The chromosome folding problem and how cells solve it

Abstract

Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.

Figure 1. Evolving physical models over the last decades.

Over the last 50 years, Polymer Physics has put forth increasingly refined models of chromosome conformation. See text for details.

Figure 2:. Two processes for nuclear organization: compartmentalization through homotypic affinities and tethering to the nuclear periphery.

A. Eukaryotic chromosomes are composed of alternating A and B compartments. In conventional nuclear organization, strong B-B affinities lead to spatial separation of A and B compartments. A-A affinities are much weaker and contribute to a lesser extent. In addition, Some B compartments are tethered to the nuclear periphery, resulting in enrichment of heterochromatin at the nuclear periphery, leaving euchromatin located centrally. B. In the absence of tethering of B compartment domains to the nuclear periphery, A/B compartmentalization occurs normally, but the strong B-B affinities result in clustering of all B compartments in the center of the nucleus, with A compartments located at the periphery (inverted nucleus). C. A more complex picture when more than 2 compartment types are present. A and B compartments can be split in different subcompartments that can also display significant preferential homotypic affinities, leading to their spatial segregation.

Figure 3:. Two regimes of loop extrusion produce different conformations, consistent with interphase and mitosis.

A. Activity of a loop extruder: the complex loads, extrudes some amount of time after which it may dissociate, or is actively unloaded. B. During interphase (in vertebrates), cohesin is the main loop extrusion complex. It has a short residence time, generating a low density of transient loops, and the chromosomes appear diffuse in shape. Cohesin can be blocked by CTCF-bound sites, generating enrichment of positioned loops at these elements. C. During mitosis, condensins are the main loop extrusion complexes. Condensin II has a long residence time, generating stable arrays of consecutive loops that lead to compaction into the rod-shaped mitotic chromosomes. Condensin is not blocked by CTCF, and the loop array is not positioned at reproducible loci in the cell population. C. In bacteria, repeated loading of loop extruding complexes at defined loading sites can lead to juxtaposition of the chromosome arms, sequences on either side of the loading site.

Figure 4:. Rules of engagement for different SMCs results in different loop organization and structures of compacted chromosomes.

A. Three possible outcomes of an encounter between loop-extruding SMCs (orange and purple): they can block each other, leading to formation of consecutive loops; bypass each other forming so-called Z-loop; or one can facilitate dissociation of another (other outcomes are also possible, e.g. one pushing the other back, etc). B. Two possible outcomes of interactions between cohesive cohesins (blue rings) and loop extruding SMCs (purple). Top: when extruders are blocked by cohesive complexes, sister chromatids are predicted to be connected at the bases of the loops, forming a single axis (as in meiotic prophase I and early mitotic prophase). When extruders can bypass cohesive complexes, sister chromatids are predicted to be connected through the tips of their loops (as in mitotic prometaphase).

Figure 5:. Current models of interphase chromosome organization through integrated activity of multiple mechanisms.

Schematic depiction of interphase chromosome conformation in eukaryotes as the combined and integrated result of multiple folding mechanisms. The chromosome is a worm-like chain that phase separates in distinct compartments (A/B compartments or finer subcompartments) driven by homotypic affinities. Tethering of domains to sub-nuclear structures such as the nuclear lamina, the nucleolus, or nuclear bodies including speckles, leads to positioning of loci and chromosomes at specific nuclear locations. Topological contraints prevent mixing in interphase but self-entanglements are formed in mitosis, facilitating full and fast compaction. At the scale of hundreds of Kb, loop extrusion, guided by cis elements that determine loading, unloading, and blocking (CTCF) of loop extruders, and with extensive interplay with other folding mechanisms, including compartmentalization, adds an additional layer of chromosome folding.

Figure 6:. The interplay of Loop extrusion, topologically associating domain formation, and guidance of promoter-enhancer interactions

Enhancers can reach nearby promoters (separated by less than 50 kb) and interact via affinity-driven contacts, without a need for loop extrusion to facilitate their interaction. Cohesin facilitates contacts between enhancers and promoters when they are separated by more than 50 kb. Repeated enhancer-promoter contacts may be required to activate the gene (green arrows), leading to reduced correlation between contact and transcription in real time. For longer-range enhancer-promoter pairs: when clusters of multiple CTCF sites are located in between them, they will block loop extrusion, induce a TAD boundary, and inhibit enhancer-promoter contacts, preventing enhancers from activating the gene. Single CTCF sites can create weak and permeable boundaries that may not fully prevent enhancer-mediated activation leading to some activation (smaller green arrow). Orange triangles, in different shades represent Hi-C interaction data and TADs.