High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

Abstract

Chromosomes must be highly compacted and organized within cells, but how this is achieved in vivo remains poorly understood. We report the use of Hi-C to map the structure of bacterial chromosomes. 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 evidence that domain boundaries are established by highly-expressed genes and the formation of plectoneme-free regions, whereas the histone-like protein HU and SMC promote short-range compaction and the cohesion of chromosomal arms, respectively. Collectively, our results reveal general principles for the organization and structure of chromosomes in vivo.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation

“…Similarly, recent experimental work in Caulobacter reveals that highly transcribed genes appear to demarcate topological domains in the chromosome (7), and in vivo measurements of interloci distances in Caulobacter resemble those theoretically predicted for a branched supercoiled conformation with densely packed plectonemes (65). In all three of these organisms, topological domains are measured to possess average sizes of~10 kilobases (7,33) and the importance of transcription in regulating the size of these topological domains is suggested by the high conservation of genomic interspacing of highly expressed genes in the chromosomes of phylogenetically distant bacteria (33). Thus, the linking deficits and length scales simulated in this work are of direct relevance to the length scales and linking deficit regimes that are implicated in transcriptional regulation of chromosomal topology, and may have important implications for chromosomal organization and dynamics.…”

“…In Escherichia coli and other bacteria, the circular DNA chromosome is regulated in an underwound topological linking state by topoisomerases, which gives rise to supercoiling of the chromosome. The degree of supercoiling is dynamically adapted to environmental cues (4), and the chromosome is further dynamically partitioned into looped topological domains with average sizes of~10 kilobases (5)(6)(7). In both eukaryotes and prokaryotes, supercoiling facilitates compaction of the genome into the cell (1) and is believed to be intimately connected to regulation of gene expression (7)(8)(9).…”

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

“…Our results indicate that colocalization of rRNA operons crosses not only macrodomain but also replichore boundaries. Cross-replichore interactions have also been reported in the C. crescentus (Le et al 2013) and Bacillus subtilis (Wang et al 2015) genomes. However, those interactions appear to be based on distance from the origin of replication rather than a shared function of the interacting gene pairs.…”

“…The positions of individual loci in space are dynamic (Espeli et al 2008), but systematic, genome-wide cytological analyses of both the E. coli and Caulobacter crescentus chromosomes concluded that the linear order of genes in space recapitulates the genetic map (Viollier et al 2004; for review, see Wang and Rudner 2014). The linear array has been pictured as a "bottlebrush" in which interwound loops extrude from a central nucleoid scaffold (Le et al 2013;Wang and Rudner 2014). The ter macrodomain is organized by the MatP and YfbV proteins (Thiel et al 2012), but the identities of the short-and long-range interactions that might organize other parts of the chromosome remain unclear.…”

Rapid pairing and resegregation of distant homologous loci enables double-strand break repair in bacteria

“…To assess the possible effects of a DSB on global chromosome organization, we used chromosome conformation capture with deep sequencing, or Hi-C (Le et al, 2013). Prior Hi-C analysis of undamaged cells demonstrated that the C. crescentus chromosome contains ∼23 chromosomal interaction domains where loci interact preferentially with other loci in the same domain.…”