Somnath Paul

Automated micronucleus (MN) scoring is increasingly proposed as a remedy for the subjectivity and labour burden of manual scoring yet reported performance has not been appraised systematically. This critical systematic review with quantitative synthesis follows PRISMA 2020. PubMed was searched for studies applying computer‐vision, machine‐learning, or deep‐learning methods to MN determination against expert or expert‐derived reference standards. Twenty‐four records were screened and eight (2020–2025) met eligibility, spanning fluorescence microscopy, brightfield/Giemsa preparations, imaging flow cytometry, and whole‐slide imaging. Because no study reported a reconstructable 2 × 2 table, bivariate diagnostic‐accuracy meta‐analysis was not possible; reported scalar metrics were instead logit‐transformed and combined by DerSimonian–Laird random effects as explicitly descriptive summaries, with correlations combined on the Fisher‐z scale. Summarized recall was 0.924 (95% CI 0.845–0.965) and precision 0.874 (0.790–0.927), both with near‐total heterogeneity (I ² ≈ 97%), whereas agreement between automated and reference counts was high and homogeneous (Pearson r = 0.920, 0.911–0.929; I ² = 0%). Metric definition was the dominant moderator of heterogeneity; residual variation in precision tracked imaging modality rather than network architecture. Although there are bias regarding choice of staining or systems used for analysis as discussed here, current evidence supports a future of automated MN frequency estimation for regulatory and biomonitoring endpoints; but not object‐level equivalence with expert scoring.

Micronuclei (MN) are small extranuclear chromosomal fragments that arise from genomic instability and serve as established biomarkers for genotoxicity and disease susceptibility. Once considered only markers of disease, they are now recognized as active, causative drivers of disease progression, driven by emerging evidence of epigenetic regulation within these structures. The micronucleus assay is recognized as a cost‐effective and minimally invasive method for monitoring genotoxicity resulting from both chronic and early exposure to environmental factors such as arsenic and lead, as well as from genetic instability associated with cancer progression. This review critically examines the expanding role of MN beyond traditional cytogenetic endpoints, with particular emphasis on recent insights into their epigenetic landscape. Mass spectrometry‐based studies have demonstrated that MN possess distinct histone posttranslational modification signatures compared to primary nuclei, including alterations in H3K27ac, H3K9ac, and H3K18ac. These modifications affect chromatin structure, gene expression, and DNA repair mechanisms. In the context of xenobiotic exposures, MN‐associated epigenetic changes may function as early indicators of disease progression. Additionally, rupture of the MN envelope can activate innate immune responses through the cGAS–STING pathway or result in chromothripsis, both of which contribute to cancer progression. The concept of “Micronuclear Epigenetics” is highlighted, with its potential application in high‐throughput diagnostic platforms, particularly liquid biopsy, discussed. This approach may enhance early detection and risk stratification in exposure‐induced toxicity and diseases such as cancer.

The INO80 complex stood out in a large family of ATP-dependent chromatin remodelers because of its ATPase domain binding and translocating on DNA at the edge of nucleosomes, rather than at two helical turns from the center of DNA that is wrapped around nucleosomes. This unique property of INO80 was thought to account for its singular role in nucleosome placement at gene promoters in a DNA-sequence dependent manner that is crucial for transcription regulation. Now, we uncover INO80 functions differently than previously thought with its ATPase domain translocating on DNA close to the center of nucleosomes, like other remodelers. Our discovery also reveals the physical properties of the first ~36 bp of DNA on the entry side of nucleosomes is the main determinant for the DNA specificity of INO80 rather than the properties of the extranucleosomal DNA. The DNA sequence sensitive step of INO80 is after DNA is displaced from the histone octamer on the entry side of nucleosomes and 20 bp of DNA are moved out the exit side. We find the ATPase domain and Arp5 subunit of INO80 are likely involved in INO80’s DNA specificity and the mechanism of INO80 remodeling is substantially different than originally proposed.

All ATP-dependent chromatin remodelers have a DNA translocase domain that moves along double-stranded DNA when hydrolyzing ATP, which is the key action leading to DNA moving through nucleosomes. Recent structural and biochemical data from a variety of different chromatin remodelers have revealed that there are three basic ways in which these remodelers self-regulate their chromatin remodeling activity. In several instances, different domains within the catalytic subunit or accessory subunits through direct protein–protein interactions can modulate the ATPase and DNA translocation properties of the DNA translocase domain. These domains or subunits can stabilize conformations that either promote or interfere with the ability of the translocase domain to bind or retain DNA during translocation or alter the ability of the enzyme to hydrolyze ATP. Second, other domains or subunits are often necessary to anchor the remodeler to nucleosomes to couple DNA translocation and ATP hydrolysis to DNA movement around the histone octamer. These anchors provide a fixed point by which remodelers can generate sufficient torque to disrupt histone–DNA interactions and mobilize nucleosomes. The third type of self-regulation is in those chromatin remodelers that space nucleosomes or stop moving nucleosomes when a particular length of linker DNA has been reached. We refer to this third class as DNA sensors that can allosterically regulate nucleosome mobilization. In this review, we will show examples of these from primarily the INO80/SWR1, SWI/SNF and ISWI/CHD families of remodelers.

Nuclear actin and actin-related proteins (Arps) are key components of chromatin remodeling and modifying complexes. Although Arps are essential for the functions of chromatin remodelers, their specific roles and mechanisms are unclear. Here we define the nucleosome binding interfaces and functions of the evolutionarily conserved Arps in the yeast INO80 chromatin remodeling complex. We show that the N-terminus of Arp8, C-terminus of Arp4 and the HSA domain of Ino80 bind extranucleosomal DNA 37–51 base pairs from the edge of nucleosomes and function as a DNA-length sensor that regulates nucleosome sliding by INO80. Disruption of Arp8 and Arp4 binding to DNA uncouples ATP hydrolysis from nucleosome mobilization by disengaging Arp5 from the acidic patch on histone H2A-H2B and the Ino80-ATPase domain from the Super-helical Location (SHL) -6 of nucleosomes. Our data suggest a functional interplay between INO80’s Arp8-Arp4-actin and Arp5 modules in sensing the DNA length separating nucleosomes and regulating nucleosome positioning.