Spatially confined folding of chromatin in the interphase nucleus

Abstract

Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability P for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10 -30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5-to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin-chromatin interactions and determine the 3-dimensional organization of the chromatin fiber.genome organization ͉ polymer model ͉ chromatin folding T he chromatin fiber inside the interphase nucleus of higher eukaryotes is folded and compacted on several length scales. On the smallest scale the basic filament is formed by wrapping double-stranded DNA around a histone protein octamer, forming a nucleosomal unit every Ϸ200 bp. This beads-on-a-string type filament in turn condenses to a fiber of 30-nm diameter, which detailed organization is still under debate (1-3). At bigger length scales the spatial organization of chromatin in the interphase nucleus is even more unclear. Imaging techniques do not allow one to directly follow the folding path of the chromatin fiber in the interphase nucleus. Therefore, indirect approaches have been used to obtain information about chromatin folding. One way, pursued in this study, is fluorescence in situ hybridization (FISH) to measure the relationship between the physical distance between genomic sequence elements (in m) and their genomic distance (in megabases). There have been several attempts to explain the folding of chromatin in the interphase nucleus using polymer models. The strength of polymer models is their ability to make predictions on the structure of chromatin by pointing out the driving forces for observed folding motifs. These predictions can then be tested experimentally. However, a polymer model that is able to explain chromatin folding spanning differen...

Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

“…Although the origin of chromosomal territories is controversial because equilibrium polymer configurations with many loops naturally produce segregated domains as well [14,15], a major non-equilibrium effect, glassy dynamics of the genome under strong confinement, should not be overlooked from a contributing factor in chromosome folding. The relaxation time of a polymer via disentanglement [16] (τ rep ∼ N 3 [12,13,17,18]) could be far longer, effectively permanent for higher organisms, than the cell cycle time (τ cell ) [12,13] for a large N .…”

“…The scaling exponent α of the contact probability between two sites separated by the chain contour s, P (s) ∼ s −α , is one way to assess the chain organization (Alternatively, the average distance between two loci separated by s, R(s) ∼ s ν , can be used [9,15]. See Fig.S3).…”

Conformational properties of compact polymers

“…Special interest is on the distance distribution between the end points of the chain as well as the distance distribution between smaller segments of the chain. Stunningly this quantity has not been analyzed in previous publications, although it is of severe importance for biological applications as the distributions can be compared directly to experimental data [7]. Furthermore, we provide a comparison of compact polymers to a polymer melt of equal density, which has been suggested to behave similarly [1,16].…”

“…In a third step, we apply the results of our simulational study to recent experimental data concerning the folding of chromatin inside the interphase nucleus. We show that chromatin on a scale above 150 kb does not organize simply in a compact state as the behaviour of the mean square displacement with genomic distance might suggest [7], but shows important hallmarks of a disordered system as described by the random loop model [7,17].…”

“…distribution between two arbitrary monomers along the chain which are separated by a certain contour length n. For example, this quantity becomes important in experiments measuring the spatial arrangement of two flourescently labelled parts of the human genome [7]. Therefore, we have to evaluate how the distribution changes when looking at intrachain segments.…”