A physical model of transcription factor dynamics through human chromosomes: data and code

This record contains the data and analysis code supporting the manuscript:“3D genome architecture regulates the traffic of transcription factors throughout human chromosomes.”

The repository includes curated, post-aggregation outputs from an in-silico model to simulate the dynamics of a specific transcription factor protein through 3D architecture of a specific human chromosme. We have also included analysis scripts and documentation required to reproduce the reported results and figures. The repository contains sample trajectory files containing list of x, y, z positions of all TF molecules from all timepoints of a demo simulation, and all the pooled datasets containing TF residence times on binding sites, all the hopping spatial and genomic distance of the TFs from all our simulations.

A demo simulation and analysis code are provided, including python classes that are used to create the polymer model of chromosomes. The binding sites locations, extracted from ChIPseq data of the TF on the given chromosome, are overlayed on the polymer. All the ChIPseq analysis codes and resultant location data of binding sites are also included. 

Raw molecular dynamics trajectories and intermediate per-trajectory analysis files (multiple terabytes) are not included due to their size. The repository instead provides final processed datasets and matlab scripts sufficient to reproduce all figures.

Input chromatin structures were generated using a previously published ensembe (Cheng et al eLife 9, e60312 (2020)). A small subset of representative structures is included for inspection. The full ensemble is not redistributed here and is available at: https://ndb.rice.edu. 

Processed datasets are also available as a downloadable archive; see repository README for directory structure and file descriptions.