BPS2026 – Image-based analysis of the genome’s fractality during the cell cycle

The human genome consists of about 2 m of DNA packed inside the 10-μm cell nucleus. DNA is complexed with histones, forming chromatin fiber, which folds inside the nucleus into loops, topologically associating domains, A/B compartments, and chromosome territories. This organization is knot-free and self-similar across length scales, leading to a hypothesis that the genome presents a fractal globule, as corroborated by chromosome conformation capture experiments. In addition, many microscopy techniques have been used to obtain the fractal dimension of the genome’s spatial distribution from its images. However, different techniques often adapted different definitions of fractal dimension, making the comparison of these results non-trivial. In this study, we use spinning disk confocal microscopy to collect high-resolution images of nuclei in live human cells during the cell cycle. We then systematically compare existing image-based fractal analyses—including mass-scaling, box-counting, lacunarity, and multifractal spectrum—by applying them to the images and investigate changes in the genome’s spatial organization during the cell cycle. Our data reveal that different fractal measurements offer distinct metrics, highlighting different features of the genome’s spatial organization. Yet, all these metrics consistently indicate the following trend for the changes in the genome’s organization during the cell cycle—the genome being compactly packed in early G1 phase, followed by a decondensation throughout the G1 phase, and a subsequent condensation in the S and G2 phases. Our comprehensive comparison of image-based fractal analyses reconciles the perceived discrepancies between different methods. Moreover, our results offer new insights into the physical principles underlying the genome’s organization and its changes during the cell cycle (Lee et al, Biophys. J. , 2025). This research was supported by the National Institutes of Health grant R01-GM145924 and by the National Science Foundation grants CAREER PHY-155488, CMMI-1762506, and PHY-2210541.