Abstract
We have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome by combining genome-wide chromatin interaction detection, live-cell imaging, and computational modeling. Using chromosome conformation capture carbon copy (5C), we derive ~13 kb resolution 3D models of the Caulobacter genome. The resulting models illustrate that the genome is ellipsoidal with periodically arranged arms. The parS sites, a pair of short contiguous sequence elements known to be involved in chromosome segregation, are positioned at one pole, where they anchor the chromosome to the cell and contribute to the formation of a compact chromatin conformation. Repositioning these elements resulted in rotations of the chromosome that changed the subcellular positions of most genes. Such rotations did not lead to large-scale changes in gene expression, indicating that genome folding does not strongly affect gene regulation. Collectively, our data suggest that genome folding is globally dictated by the parS sites and chromosome segregation.
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📊 Figures
Figure 1
Genome-wide 5C reveals that the swarmer chromosome is ellipsoidal
(A) Outline of our 3C and 5C approaches. (Top) Formaldehyde is added to a culture of synchronized swarmer cells, cross-linking physically touching chromosomal loci (e.g. the red and purple regions den...
Figure 2
Modeling reveals the 3D architecture of the swarmer genome
(A) Outline of our modeling methodology. Restriction fragments were modeled as points connected by springs. The distance derived from the contact frequency between pair of fragments was used (I) to de...
Figure 3
5C Analyses of strains carrying genomic inversions reveal that the parS elements are critical to defining chromosome orientation
(A) Genomic maps for strains CB15N (wild-type), and inversion strains ET166, and ET163. The inverted region is indicated in yellow and green. (B/D) Contact maps for strain ET166 and ET163 swarmer cell...
Figure 4
The genomic positions of the parS sites affect the orientation of the entire Caulobacter genome within the cell
(A) Representative images showing the position of parS (yellow), and a lacO array (blue) inserted 2898 Kb from the origin (cyan), in wild-type and the inversion strains, ET166 and ET163. (Bu2013C) Sub...
Figure 5
Inter-arm alignments reveal interaction asymmetries in ET166 swarmer cells
(A) (Top) Wild-type cluster 1 swarmer long-axis alignment plot. The genomic distance of each fragment to the most polar fragment ( parS elements) is plotted against the genomic distance of the closest...
Figure 6
The parS sites nucleate a compact region of the genome
(A) (Top) Wild-type (black) and ET166 (green) genome compaction profile generated from the models in cluster 1. This profile presents the local compaction (derived from the 3D distances between neighb...
Figure 7
The Caulobacter chromosome is free to rotate around the long cell axis
(A) (Left) Schematic of a Caulobacter swarmer cell indicating the positions of the new and old poles as well as the dorsal and ventral sides of the cell. Negative and positive signs refer to the conve...
Figure images are served from the NIH/NLM PubMed Central Open Access Subset or Europe PMC; copyright remains with the publishers and authors.
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