Early dynamics of chromatin decompaction drive nuclear stiffening

Chromatin regulatory processes involve dynamic modifications to DNA and histone proteins that modulate chromatin structure and accessibility, which in turn control gene expression and genome stability. The cell nucleus must continuously respond to both extracellular and intracellular physical forces and adapt accordingly to preserve proper genome organization across different time scales. Early studies from two decades ago revealed that the nucleus exhibits viscoelastic behavior, characterized by both elastic deformation and time-dependent viscous flow (1). This complex mechanical behavior arises from intricate interactions and structural coupling between chromatin, nuclear lamina, and other nuclear components which comprise the nucleoplasmic fluid. Chromatin decompaction loosens the chromatin structure and is key to facilitating access to DNA for essential processes like transcription, repair, and replication. It also plays an important role in the cell’s response to external forces due to altered mechanical properties. Our understanding of how transient chromatin decompactions affect nuclear stiffness is still limited. Mitra et al. found that acute chromatin decompaction paradoxically increases nuclear stiffness, followed by softening in a time-dependent manner. This transient stiffening is associated with nuclear import, volume increase, and lamin recruitment to the nuclear periphery (Fig. 1A) (2).

Fig. 1.

(A) Histone deacetylase (HDAC) inhibitors, such as Trichostatin A (TSA), increase chromatin acetylation and promote decompaction. Rapid chromatin loosening initially increases nuclear stiffness, which is followed by softening over time. This temporary stiffening is associated with nuclear import, increased nuclear volume, and recruitment of lamin proteins to the nuclear periphery. (B) Acute chromatin decompaction, which causes transient nuclear stiffening, hinders cancer cells’ ability to migrate in confined spaces, but this coupling is disrupted in highly metastatic cells.

Mitra et al. found that acute chromatin decompaction paradoxically increases nuclear stiffness, followed by softening in a time-dependent manner.

Nuclear lamins are type V intermediate filament proteins that form a thin meshwork at the outer layer of the nucleus. Lamin A/C, encoded by the LMNA gene, is primarily found in differentiated cells and plays a role in gene regulation and nuclear stability, while Lamin B, encoded by the LMNB1 and LMNB2 genes, is essential in all cells and helps anchor chromatin to the nuclear envelope (3). Type A and B Lamins form separate but interconnected networks, have different mobility, directly bind to chromatin, organize chromosome positioning within the nucleus, and interact with regulatory factors that influence chromatin structure (4). Distinct deformation regimes have been found, with chromatin responding to small extensions and A-type lamin levels controlling nuclear strain stiffening at large extensions (5). Over a century ago, Heitz introduced the term heterochromatin to describe tightly packed, transcriptionally inactive chromosomal regions, distinguishing them from the more relaxed, transcriptionally active regions referred to as euchromatin (6). Since then, our understanding of chromosome architecture has advanced significantly. Using replication-dependent histone labeling—which distinguishes euchromatin and heterochromatin in living mammalian cells based on replication timing and allows measurement of nucleosome motion in different chromatin regions—it was found that euchromatin exhibits greater local motion, indicating a more fluid, liquid-like state. In contrast, heterochromatin is more constrained and gel-like, likely due to structural crosslinkers such as HP1 and the nuclear lamina (7). Chromatin decompaction can be achieved through chemical modifications to histones, such as acetylation, which reduces the positive charge on histone tails and weakens their interaction with negatively charged DNA (8). Inducing chromatin decompaction by altering chromatin histone modification state with histone deacetylase inhibitors, which causes a general increase in decompact euchromatin, softens the nucleus (9). Change in chromatin mobility through calcium-dependent softening has been shown to be part of the mechanoprotective mechanism against DNA damage during deformations (10). In beating cardiomyocytes, loss of the peripheral heterochromatin by the HMGN5, a member of the HMGN protein family which binds to nucleosomes and reduces histone H1’s interaction with chromatin also decreases nuclear elasticity and disrupts lamina which compromises the ability to withstand mechanical forces (11). Multiple studies employing diverse methodologies to assess nuclear stiffness have demonstrated that chromatin decompaction, through increased euchromatin content, results in a reduction in nuclear rigidity (5, 12, 13). However, these studies primarily focused on longer treatment times for chromatin decompaction or short-time treatment but on isolated nuclei (14). Mitra et al. used a common HDAC inhibitor Trichostatin A, a natural derivative of dienohydroxamic acid derived from a fungal metabolite, to increase chromatin acetylation and therefore decompaction in Hela cells (2). Transmission electron microscopy confirmed a reduction in heterochromatin regions along the nuclear envelope and around the nucleoli, with increased chromatin decondensation observed throughout the nuclear interior. Stiffness was measured by quantifying the indentation depth into the nucleus using vertically aligned nanopillars, with results supported by atomic force microscopy experiments. Nuclear rigidity increased during the first 4 h after chromatin decompaction—timeframes particularly relevant to restricted migration. The authors also showed that moderate nuclear stiffening also occurs following genetic depletion of AKTIP, a telomeric protein that interacts with both type A and B lamins. This depletion induces stable chromatin decompaction and is also accompanied by an increase in the nuclear volume with lasting effects. Dynamic changes in chromatin organization over short time scales are critical for processes such as cell migration, which requires global chromatin condensation (15) or DNA damage repair, which relies on chromatin decompaction (16). Therefore, Mitra et al.’s work is timely and contributes to our understanding of nuclear mechanoadaptation. Perturbations in nuclear mechanical properties are a hallmark of various pathologies including cancer (17). Mechanical and structural alterations of the nucleus lead to abnormal nuclear morphology, which has been used for nearly a century as a diagnostic marker for cancer. Recent advancements in machine learning have enabled highly accurate classification of cancerous cells through the analysis of nuclear morphology in cell nucleus images (18). Superresolution imaging reveals fragmentation and decompaction of heterochromatin in the early stages of carcinogenesis in normal-appearing tissue at risk for tumorigenesis. In addition, integrated genomic and transcriptomic analyses show a more open chromatin structure with disrupted heterochromatin in satellite repeats, leading to increased gene expression, enhanced transcription, and impaired genomic stability, highlighting heterochromatin decompaction as a key feature across multiple tumor types and a potential tool for early cancer detection and risk assessment (19). What promotes cancer cells invasiveness and how cancer become metastatic are among the outstanding questions in cancer biology, with much still left to understand. Mitra et al. performed analysis of the mechanical response and migration efficiency of poorly malignant breast, ovarian, and lung cancer cell lines, comparing them with corresponding cells of higher metastatic potential in response to acute chromatin decompaction (2). They found that the correlation between chromatin decompaction and nuclear stiffening is weakened in malignant cells (Fig. 1B), and this is associated with increased markers of compact heterochromatin, which favors migration, consistent with other studies (20). Cancer mechanobiology, which spans from the physical environment to cell mechanics and the nucleoskeletal framework, can influence both cancer cell behavior and the expression of cancer-related genes. A deeper understanding of the interplay between these components can help us develop better diagnostic and therapeutic tools to fight cancer progression.