Differential Chromosome Conformations as Hallmarks of Cellular Identity Revealed by Mathematical Polymer Modeling

Abstract

Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MAT a cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.

The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer

“…The existence and role of pre-folding of chromosome III to the directionality of the mating type switch has been debated, because the motion of HML α was mating type and RE-dependent in strains disomic for chromosome III (Bressan et al, 2004), but in contrast tethering the HM loci to MAT did not alter donor preference (Simon et al, 2002). Also, nuclear positioning of the mating type loci did not seem to differ in a and α cells (Bystricky et al, 2009a) while mating type specific features of the folding of chromosome III could be seen in a subset of cells (Lassadi et al, 2015). …”

Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae

“…One noteworthy difference between a cells and a cells is the spatial conformation of chromosome III (Belton et al 2015;Lassadi et al 2015). In comparison to a cells, a cells show more frequent interactions between the left arm of chromosome III, which contains HML and the RE, and a region on the right arm that extends from the centromere to the MAT locus.…”

“…Given that a cells and a cells show similar patterns of DNase-I sensitivity throughout this chromosome arm, the RE does not dramatically alter the local chromatin structure (Ercan and Simpson 2004). Remarkably, the RE does effect a change in the higher-order folding of chromosome III; however, this function is genetically separable from the recombination function (Belton et al 2015;Lassadi et al 2015). The mechanism by which the RE acts at a distance remains unresolved.…”

ChromoTrace: Computational Reconstruction of 3D Chromosome Configurations for Super-Resolution Microscopy

“…Such a result would be disappointing in 499 terms of the reconstruction algorithm, but fascinating in terms of how such chromosomal 500 domains are created and maintained. However, the extended conformation of many 501 chromosomes seen previously [31], along with the distribution of their contacts to the 502 nuclear lamina [32], suggest that overall compaction is an unlikely configuration, except 503 for specific cases such as mitotic chromosomes or the inactive X chromosome. The 504 second outcome is that the more highly packed regions are interspersed with more 505 extended regions.…”

“…Within territories and across the whole nucleus euchromatin 29 and heterochromatin are generally spatially separated [9], leading to heterochromatin 30 rich and gene expression poor domains at the nuclear periphery and around nucleoli. 31 Gene expression is intrinsically linked to the 3D structure of chromosomes, chromatin 32 packing densities and the accessibility of DNA by e.g. the transcriptional machinery.…”