High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

Abstract

Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10 -2 -10 3 sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.

Evidence for actin dual role in regulating chromosome organization and dynamics in yeast

“…The prefactor C characterizes how fast the chromatin locus moves, the exponent is indicative of the type of diffusion, subdiffusive if α<1 or diffusive if α=1 (in this latter case, C would be identical to the diffusion coefficient). Our finding that α≈0.5 is in agreement with previous studies on other chromosome loci, which have reported subdiffusion with similar exponents in both prokaryotes and eukaryotes Hajjoul et al, 2013;Weber et al, 2010). This shows that subtelomeres undergo subdiffusive motion.…”

“…This is in agreement with previous studies, which have shown that locus motion does not obey free diffusion but is instead constrained with a subdiffusive behavior that is ubiquitously observed in bacteria, yeast and mammals (Heun et al, 2001;Marshall et al, 1997;Weber et al, 2012). The observed subdiffusive exponent is consistent with the Rouse model of polymer dynamics that assumes spring-like interactions between consecutive monomers, or alternatively with a viscoelastic response of the nuclear medium (Bronstein et al, 2009;Cabal et al, 2006;Hajjoul et al, 2013;Lucas et al, 2014;Weber et al, 2012). Although the anomalous exponent does not depend on the locus, the prefactor C shows variations relative to the genomic position, as exemplified by the reduced mobility of subtelomeres (Bystricky et al, 2005;Hajjoul et al, 2013;Heun et al, 2001).…”

“…A position within the right arm of chromosome IV, known to be preferentially positioned away from the periphery (735 kb from the centromere; Wong et al, 2012) was tracked by using time-lapse acquisition as described above, with or without latrunculin A (Materials and Methods). In the DMSO control, all loci exhibited similar prefactor C values in agreement with previous results (above and Hajjoul et al, 2013). Interestingly, in the presence of latrunculin A, a marked decrease in subdiffusion was observed both in WT and Δcsm4 cells ( Fig.…”

“…The observed subdiffusive exponent is consistent with the Rouse model of polymer dynamics that assumes spring-like interactions between consecutive monomers, or alternatively with a viscoelastic response of the nuclear medium (Bronstein et al, 2009;Cabal et al, 2006;Hajjoul et al, 2013;Lucas et al, 2014;Weber et al, 2012). Although the anomalous exponent does not depend on the locus, the prefactor C shows variations relative to the genomic position, as exemplified by the reduced mobility of subtelomeres (Bystricky et al, 2005;Hajjoul et al, 2013;Heun et al, 2001). When actin filaments were depleted following addition of latrunculin A, the subdiffusive prefactor C was decreased, whereas the exponent α≈0.5 was maintained, suggesting that actin filaments do not affect the constraint that prevents the locus from undergoing free diffusion.…”

Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior

“…Examples include az0:7 for RNA-protein particles in E. coli (14,21) and S. cerevisiae (22), az0:7 for lipid granules in fission yeast (23), az0:5 for gold nanoparticles in several human and mammalian cell lines (24), and az0:5 À 0:8 for dextrans in HeLa cells (25). Chromosomal loci also exhibit subdiffusive behavior, with az0:4 À 0:5 for E. coli (26,27), az0:5 À 0:7 in budding yeast (28,29), and az0:3 for mammalian telomeres at timescales <10 s (30). Note that subdiffusive behavior does not necessarily imply nonGaussian behavior, as models such as fractional Brownian motion exhibit Gaussian, anticorrelated increments resulting in anomalous diffusion (31).…”