biostudies-literatureUnknown645(8082)Gavrilov AAUnravelling how genomes are spatially organized and how their three-dimensional (3D) architecture drives cellular functions remains a major challenge in biology^1,2. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid^3-5. Despite progress in characterizing bacterial 3D genome architecture over recent decades^6-8, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods such as Hi-C^9-11. Here we developed an enhanced Micro-C chromosome conformation capture, achieving 10-base pair (bp) resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the Escherichia coli nucleoid, including chromosomal hairpins (CHINs) aNature1060-1070https://www.ebi.ac.uk/biostudies/studies/S-EPMC12460168biostudies-literatureElementary 3D organization of active and silenced E. coli genome.PMC12460168Shamovsky IBlavatnik AProshkin SLahiri SRasouly AShamovsky YEpshtein VEvko GRazin SVZhegalova INudler EGavrilov AARothenberg EfalseElementary 3D organization of active and silenced E. coli genome.Unravelling how genomes are spatially organized and how their three-dimensional (3D) architecture drives cellular functions remains a major challenge in biology^1,2. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid^3-5. Despite progress in characterizing bacterial 3D genome architecture over recent decades^6-8, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods such as Hi-C^9-11. Here we developed an enhanced Micro-C chromosome conformation capture, achieving 10-base pair (bp) resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the Escherichia coli nucleoid, including chromosomal hairpins (CHINs) a2025-01-01T00:00:00Z2025 Sep2026-07-15T06:45:40.511Z2026-06-30T03:22:39.678ZS-EPMC124601684080452710.1038/s41586-025-09396-y