This repository contains the necessary data and scripts to reproduce the main figures of the manuscript.
The data needed to execute the preprocessing step is available at GEO under the accession GSE235947. In the corresponding preprocessing folder are listed and organized by omics the different scripts used to process our data from the trimming and mapping of FASTQ files to the call of significant biological signals (peaks, interactions...).
Nonetheless, the data folder allows to skip the preprocessing step as it contains the supplementary data tables and essential processed data needed to generate most figures presented the manuscript.
The figures folder contains script and folder to (re)generate stats and figures from the manuscript.
Specific dependencies are listed in each preprocessing section:
| Datatype | Short description |
|---|---|
| ChIP-Seq | Trimming, mapping, peak-calling, and differential analysis |
| Hi-C | Mapping, filtering, normalization, compartment- and TAD-calling |
| PCHi-C | Mapping and significant interactions calling |
| RNA-seq | Trimming, mapping and differential expression analysis |
and in the figures section:
| Figure 1 | A/B compartment changes along p53 activation. |
| Figure 2 | TAD dynamics along p53 activation. |
| Figure 3 | p53 binding to chromatin leads to direct changes in 3D genome topology. |
| Figure 4 | Promoter interactions shift during p53 activation. |
| Figure 5 | Identification of new p53 distal target genes through enhancer-promoter interactions. |
| Figure 6 | p53 drives the formation of promoter-enhancer interactions or uses pre-established ones to control gene transcription over distance. |
| Figure 7 | Cohesin depletion impedes p53-mediates transcriptional response. |
| Supplementary | Scripts related to supplementary panels. |
Serra, F., Nieto-Aliseda, A., Fanlo-Escudero, L. et al.
p53 rapidly restructures 3D chromatin organization to trigger a transcriptional response.
Nat Commun 15, 2821 (2024). doi:10.1038/s41467-024-46666-1