Light-dependent changes in the higher-order DNA structure of the cyanobacterium Synechocystis sp. PCC 6803

Chromosome spatial organization plays critical roles in transcriptional regulation and DNA protection. In cyanobacteria--oxygenic photosynthetic bacteria that experience dramatic fluctuations in light intensity--chromosome reorganization may facilitate rapid transcriptional reprogramming and protect DNA from photodamage. However, direct observation of chromosome organization in these polyploid organisms has remained technically challenging, leaving light-dependent chromosomal responses unexplored. Here we show that local chromosome organization in Synechocystis sp. PCC 6803 is reorganized in response to high-light stress. We established fluorescence in situ hybridization (FISH) methods for this model cyanobacterium carrying multi-copy genomes, together with a computational pipeline for optimal same-genome-copy probe pairing. Under standard conditions, spatial distance between paired signals increased with genomic distance (slope {beta} = 0.972 nm/kbp, R{superscript 2} = 0.12), demonstrating that linear genome organization is reflected in three-dimensional chromosome structure at the 25-124 kbp scale. This genomic-spatial distance relationship substantially weakened under high-light conditions ({beta} = 0.450 nm/kbp, R{superscript 2} = 0.02), indicating that local chromosome organization is disrupted by elevated light intensity. Same-color nearest-neighbor distances further revealed that the spatial distribution of genome copies differed between conditions, independently supporting condition-dependent chromosome reorganization. Hi-C analysis corroborated these findings, revealing reduced short-range interactions within the 10-100 kbp genomic range under high-light conditions. Our integrative single-cell and population-level approach provides a framework for investigating how environmental signals modulate higher-order chromosome structure in polyploid bacteria.