirality Γ(c) and the magnetic chirality γ(m) of the FeGe single crystals. Similar to previous observations for FeSi-based compounds, FeGe demonstrates left- (right-)handed crystalline chirality acompained by right (left) handedness of the magnetic helix (Γ(c) γ(m) = -1). At variance, MnSi related compounds show the opposite behavior (Γ(c)γ(m) = 1). Since the magnetic chirality γ(m) relates to the sign of the Dzyaloshinskii-Moriya interaction (DMI), for the same geometrical arrangement (Γ(c)) the sign of DMI can be set by the proper choice of the transition metal.

Crystal handedness and spin helix chirality in Fe1-xCoxSi

We show, with the help of polarized neutrons, that the cubic magnets Fe1-xCoxSi with Dzyaloshinskii-Moriya interaction can be switched between left (for x=0.1, 0.15) and right (for x=0.2, 0.25, 0.3, 0.5) chiral states of the spin helix. The absolute structure was evaluated using x-ray diffraction. The crystals are shown to be enantiopure and the structural chirality changes from right handed for x<0.2 to left handed for x>0.2. These compounds are compared with the etalon sample of MnSi which is identified as having the left-handed chirality both in the magnetic and crystallographic sense.

Field induced chirality in the helix structure of Dy/Y multilayer films and experimental evidence for Dzyaloshinskii-Moriya interaction on the interfaces

Polarized neutron scattering experiments have demonstrated that Dy/Y multilayer structures possess a coherent spin helix with a preferable chirality induced by the magnetic field. The average chirality, being proportional to the difference in the left- and right-handed helix population numbers, is measured as a polarization-dependent asymmetric part of the magnetic neutron scattering. The magnetic field applied in the plane of the sample upon cooling below T(N) is able to repopulate the otherwise equal population numbers for the left- and right-handed helixes. The experimental results strongly indicate that the chirality is caused by Dzyaloshinskii-Moriya interaction due to the lack of the symmetry inversion on the interfaces.