A multifaceted journey into higher-order chromatin organization: Insights from experimental and computational...

Chromatin organization in the nucleus is a nonrandom and highly organized process. This nonrandom chromatin arrangement in the nucleus is the crucial regulator of genome function and stability. Over the recent decades, the development of various high-throughput experimental methods has revealed chromatin architecture across multiple genomic scales from nucleosome positioning to topologically associating domains (TADs) and chromosome territories. The increasing complexity and volume of experimental data necessitate the development of sophisticated computational tools for data integration, modeling, and interpretation. Given the rapid evolution of both experimental techniques and computational frameworks, a comprehensive and critical review of current approaches is timely. This review discusses methods for studying higher-order chromatin organization, including microscopy-based techniques, sequencing-based approaches, and informatics-driven computational analyses. We emphasize their strengths, limitations, and significance in advancing our understanding of chromatin organization within the three-dimensional space of the nucleus. By providing an integrated perspective, this review aims to guide researchers in selecting appropriate tools and highlighting future directions for exploring the critical domain of genome architecture.