The transcriptomics of phenotypic nonspecificity in <i>Drosophila melanogaster</i>

Transcription factor (TF) function is redundant: TF phenotypes are frequently rescued by TFs not resident to the TF locus, a phenomenon termed phenotypic nonspecificity. Phenotypic nonspecificity in Drosophila melanogaster is not dependent on the DNA binding specificity of the TFs and generally due to genetic complementation. Two TF phenotypes (doublesex [dsx] and apterous [ap]) are rescued by multiple TFs. The rescue by resident TFs (DSXF or AP) and the rescue and non-rescue by nonresident TFs of these 2 phenotypes were used to distinguish between 3 possible outcomes of the comparison of the TF-dependent mRNA accumulation in these 2 systems. First, the sets of TF-dependent mRNAs are independent and nonoverlapping; second, the sets of TF-dependent mRNAs are independent and overlapping; and third, the sets of TF-dependent mRNAs are constrained and have extensive overlap. The transcriptomes associated with rescue by resident TFs, and rescue and non-rescue by nonresident TFs, of the 2 TF phenotypes (dsx and ap) provided many examples of extensive overlap indicating regulation of constrained sets of genes. However, the strength of correlation of transcript accumulation observed between the resident and nonresident TFs was not a strong predictor for rescue of the phenotype by the nonresident TFs. The accumulation of a constrained set of mRNAs is discussed in relation to 3 potential explanations of phenotypic nonspecificity: limited specificity of TF function, the hypothetical assembly of TFs into wolfpacks, and chromatin accessibility.