Transcription factor-target relationships complicated by knockout analysis

Knockout analysis is a common tool to reveal transcription factor (TF) functions. However, such a reverse genetic analysis based on observed phenotype changes in mutant cell may lead to a misunderstanding of TF wild-type functions. Here, a model was proposed, in which the knockout-observed TF-target regulatory relationships might only occur in mutant cell, and they do not reflect TF normal functions in wild-type cell. Actually, the knockout of one TF might release another TF which is the protein-protein interaction partner of the deleted TF. The free TF could bind its new target genes and cause their significant expression changes. These seemingly TF knockout affected genes are thus not directly regulated by the deleted TF, but are gain-of-regulated genes of the latter TF in mutant cell. Based on this model, multiple sources of genome-wide data were used to identify 20 such TF pairs, and one pair was validated using other independent data. TF wild-type regulatory genes are not associated with their gain-of-regulated genes. My findings revealed TF-target relationships complicated by TF knockout analysis.