2023
1
Polymer folding through active processes recreates features of genome organization
Andriy Goychuk*; Deepti Kannan*; Arup K. Chakraborty†; Mehran Kardar†
* Equal contribution † Corresponding author
In: Proceedings of the National Academy of Sciences, vol. 120, no. 20, pp. e2221726120, 2023, ISSN: 0027-8424, 1091-6490.
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Active ProcessesAnalytical TheoryGenome OrganizationPolymer MechanicsSimulationStochastic Processes
@article{goychuk_polymer_2023,
title = {Polymer folding through active processes recreates features of genome organization},
author = {Andriy Goychuk and Deepti Kannan and Arup K. Chakraborty and Mehran Kardar},
doi = {10.1073/pnas.2221726120},
issn = {0027-8424, 1091-6490},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {120},
number = {20},
pages = {e2221726120},
abstract = {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. Moreover, chromatin motion varies with genomic coordinate, pointing toward 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 nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.},
keywords = {Active Processes, Analytical Theory, Genome Organization, Polymer Mechanics, Simulation, Stochastic Processes},
pubstate = {published},
tppubtype = {article}
}
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. Moreover, chromatin motion varies with genomic coordinate, pointing toward 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 nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.