Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Area of Science:

• Molecular Biology
• Genetics
• Biophysics

Background:

• Chromosome spatial organization is crucial for cellular function.
• Loop-extrusion and phase-separation are proposed mechanisms.
• Their relative contributions and interplay remain unclear.

Purpose of the Study:

• Compare loop-extrusion and phase-separation models.
• Investigate their co-existence at the single-molecule level.
• Explain chromatin architecture data.

Main Methods:

• Polymer physics modeling.
• Comparison against multiplexed FISH data from human cell lines (IMR90, HCT116).
• Analysis of bulk Hi-C and microscopy data.

Main Results:

• All models recapitulated bulk Hi-C and average microscopy data.
• Phase-separation models best captured single-molecule conformations and globule segregation.
• Cell-to-cell variability explained by epigenetic heterogeneity and folding degeneracy.
• Combined loop-extrusion and phase-separation model accurately described data, especially higher-order contacts.

Conclusions:

• Loop-extrusion and phase-separation can co-exist in shaping chromatin architecture.
• Phase-separation models provide superior explanation for single-molecule chromatin conformations.
• Combined models offer a comprehensive understanding of genome organization.