Comprehensive Hub for Alternative Regulatory Mapping (CHARM)

CHARM is an R Shiny web application for exploring the regulatory roles of RNA-binding proteins (RBPs) in gene expression, splicing regulation, and direct RNA binding.

The app integrates data from the ENCODE project (Luo et al., 2020), including eCLIP and RNA-seq datasets from RBP knockdown/knockout experiments in HEPG2 (liver cancer) and K562 (leukemia) cell lines.

CHARM serves as both a repository of this curated data and a discovery tool:

• Explore how 168 RBPs from ENCODE affect expression, splicing, and binding.
• Infer potential networks between these regulatory layers, revealing new pathways and mechanisms.
• Upload your own expression, splicing, or binding datasets to identify RBPs most likely altered in your system.

CHARM integrates three main data types:

• Expression: Differential expression upon RBP knockdown/knockout, with pathway-level insights from Gene Set Enrichment Analysis.

• Splicing: Alternative splicing changes quantified with betAS (Ferreira et al., 2024), using VastDB nomenclature (Tapial et al., 2017).

• Binding: Altered RNA binding patterns of the silenced RBP and other RBPs, characterized with the eCLIPSE tool (see below).

eCLIPSE is a companion tool that processes eCLIP data from ENCODE to generate RNA splicing maps. It aligns binding profiles to the genomic coordinates of splicing events defined in VastDB (Tapial et al., 2017).

This allows assessment of how each RBP regulates splicing events both directly (through its own binding) and indirectly (through effects on other RBPs).

eCLIPSE was used to generate the binding layer in CHARM. The tool is freely available and can also be applied to user-submitted eCLIP datasets to map splicing regulation of additional RBPs.