Fundamentally different strategies for transcriptional regulation are revealed by information-theoretical analysis of binding motifs

2008/12/19 by Mirny, Leonid A., Wunderlich, Zeba
#Biomolecules (q-bio.BM) #FOS: Biological sciences #Genomics (q-bio.GN) #Molecular Networks (q-bio.MN) #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM) #Subcellular Processes (q-bio.SC)

paper · doi:10.48550/arxiv.0812.3910

Abstract

To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10⁶-10⁹ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.

Related

• Transcription Factors and DNA Play Hide and Seek
• Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors
• Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs
• Systematic Target Function Annotation of Human Transcription Factors
• Finding regulatory sites from statistical analysis of nucleotide frequencies in the upstream region of eukaryotic genes