The WNT/β-catenin pathway regulates tissue development and homeostasis, and its dysregulation drives many human diseases, including colorectal cancer. Central to this pathway is the β-catenin Destruction Complex (BDC), which controls β-catenin stability through a network of protein–protein interactions.To better understand how specific sequence elements within BDC components regulate signaling in vivo, we conducted CRISPR base editing screens targeting multiple BDC genes. These screens enable systematic mutational analysis at endogenous loci, revealing activating and regulatory mutations that refine our understanding of WNT/β-catenin pathway control.
The R script in this repository implements the computational pipeline used to process and analyze base editing screen data.
- Processing raw next-generation sequencing (NGS) data
- Quantification of guide RNA read counts
- Statistical modeling to identify variants affecting WNT signaling activity
- Annotation of predicted mutations based on genomic position and codon context
- Classification of mutations by functional impact:
- Synonymous
- Missense
- Nonsense
- Splice site
Together, these analyses provide a comprehensive view of how specific mutations affect β-catenin destruction complex function and WNT/β-catenin pathway regulation.
Operating System:
macOS Sequoia 15.6.1
R Version:
R 4.3.2
Hardware:
No specialized hardware required. Runs on standard personal computers or servers.
- dplyr (1.1.4)
- tibble (3.2.1)
- janitor (2.2.1)
- readxl (1.4.5)
- openxlsx (4.2.8)
- ggplot2 (3.5.2)
- ggpubr
- data.table (1.17.0)
- stringr (1.5.1)
- plotly (4.10.4)
- Biostrings (2.70.3)
- GenomicAlignments (1.38.2)
- GenomicFeatures
- Rsamtools (2.18.0)
- QuasR (1.42.1)
- ShortRead (1.60.0)
- Rsubread (2.16.1)
- R version 4.3.2
- Internet connection for package installation
- RStudio (recommended)
install.packages(c(
"dplyr",
"tibble",
"janitor",
"readxl",
"openxlsx",
"ggplot2",
"ggpubr",
"data.table",
"stringr",
"plotly"
))