Additional Code for "PAX3-FOXO1 uses its activation domain to recruit CBP/P300 and shape RNA Pol2 cluster distribution"

Code provided by: Yaw Asante and Bhava Udhayakumar Questions and data request can be made to: yaw.asante@case.edu

This repo contains the code and tools used to create the figures and datasets in Asante, Benischke and Osman et al, 2023. Any omissions or uncertainty can be reported to yaw.asante@case.edu

Figures made, by Tool:

ChIP-seq Track Visualization with IGV

Source: External, https://software.broadinstitute.org/software/igv/

Figure 3F, Figure 3H, Figure 5M

Principal Component Analysis of RNA Seq

Source: In-House, in the RNA-seq pipeline in VisualizeRNAseq

Figure 3A

Ranked Gene Set Enrichment Analysis of Gene Expression

Source: In-House, GSEA ranklist on GitHub

Figure 3C, Figure 4H, Figure 5H

Analysis of HiChIP Data

Source: In-House, using peaks3d and aquatools.

Figures 6 (all panels), Figure 7 (all panels) and Figure 8 (all panels)

Tools used by Figure:

Figure 3

Panel A is a principal component analysis of RNA-seq derived TPM data, made with the RNA-seq pipeline in VisualizeRNASeq.

Panel B is a heatmap of expression made with the RNA-seq pipeline in VisualizeRNASeq.

Panel C is a rank plot of gene set enrichment made with the GSEA ranklist script in VisualizeRNASeq.

Panel D is a scatterplot made with GraphPad Prism.

Panel E is a pie chart made with GraphPad Prism.

Panel F and Panel H consist of ChIP-seq data tracks plotted with the Integrated Genome Viewer (IGV) .

Panel G is a bar plot made with GraphPad Prism.

Panel I pairs a profile plot and a heatmap and was made with plotBEDheat from the ChIPseqPipe repo (which employs deeptools).

Figure 4

Panel A contains a volcano plot made with GraphPad Prism.

Panel F pairs profile plots of read-pileup with corresponding heatmaps and were made with plotBEDheat from the ChIPseqPipe repo (which employs deeptools). Acetylation Levels and Chromatin Accessibility at p300 binding sites in RH4 cells.

Panel G is a principal component analysis of RNA-seq data, made with the RNA-seq pipeline in VisualizeRNASeq.

Panel H is a rank plot of gene set enrichment made with GSEA ranklist script in VisualizeRNASeq.

Figure 5

Panel H consists of rank plots of gene set enrichment made with GSEA ranklist script in VisualizeRNASeq.

Panel J is a bar plot made with GraphPad Prism.

Panel K is a line plot made with GraphPad Prism.

Panel M consists of ChIP-seq data tracks plotted with Integrated Genome Viewer (IGV) .

Panel N consists of profile plots of read-pileup with corresponding heatmaps and were made with plotBEDheat from the ChIPseqPipe repo (which employs deeptools).

Figure 6

Panel A (right) is output from the Genic Rank of Active Clustered Elements (GRACE) tool provided at peaks3d.

Panel B and Panel D were made in R with output from GRACE.

Panel E consists of boxplots made using RNA-seq and HiChIP data via code novel to the resumbission, able to be provided upon reasonable request. Changes in RH4 gene expression due to dCBP1, split across features associated with genes near and distal from p300 enhancers.

Panel F (left) are heatmaps and profile plots made with plotBEDheat from the ChIPseqPipe repo.

Panel F (right) is an Aggregate Peak Analysis plot made with peaks3d.

Panel G consists of moving average plots made with BedCovCompare from ChIPseqPipe repo.

Panel H consists of rankplots of HiChIP data using BedCovCompare (as previously described here), created with code that can be provided upon reasonable request. The impact of P300/CBP degraders on RH5 H3K27ac, segregated by enhancer and promoter regions (compared to impact on RH4 Pol2).

Figure 7

Panel A is a boxplot of HiChIP signal made with BedCovCompare from ChIPseqPipe.

Panel B was made using motif information from HOMER (version 4.9.1, http://homer.ucsd.edu/homer/index.html).

Panel C is a donut plot made with data from the HiChIP analysis obtained via peaks3d.

Panel D is a boxplot made using same HiChIP data from Panel C overlapped with p300 and P3F binding sites from ChIP-seq as described, with code which can be provided upon reasonable request. 3D genome looping at Pol2 sites strongly bound by P300 with and without P3F.

Panel E is a histogram made using the same HiChIP data from Panel C.

Figure 8

Panel B made using HiChIP data viewed via Juicebox, Integrated Genome Viewer (IGV) and analyzed with plotAPA and runpeaks3d (generation of loops) from peaks3d.

Panel D consists of Aggregate Peak Analysis (APA) plots of RH4 HiChIP data (with dTAG47 KO of P3F) made with plotAPA from peaks3d. APA plots made with the parameters described in the figure, but code can be provided upon reasonable request.