Chromatin condensed domains revealed by AFM, and their transformation in mechanically deformed normal and malignant cell nuclei

• Published in: Biochemical and biophysical research communications 2024-12, Vol.736, p.150861, Article 150861
• Main Authors: Bairamukov, V. Yu, Ankudinov, A.V., Kovalev, R.A., Pantina, R.A., Grigoriev, S.V., Varfolomeeva, E. Yu
• Format: Article
• Language: English
• Subjects: AFM; Cell Line, Tumor; Cell Nucleus - metabolism; Cell Nucleus - ultrastructure; Chromatin - chemistry; Chromatin - metabolism; Chromatin - ultrastructure; Chromatin condensed domain; DNA supercoiling domains; DNA, Superhelical - chemistry; DNA, Superhelical - metabolism; DNA, Superhelical - ultrastructure; Fibroblasts - cytology; Fibroblasts - metabolism; Fibrosarcoma - genetics; Fibrosarcoma - metabolism; Fibrosarcoma - pathology; Humans; Microscopy, Atomic Force - methods; Nucleosome clutches; Transcription
• ISSN: 0006-291X; 1090-2104; 1090-2104
• DOI: 10.1016/j.bbrc.2024.150861

It has been generally accepted that heterochromatin is represented by a regular, dense and closed structure, while euchromatin is open and sparse. Recent evidence indicates that chromatin is comprised of irregular nucleosome clutches compacted within the nucleus. Transcriptional events transform the chromatin architecture, resulting in appearance of 100–300 nm nucleosomal aggregates. Meanwhile, the current paradigm of chromatin architecture is largely fragmented. In this communication, we unraveled chromatin ultrastructure of normal and malignant cell nuclei through mechanical deformation of the nuclei and Atomic Force Microscopy (AFM) analysis of the resulting landscape. In human skin fibroblasts cell nuclei, nanodomains of about 16.5–33.5 nm were revealed. Hierarchical folding of the chromatin of normal nuclei was observed: the nanodomains formed irregular fiber-like structures that coalesced into the macroscale chromatin compartments. In fibrosarcoma cell nuclei DNA supercoiling domains (SDs) of about 66.3–113.0 nm, uniformly distributed within the nuclei, were revealed. Transformation of the morphology of the condensed chromatin domains through up- and downregulation of supercoiling was demonstrated. [Display omitted] •Chromatin ultrastructure was revealed by AFM via nuclei's mechanical stress.•Nanodomains of 16.5–33.5 nm were revealed in skin fibroblasts cell nuclei.•DNA supercoiling domains of 66.3–113.0 nm were revealed in fibrosarcoma cell nuclei.•The morphology of the chromatin domain is transformed through supercoiling regulation.