MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation...

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• Transcription factors (TFs) regulate gene expression through DNA binding.
• DNA methylation and cofactor interactions influence TF binding and target gene specificity.
• Existing databases often lack integrated epigenetic and cofactor information for TF-binding motifs.

Purpose of the Study:

• To enhance the MethMotif database with expanded TF-binding profiles, DNA methylation patterns, and cofactor information.
• To provide context-specific TF functions by integrating epigenetic data.
• To broaden the database's applicability to multiple species.

Main Methods:

• Expanded the database to include over 700 position weight matrices (PWMs) with DNA methylation profiles.
• Segregated TF-binding motifs based on cofactor and DNA methylation status.
• Integrated precomputed Gene Ontology (GO) annotations for human TFs and TF-co-TF complexes.
• Added data for Mus musculus and Arabidopsis thaliana.

Main Results:

• The updated MethMotif database contains over 700 TF-binding motifs with associated DNA methylation profiles.
• TF-binding motifs are now categorized by cofactor and methylation status, enabling context-specific analysis.
• Precomputed GO annotations facilitate the study of TF functions in relation to cofactors and methylation.
• The database now supports human, mouse, and Arabidopsis.

Conclusions:

• MethMotif is the first database to integrate context-specific PWMs with epigenetic information for TF-binding motifs.
• The enhanced database provides deeper insights into context-specific TF functions and regulatory mechanisms.
• The expanded species coverage increases the utility for a wider research community.