Abstract
Drosophila transcription factor (TF) function is phenotypically nonspecific. Phenotypic nonspecificity is defined as one phenotype being induced or rescued by multiple TFs. To explain this unexpected result, a hypothetical world of limited specificity is explored where all TFs have unique random distributions along the genome due to low information content of DNA sequence recognition and somewhat promiscuous cooperative interactions with other TFs. Transcription is an emergent property of these two conditions. From this model, explicit predictions are made. First, many more cases of TF nonspecificity are expected when examined. Second, the genetic analysis of regulatory sequences should uncover cis-element bypass and, third, genetic analysis of TF function should generally uncover differential pleiotropy. In addition, limited specificity provides evolutionary opportunity and explains the inefficiency of expression analysis in identifying genes required for biological processes.
Highlights
The Specific World of transcription factor (TF)In Biology gene expression is a major concern and is focused on how a single genotype exhibits multiple phenotypes
One major mechanism of regulation is the control of the initiation of transcription, which is mediated by TFs
Eukaryotic TFs are generally thought to be composed of multiple functional domains: a DNA binding domain that recognizes a specific DNA sequence, a transcriptional regulation domain, and allosteric regulation domain(s) [2, 3]
Summary
In Biology gene expression is a major concern and is focused on how a single genotype exhibits multiple phenotypes. The DNA binding domain of TAL TFs is a series of repeats of 34 amino acids with each repeat recognizing a specific base (Figure 1(b)) This one to one repeat to base recognition allows the engineering of proteins that can recognize any DNA sequence in a genome [6]. In order to have high specificity for binding site recognition and a dynamic system, weak interactions between TFs in prokaryotes and eukaryotes occur and are a mechanism of cooperativity [20]. TF activity is regulated after the formation of the DNA protein complex An example of this is the yeast Gal4p transcription factor being bound to the cisregulatory sequences in the presence or absence of galactose [28]. In describing this model, I do not incorporate or discuss much from the specific world; I do acknowledge that there are specific mechanisms regulating TF function, which would have to be incorporated into a more complete model for the regulation of the initiation of transcription of all genes in the genome
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