Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

Keizer, Veer I. P.; Grosse‐Holz, Simon; Woringer, Maxime; Zambon, Laura; Aïzel, Koceila; Bongaerts, Maud; Delille, Fanny; Kolar-Znika, Lorena; Scolari, Vittore F.; Hoffmann, Sebastian; Banigan, Edward J.; Mirny, Leonid A.; Dahan, Maxime; Fachinetti, Daniele; Coulon, Antoine

doi:10.1126/science.abi9810

Cited by 60 publications

(60 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in the picture of higher-order catalysis, the multi-way contacts come and go quickly, rearranging chromatin constantly. Such nonequilibrium activities allow chromatin to stay in a highly dynamic, liquid-like state, which is consistent with recent experimental observations 58 .…”

Section: Discussionsupporting

confidence: 91%

Phase separation as higher-order catalyst

Huang

Quan

Qin

2022

Preprint

View full text Add to dashboard Cite

The long-distance communication between multiple cis-regulatory elements (CREs), the self-limiting size and lifetime of regulatory condensates, are two puzzling phenomena in biology. To reconcile these puzzles, we introduce the concept of higher-order catalysis into chromatin-mediated reactions. Essentially, multi-way contact between the CREs defines a transition state that is required for the downstream cascade of chemical reactions. The entropic penalty of chromatin reorganization sets a high activation barrier to enter this transition state. Phase separation of trans-acting agents induced by the CREs reduces this barrier and stabilizes the transition state via forming a regulatory condensate. The downstream reaction then pays back energy to dissolve the condensate and resets the agents to a metastable single-phase state. Accelerating the reactions without consuming agents or changing their state, the cycled phase transitions construct a higher-order catalyst or super-enzyme that is beyond the form of a single molecule. We discuss how chromatin employs such super-enzymes to catalyze higher-order reactions mediated by itself.

show abstract

Section: Discussionsupporting

confidence: 91%

Phase separation as higher-order catalyst

Huang

Quan

Qin

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Moreover, our previous work has shown that removal of cytoskeletal forces does not cause relaxation of the nucleus to a spherical morphology, implying nuclear deformations in spread cells are irreversible [38]. Consistent with these findings, elastic forces in the nuclear interior have been found to rapidly dissipate on the time scale of seconds and that the nuclear contents behave as a viscous fluid on this time scale [45; 46]. From literature estimates of the area dilation modulus (∼390 nN/µm; [47]), the nuclear bulk modulus (∼5 nN/µm 2 [48]), and the cortical tension (∼0.5 nN/µm; [42]), the areal extension of the lamina and changes in volume due to compression in the flattened nucleus during spreading are expected to be less than 1%, based on pressures and tensions calculated from Eq.…”

Section: Discussionmentioning

confidence: 57%

A predictive unifying explanation for nuclear shapes based on a simple geometric principle

Dickinson

Lele

2022

Preprint

View full text Add to dashboard Cite

Nuclei have characteristic shapes dependent on cell type, which are critical for proper cell function, and nuclei lose their distinct shapes in multiple diseases including cancer, laminopathies, and progeria. Nuclear shapes result from deformations of the sub-nuclear components-nuclear lamina and chromatin. How these structures respond to cytoskeletal forces to form the nuclear shape remains unresolved. Although the mechanisms regulating nuclear shape in human tissues are not fully understood, it is known that different nuclear shapes arise from cumulative nuclear deformations post-mitosis, ranging from the rounded morphologies that develop immediately after mitosis to the various nuclear shapes that roughly correspond to cell shape (e.g., elongated nuclei in elongated cells, flat nuclei in flat cells). Here we establish a simple geometric principle of nuclear shaping: the excess surface area of the nucleus (relative to that of a sphere of the same volume) permits a wide range highly deformed nuclear shapes under the constraints of constant surface area and constant volume, and, when the lamina is smooth (tensed), the nuclear shape can be predicted entirely from these geometric constraints alone for a given cell shape. This principle explains why flattened nuclear shapes in fully spread cells are insensitive to the magnitude of the cytoskeletal forces. We demonstrate this principle by predicting limiting nuclear shapes (i.e. with smooth lamina) in various cell geometries, including isolated on a flat surface, on patterned rectangles and lines, within a monolayer, isolated in a well, or when the nucleus is impinging against a slender obstacle. We also show that the lamina surface tension and nuclear pressure can be estimated from the predicted cell and nuclear shapes when the cell cortical tension is known, and the predictions are consistent with measured forces. These results show that excess lamina surface area is the key determinant of nuclear shapes, and that nuclear shapes can be determined purely by the geometric constraints of constant (but excess) nuclear surface area and nuclear volume, not by the magnitude of the cytoskeletal forces involved.

show abstract

“…Our model could thus be applicable to chromatin, which shows a much larger cell-to-cell variability than stable protein structures (88, 89). In this context, we zoom out to large length scales where chromatin behaves like a Rouse polymer (90–92), and molecular drivers of active processes [Fig. 1] produce effective athermal excitations.…”

Section: Discussionmentioning

confidence: 99%

Polymer folding through active processes recreates features of genome organization

Goychuk

Kannan

Chakraborty

et al. 2022

Preprint

View full text Add to dashboard Cite

From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate (ATP). Moreover, chromatin motion varies with genomic coordinate, pointing towards a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers non-equilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward disentangling active and passive mechanisms of folding, we discuss a data-driven approach to discern if and how active processes affect genome organization.

show abstract

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

Cited by 60 publications

References 49 publications

Phase separation as higher-order catalyst

Phase separation as higher-order catalyst

A predictive unifying explanation for nuclear shapes based on a simple geometric principle

Polymer folding through active processes recreates features of genome organization

Contact Info

Product

Resources

About