Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling

Abstract

Layers of genome organization are becoming increasingly better characterized, but less is known about how these structures respond to perturbation or shape changes. Low-salt swelling of isolated chromatin fibers or nuclei has been used for decades to investigate the structural properties of chromatin. But, visible changes in chromatin appearance have not been linked to known building blocks of genome structure or features along the genome sequence. We combine low-salt swelling of isolated nuclei with genome-wide chromosome conformation capture (Hi-C) and imaging approaches to probe the effects of chromatin extension genome-wide. Photoconverted patterns on nuclei during expansion and contraction indicate that global genome structure is preserved after dramatic nuclear volume swelling, suggesting a highly elastic chromosome topology. Hi-C experiments before, during, and after nuclear swelling show changes in average contact probabilities at short length scales, reflecting the extension of the local chromatin fiber. But, surprisingly, during this large increase in nuclear volume, there is a striking maintenance of loops, TADs, active and inactive compartments, and chromosome territories. Subtle differences after expansion are observed, suggesting that the local chromatin state, protein interactions, and location in the nucleus can affect how strongly a given structure is maintained under stress. From these observations, we propose that genome topology is robust to extension of the chromatin fiber and isotropic shape change, and that this elasticity may be beneficial in physiological circumstances of changes in nuclear size and volume.

Constricted migration is associated with stable 3D genome structure differences in cancer cells

“…Notably, this phenomenon was also previously observed with constricted migration in neutrophils (Jacobson et al, 2018). Furthermore, we observe this loss of B-B interaction strength in the purely physical perturbation of low-salt expansion in isolated nuclei (preprint: Liu & Dekker, 2021;Sanders et al, 2022). Conversely, in lung cancer cells, the loss of SETDB1 methyltransferase was shown to lead to an increase in B-B compartment interactions and increased segregation of compartments overall, while also stiffening the nucleus and decreasing cell migration (preprint: Zakharova et al, 2021).…”

“…To image nuclei in cells migrating through collagen, A375 cells were transfected with Dendra2‐histone H4. The creation of this plasmid was described previously (Sanders et al , 2022) and is available upon request.…”

Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

“…But they show that increased nucleus size leads to compartment strength weakening, similar to what we and others 23 observe in neuronal Hi-C. However, nuclear swelling does not affect the genomic positioning of compartments 28 , while compartments in neurons are largely different from non-neurons. Therefore, we propose that the observed compartmentalization differences in NeuN(+) cells, such as lower strength, altered positioning and lower correlation with histone marks, may be attributed to the more active loop extrusion in neurons counteracting compartmentalization, similar to what Schwarzer et al observe upon NIPBL knockout 34 .…”

3D genome organization

“…While slight changes were observed in short distance interactions, higher order structures such as loops, TADs compartments, and chromosome territories maintained their global organization. The authors conclude that this robustness of genome topology offers resilience against physiological changes that take place in nuclear morphology 10 .…”