HTHmotif

HTHmotif identifies transcription factor binding sites in prokaryotic genomes by combining specificity-determining residues from DNA–protein crystal structures with sequence-based motif discovery to delineate regulatory motifs.

Key Features:

• Sequence-Based Approach: Uses nucleotide sequence data, including inputs derived from next-generation sequencing, to predict transcription factor binding sites.
• Specificity Determination: Identifies specificity-determining (critical) residues from crystal structures of DNA–protein complexes.
• Classification into Specificity Classes: Groups transcription factors that share critical residues into specificity classes.
• Defining Putative Binding Regions: Defines putative binding regions by considering autoregulatory promoters and the immediately upstream and downstream operons.
• Motif Discovery with MEME: Applies the Multiple EM for Motif Elicitation (MEME) algorithm to discover motifs within each specificity class.

Scientific Applications:

• Prokaryotic regulatory site identification: Enables identification and characterization of transcription factor binding sites to study transcriptional regulation in microbial genomes.
• Validation on TF families: Validated on LacI and TetR families using annotated sites from RegulonDB, achieving sensitivities of 86% for LacI and 80% for TetR.

Methodology:

Identification of critical residues from crystallographic DNA–protein complexes; grouping transcription factors into specificity classes based on shared critical residues; defining putative binding regions by analyzing autoregulatory promoters and adjacent operons; and motif prediction using MEME on class-specific sequence sets.