This repository contains R scripts used to generate the main figures for the manuscript:

Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization

Gony Shanel, Tsung-Han S. Hsieh, Claudia Cattoglio, Hadar Amira Haham, Hsin-Jung Chou, Jack Z. Li, Ron Shamir, Xavier Darzacq, and Ran Elkon.

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Overview

This repository provides original R scripts developed for specific analyses in Figures 2–6 of the manuscript.
The scripts are organized by figure and cover tasks such as A/B compartment assignment, TAD boundary analysis, chromatin loop quantification, enhancer-promoter loop identification, and integration of gene expression and chromatin architecture in response to p53 activation.

Each script operates on example input files provided in the data/ folder and can be run independently.
Supporting functions are collected in _functions.r and _functions_hic.r.

Note: This repository contains only the custom R scripts created for the study.
Operation preformed with external command-line tools (deeptools, FAN-C, ect.) are not included here.

Scripts are organized into folders by figure number:

• Figure_2/: A/B compartment analysis
• Figure_3/: TAD detection and characterization
• Figure_4/: Chromatin loop detection and quantification
• Figure_5/: Identification of functional enhancer-promoter loops
• Figure_6/: Analysis of p53-induced transcriptional responses

Supporting R functions used across analyses are provided in:

• _functions.r
• _functions_hic.r

Small example data files needed to run the scripts are provided in the data/ folder.

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Requirements

R packages:

• data.table
• ggplot2
• bedtoolsr
• parallel
• DESeq2

External tools:

• bedtools

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Usage

1. Example input files are placed in the data/ folder.
2. Scripts can be run independently within each Figure_X/ folder.
3. Paths to data files must be manually set at the beginning of each script if needed.
4. Supporting functions are sourced automatically from _functions.r and _functions_hic.r.

⚠️ These scripts are designed for reproducibility and demonstration purposes using small example files, not for full-scale reprocessing of raw datasets.

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Citation

If you use these scripts, please cite:

Gony Shanel et al.,
"Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization." (2025)

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