The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Area of Science:

• Genomics
• Computational Biology
• Structural Biology

Background:

• Understanding the three-dimensional (3D) genome organization is crucial for deciphering gene regulation and function.
• Existing tools often lack integrated simulation and analysis capabilities for chromosomal dynamics.

Purpose of the Study:

• To introduce the Nucleome Data Bank (NDB), a comprehensive web-based platform for simulating and analyzing 3D genome organization.
• To provide a resource for predicting chromosomal structural dynamics and generating sub-compartment annotations.

Main Methods:

• Physics-based simulation of chromosomal structural dynamics using the MEGABASE + MiChroM computational pipeline.
• Utilizing epigenetic information from the Encode database as input.
• Developing custom web-based tools for data analysis and visualization.

Main Results:

• The NDB accurately predicts Hi-C and fluorescence in situ hybridization (FISH) data, as well as in vivo chromosomal dynamics.
• Chromosomal sub-compartment annotations can be generated directly from epigenetic data without proximity ligation data.
• The platform hosts and provides access to experimental and computational structural genomics data.

Conclusions:

• The NDB serves as a valuable, freely accessible resource for biologists, biophysicists, and genome scientists.
• It facilitates the study of spatial distributions of genetic and epigenetic features by overlaying 1D data onto 3D chromosome structures.
• The platform enhances the understanding of genome organization and dynamics through integrated simulation and analysis tools.