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.

Application of atomic force microscopy for investigation of Na(+),K(+)-ATPase signal-transducing function

The Young's modulus of 10-12-day-old chick embryos' sensory neurons cultivated in dissociated cell culture was measured using a PeakForce Quantitative Nanomechanical Mapping atomic force microscopy. The native cells were tested in control experiments and after application of ouabain. At low "endogenous" concentration of 10⁻¹⁰ M, ouabain tended to increase the rigidity of sensory neurons. We hypothesize that this trend resulted from activation of Na⁺,K⁺-ATPase signal-transducing function.

Investigation of the light field of a semiconductor diode laser

Scanning near-field optical microscopy was applied to study, with sub-wavelength spatial resolution, the near- and the far-field distributions of propagating modes from a high-power laser diode. Simple modeling was also performed and compared with experimental results. The simulated distributions were consistent with the experiment and permitted clarification of the configuration of the transverse modes of the laser.