Elementary 3D organization of active and silenced E. coli genome
Unraveling how genomes are spatially organized and how their 3D architecture drives cellular functions remains a major challenge in biology. In bacteria, genomic DNA is compacted into a highly ordered, condensed state called nucleoid. Despite progress in characterizing bacterial 3D genome architecture over recent decades, the fine structure and functional organization of the nucleoid remain elusive due to low-resolution contact maps from methods like Hi-C. In this study, we developed an enhanced Micro-C chromosome conformation capture, achieving 10 bp resolution. This ultra-high-resolution analysis reveals elemental spatial structures in the E. coli nucleoid, including chromosomal hairpins (CHINs) and chromosomal hairpin domains (CHIDs). These structures, organized by histone-like proteins H-NS and StpA, play key roles in repressing horizontally transferred genes (HTGs). Disruption of H-NS causes drastic reorganization of the 3D genome, decreasing CHINs and CHIDs, while removing both H-NS and StpA results in their complete disassembly, increased HTGs transcription, and delayed growth. Similar effects are observed with netropsin, which competes with H-NS and StpA for AT-rich DNA binding. Interactions between CHINs further organize the genome into isolated loops, potentially insulating active operons. Our Micro-C analysis reveals all actively transcribed genes form distinct operon-sized chromosomal interaction domains (OPCIDs) in a transcription-dependent manner. These structures appear as square patterns on Micro-C maps, reflecting continuous contacts throughout transcribed regions. This work unveils the fundamental structural elements of the E. coli nucleoid, highlighting their connection to nucleoid-associated proteins and transcription machinery. Overall design: Using the Micro-C technique, we generated contact maps of the E. coli genome at a resolution up to 10 bp. We analyzed wild-type E. coli cells, cells subjected to heat shock, cells treated with different antibiotics and drugs (rifampicin, bleomycin, novobiocin, ciprofloxacin, netropsin), as well as different knockout strains (deltaHNS, deltaStpA, deltaHNSdeltaStpA, deltaFis, deltaMukBEF). We performed gene expression profiling analysis using data obtained from Red-C and RNA-seq. We also performed Hi-C analysis of wild-type E.coli cells.