Quantifying Conformational Heterogeneity of 3D Genome Organization in Fruit Fly

Area of Science:

• Genomics
• Computational Biology
• Cell Biology

Background:

• The three-dimensional (3D) genome organization in eukaryotes exhibits significant cell-to-cell variability.
• Understanding this stochasticity is crucial for deciphering gene regulation and nuclear organization.

Purpose of the Study:

• To introduce a novel metric, Conformational Heterogeneity (C.H.), for quantifying 3D chromatin conformation variability across single cells.
• To analyze and compare cell-to-cell heterogeneity in fruit fly X chromosome structures using different modeling approaches.

Main Methods:

• Defined Conformational Heterogeneity (C.H.) as the standard deviation of per-cell average inter-loci distances for a given genomic separation.
• Applied C.H. metric to analyze chromatin models derived from bulk Hi-C, lamina-DamID, and single-cell Hi-C data.
• Developed an algorithm to compare C.H. across models of varying resolutions.

Main Results:

• Higher resolution chromatin models generally exhibit increased Conformational Heterogeneity.
• Model resolution impacts C.H. most significantly at genomic distances near the resolution limit, with diminishing effects beyond ~100 kb.
• A notable divergence in C.H. trends was observed for genomic separations beyond the TAD size, with single-cell Hi-C models showing an inverse trend compared to bulk Hi-C models.
• Depletion of nuclear lamins resulted in increased structural heterogeneity.

Conclusions:

• The choice of modeling approach, particularly the type of Hi-C data used, significantly influences the quantification of 3D chromatin heterogeneity.
• Integrating bulk Hi-C data into single-cell Hi-C based models may improve accuracy.
• Nuclear lamins play a role in maintaining chromatin structural stability, and their depletion can lead to greater variability in nuclear organization.