Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci

Area of Science:

• Cell Biology
• Genetics
• Biophysics

Background:

• Tracking chromatin configuration in live cells is crucial for understanding genome dynamics.
• Current methods using distinguishable labels limit the number of observable loci.
• Using identical labels requires a framework for identifying locus identity.

Purpose of the Study:

• To theoretically analyze how single-particle tracking of identically-labeled loci can determine locus identity.
• To investigate the feasibility of inferring temporal dynamics of chromatin configuration in living cells.

Main Methods:

• Simulations of Rouse-model polymers to analyze locus identity determination.
• Theoretical analysis of single-particle tracking with identical and alternating labels.
• Modeling of dynamic loops in a modified Rouse-model polymer.

Main Results:

• Probability of correct locus assignment converges exponentially with increasing observed configurations.
• High-fidelity identification is achievable with approximately 8 independent configurations for identically-labeled loci.
• Alternating labels offer faster convergence, requiring fewer configurations for identification.
• Dynamic loop models also show exponential convergence, slightly slower than classical Rouse models.

Conclusions:

• Single-particle tracking of identically- or alternately-labeled loci is a feasible method for inferring chromatin polymer dynamics.
• This approach allows for the temporal study of coarse-grained chromatin configuration in individual live cells.
• The findings provide a framework for advanced live-cell chromatin research.