Condensin-driven remodelling of X chromosome topology during dosage compensation

Abstract

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct higher-order structure onto X while regulating gene expression chromosome wide.

Iteratively improving Hi-C experiments one step at a time

“…Overall, all of these approaches lead to reproducible final Hi-C libraries according to concordance scores calculated by GenomeDISCO [38] and visual comparisons of the resulting heatmaps at 40 kb resolution ( Figure 2B and C). TAD boundary locations and strengths at 40 kb resolution are also overall similar according to an insulation score profile ( Figure 2D) [37]. Thus, the major gain in these particular optimizations will lie primarily in the fraction of useful reads gained from a certain number of cells and improvements in heatmaps at higher resolution.…”

Cell Biology of theCaenorhabditis elegansNucleus

“…In this way it is possible to examine the proximity of either selected sequences or all chromosomal sequences relative to all other sequences. Two recent C. elegans studies, one employing Hi-C and the other a variation of tethered chromatin capture, revealed unique features of the C. elegans chromosome organization (Crane et al 2015;Gabdank et al 2016).…”

“…It should be kept in mind that these chromosome conformation capture analyses are nearly always done on a population of cells. Therefore, it is formally possible that worm cells have well-defined TADs, but they differ from cell to cell (in embryos, Crane et al 2015) or from tissue to tissue (Gabdank et al 2016). However, this would still be different from classical TADs, which are largely conserved within all cells of an organism.…”

“…Thus, the significance, if any, of these ill-defined autosomal TADs in regulating autosome function in C. elegans remains to be determined. The X chromosome, on the other hand, does have defined TADs (Crane et al 2015;Gabdank et al 2016;see below).…”

“…The organization in TADs is more pronounced for the X chromosome than for autosomes (chromosome I shown as example). Figure courtesy of Barbara Meyer; data from Crane et al (2015).…”