Molecular basis and biological function of variability in spatial genome organization

Abstract

The complex three-dimensional organization of genomes in the cell nucleus arises from a wide range of architectural features including DNA loops, chromatin domains, and higher-order compartments. Although these features are universally present in most cell types and tissues, recent single-cell biochemistry and imaging approaches have demonstrated stochasticity in transcription and high variability of chromatin architecture in individual cells. We review the occurrence, mechanistic basis, and functional implications of stochasticity in genome organization. We summarize recent observations on cell- and allele-specific variability of genome architecture, discuss the nature of extrinsic and intrinsic sources of variability in genome organization, and highlight potential implications of structural heterogeneity for genome function.

Fig. 1.. Variability at all levels of genome organization.

The genome is organized at multiple levels, and all of these levels show variability. DNA wraps around histone proteins at variable positions to form a chromatin fiber of variable width. Chromatin forms domains made up of individual loops, each of which occurs at only low frequency. Domains in turn assort within compartments, but their position within that compartment is variable. Similarly, chromosomes have preferred positions but can be found anywhere in the nucleus.

Fig. 2.. Classes of variability in spatial genome organization.

(A) Extrinsic variability emerges when two cell types within a population have different preferred genome conformations. This variability results in a bimodal distribution of chromatin-chromatin distances. The two alleles in a cell will behave the same. (B) Allele-specific variability is created when chromatin loops form at one allele in a cell but not the other allele. This type of variability results in a bimodal distribution, but alleles will behave differently. (C) Intrinsic variability occurs when each allele represents an individual looping event. In this case, cells will occur in the population with zero, one, or two alleles forming loops. The distance distribution will be unimodal, and the alleles will show no correlation in distances.

Fig. 3.. Stochasticity in gene expression and association.

(A) Stochastic gene expression results from random activity at gene promoters and causes a skewed distribution of transcription events, nascent mRNAs, and mature transcripts, in which at any given time a few cells produce most of the mRNA in the population. This may occur at genes with overall low expression levels (i.e., blue) or high expression levels (i.e., orange). (B) Stochastic chromatin interactions result from randomness inherent in the position and movement of the DNA fiber. They result in a population of cells in which interactions between any two regions are possible and interactions between each individual pair are rare. (C) Stochastic domain boundaries form as a result of the movement of DNA and the architectural proteins that associate with it. They result in a population of cells in which boundaries between domains can occur at any genomic position, with a preference for enriched boundary sites.

Fig. 4.. Averaging and phase separation create stability out of organizational variability.

(A) Because of the stability of the mRNA and protein products, highly variable and transient promoter-enhancer loops can nonetheless result in consistent numbers of mRNA molecules being transcribed, as well as consistent transcription profiles, within a cell or tissue. (B) Phase separation results in the segregation of molecules or DNA loci and can result in a stable nuclear body forming from a complex combination of variable associations.