The transcriptomics of phenotypic nonspecificity in Drosophila melanogaster
Transcription factor (TF) function is redundant as TF phenotypes are frequently rescued by TFs not resident to the TF locus, a phenomenon termed phenotypic nonspecificity.  Phenotypic nonspecificity 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, and the rescue and non-rescue by resident and non-resident TFs of these two phenotypes were used to distinguish between three possible outcomes of the comparison of the TF dependent mRNA accumulation in these two systems: first the sets of TF dependent mRNAs are independent and non-overlapping; 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 and non-rescue by resident and non-resident TFs of the two 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 non-resident TFs was not a strong predictor of the ability of the TFs to rescue the phenotype.  The regulation of a constrained set of genes supports the hypothetical assembly of TFs into wolfpacks, and not the hypothetical limited specificity of TF function, as a potential explanation of phenotypic nonspecificity. Overall design: Transcription factors DSXF, BAB1, ANTP, EY, ODD, FOXO, and SQZ were expressed in Drosophila melanogaster pupal abomens lacking expression of DSX using the UAS-GAL4 expression system. RNA sequencing of abdomens, including those from wildtype (OreR) and mutant (w; dsx1/dsxGAL4) lines, was performed to determine differential gene expression. Transcription factors AP, CAD, MYB, TTK, and SISA were expressed in Drosophila melanogaster wing imaginal discs lacking expression of AP using the UAS-GAL4 expression system. RNA sequencing of wing discs, including those from wildtype (y w) and mutant (y w; apnull/apGAL4) lines, was performed to determine differential gene expression.