Chromatin is frequently unknotted at the megabase scale

Abstract

Knots in the human genome would greatly impact diverse cellular processes ranging from transcription to gene regulation. To date, it has not been possible to directly examine the genome in vivo for the presence of knots. Recently, methods for serial fluorescent in situ hybridization have made it possible to measure the 3d position of dozens of consecutive genomic loci, in vivo. However, the determination of whether genomic trajectories are knotted remains challenging, because small errors in the localization of a single locus can transform an unknotted trajectory into a highlyknotted trajectory, and vice versa. Here, we use stochastic closure analysis to determine whether a genomic trajectory is knotted in the setting of experimental noise. We analyse 4727 deposited genomic trajectories of a 2Mb long chromatin interval from chromosome 21. For 243 of these trajectories, their knottedness could be reliably determined despite the possibility of localization errors. Strikingly, in each of these 243 cases, the trajectory was unknotted. We note a potential source of bias, insofar as knotted contours may be more difficult to reliably resolve. Nevertheless, our data is consistent with a model where, at the scales probed, the human genome is often free of knots.

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

“…Lack of entanglements within contiguous domains of up to several Mb was recently reported by Goundaroulis and co-workers using an entirely independent approach: their re-analysis of oligo-paint serial fluorescent labeling data from Bintu and colleagues 26 , 27 indicates chromatin domains can be largely knot free, at least for the relatively small subset of cells where the chromatin fiber could be reliably traced 27 . They did not investigate the extent to which different chromosomes or different compartments domains are entangled.…”

Active topological glass

“…Current experimental evidence for the topological state (knottedness) of the chromatin fiber also varies. While conformations inferred from contact probability measurements exhibit knots 65 , the knot analysis 66 of the direct observations of fluorescently labeled chromatin segments finds mostly unknotted segments. Unable to refine the scales of the topological constraints completely at this point, we assumed their existence for the typical observation times and examined the consequences.…”

Exploring Chromosomal Structural Heterogeneity Across Multiple Cell Lines

“…The heterogeneity has now been confirmed by direct imaging of individual chromosomal structures [14][15][16]. As a consequence of this conformational plasticity, statistical ensembles [25,26,29,30,[33][34][35][36][37][38] must be used in order to describe chromosomal structures in vivo.…”