How chromosome topologies get their shape: views from proximity ligation and microscopy methods

Abstract

The 3D organization of our genome is an important determinant for the transcriptional output of a gene in (patho)physiological contexts. The spatial organization of linear chromosomes within nucleus is dominantly inferred using two distinct approaches, chromosome conformation capture (3C) and DNA fluorescent in situ hybridization (DNA–FISH). While 3C and its derivatives score genomic interaction frequencies based on proximity ligation events, DNA–FISH methods measure physical distances between genomic loci. Despite these approaches probe different characteristics of chromosomal topologies, they provide a coherent picture of how chromosomes are organized in higher‐order structures encompassing chromosome territories, compartments, and topologically associating domains. Yet, at the finer topological level of promoter–enhancer communication, the imaging‐centered and the 3C methods give more divergent and sometimes seemingly paradoxical results. Here, we compare and contrast observations made applying visual DNA–FISH and molecular 3C approaches. We emphasize that the 3C approach, due to its inherently competitive ligation step, measures only ‘relative’ proximities. A 3C interaction enriched between loci, therefore does not necessarily translates into a decrease in absolute spatial distance. Hence, we advocate caution when modeling chromosome conformations.

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

“…Over the past decade, the advent of chromosome capture and imaging methods [13] has given key insights into the 3D spatial organization of chromosomes, with the discovery of structural features such as topologically associated domains (TADs) [14][15][16][17], phase-separated nuclear condensates [18][19][20], and larger-scale compartments [21,22]. At larger length scales, across tens to hundreds of TADs, chromosome organization has been suggested to be highly compacted in a crumpled chain configuration (often referred to as crumpled or fractal globule) [22][23][24][25][26], a long-lived polymer state with fractal dimension three.…”

“…Over the past decade, the advent of chromosome capture and imaging methods [13] has given key insights into the 3D spatial organization of chromosomes, with the discovery of structural features such as topologically associating domains (TADs) [14][15][16][17], phase-separated nuclear condensates [18][19][20], and larger-scale compartments [21,22]. These organizing structures have key implications for transcriptional regulation [23].…”

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

“…Over the past decade, the advent of chromosome capture and imaging methods (13) has given key insights into the 3D spatial organization of chromosomes, with the discovery of structural features such as topologically associating domains (TADs) (14)(15)(16)(17), phaseseparated nuclear condensates (18)(19)(20), and larger-scale compartments (21,22). These or-ganizing structures have key implications for transcriptional regulation (23), but they are not static.…”