Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive...

This article presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, the TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine-zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocols are organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) visualization of methylation-specific TF motifs using TFregulomeR, and (3) characterization of leucine-zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS-methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behavior, and visualize the impact of DNA methylation on binding specificity. The protocols also provide step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through these protocols, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine-zipper TFs in a cell-type-specific context. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Exploration of transcription factor dimerization partners Support Protocol 1: Software installation Support Protocol 2: Docker installation Support Protocol 3: Verifying installation Basic Protocol 2: Visualization of alternative cofactors Basic Protocol 3: Characterization of bZIP partners/cofactors Basic Protocol 4: Context-independent and context-dependent analysis.