High-resolution mapping of the spatial organization of Caulobacter crescentus chromosome by chromosome conformation capture in conjunction with next-generation sequencing (Hi-C)

Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the first use of Hi-C to map the structure of bacterial chromosomes at a high, unprecedented resolution. Analysis of Hi-C data and polymer modeling indicates that the Caulobacter crescentus chromosome consists of multiple, largely independent spatial domains likely comprised of supercoiled plectonemes arrayed into a bottlebrush-like fiber. These domains are stable throughout the cell cycle and re-established concomitantly with DNA replication. We provide strong evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions. Additionally, we use Hi-C to demonstrate that supercoiling, the histone-like protein HU, and SMC act at different length-scales and in complementary ways to organize and structure chromosomes within cells. Overall design: Hi-C experiments were performed on untreated wild type swarmer cells and drug-treated swarmer cells (Novobiocin or Rifampicin) of Caulobacter crescentus CB15N. Hi-C were also performed on swarmer cells of smc knock-out and hup1hup2 knock-out mutants of Caulobacter crescentus. Time-course Hi-C were performed on a synchronous population of Caulobacter crescentus at 5, 10, 30, 45, 60 and 75 minutes after synchronization. The progression of DNA replication during the cell cycle was followed by total genomic DNA sequencing.