RhizoBindingSites

RhizoBindingSites provides conserved transcription factor binding motif predictions and regulatory network data to elucidate transcriptional regulation in nitrogen-fixing bacteria of the order Rhizobiales and their symbioses with leguminous plants.

Key Features:

• Motif-Gene Association: Conserved sequences associated with genes are reported across nine symbiotic Rhizobiales species to link motifs to putative regulatory targets.
• Dyad Analysis Algorithm: A dyad analysis algorithm deduces motifs in upstream regulatory regions of orthologous genes and accepts motifs also present in the gene seed promoter at a statistical threshold of p-value 1e-4.
• Genomic Scan Analysis: Genomic scans of upstream sequences identify predicted binding sites and categorize matches by homology levels (low, medium, high) between motif matrices and regulatory sequences.
• Comprehensive Data Representation: The resource catalogs detailed motif information and conservation analysis across Rhizobiales, provides 19,613 motif matrices, and includes motif logos.
• Regulatory Networks: Regulatory networks are assembled from theoretical predictions and experimental data to represent putative transcriptional interactions.

Scientific Applications:

• Transcriptional regulation mapping: Identification and conservation analysis of regulatory motifs to elucidate gene regulatory mechanisms in Rhizobiales.
• Symbiotic nitrogen fixation research: Investigation of genetic controls underlying symbioses between Rhizobiales and leguminous plants relevant to nitrogen fixation.
• Regulatory network inference and validation: Construction and interpretation of regulatory networks combining predicted motifs with experimental data for hypothesis generation and testing.

Methodology:

RhizoBindingSites applies a dyad analysis algorithm to infer motifs in upstream regulatory regions of orthologous genes, retains motifs present in the gene seed promoter at p-value ≤ 1e-4, conducts genomic scans of upstream sequences to predict binding sites, and classifies matches by homology levels (low, medium, high) between motif matrices and regulatory sequences.