A Comprehensive Drosophila melanogaster Transcription Factor Interactome

Abstract

SUMMARY Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 protein-protein interactions (PPIs), more than doubling the number of currently known PPIs among Drosophila TFs. For quality assessment, we validated a subset of our interactions using MITOMI and bimolecular fluorescence complementation assays. We combined our interactome with prior PPI data to generate an integrated Drosophila TF-TF binary interaction network. Our analysis of ChIP-seq data, integrating PPI and gene expression information, uncovered different modes by which interacting TFs are recruited to DNA. We further demonstrate the utility of our Drosophila interactome in shedding light on human TF-TF interactions. This study reveals how TFs interact to bind regulatory elements in vivo and serves as a resource of Drosophila TF-TF binary PPIs for understanding tissue-specific gene regulation.

Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila

“…Second, an unpublished large-scale Y2H study found an interaction of BEAF with Sry-δ (http://flybi.hms.harvard.edu/results.php). Third, another large-scale Y2H study focused on transcription factors also found an interaction between BEAF and Sry-δ (SHOKRI et al 2019).…”

Eukaryotic transcription factors can track and control their target genes using DNA antennas

“…However, the affinity decrease is small relative to how much the binding site diverges from the consensus, most notably for CGTGTT in which only one consensus base is retained. To investigate this issue, we compared these results with the position weight matrix (PWM) for Engrailed obtained from bacterial one-hybrid assays 41 . The PWM recapitulates the consensus binding site ( Fig.…”

Three distinct mechanisms, Notch instructive, permissive, and independent, regulate the expression of two different pericardial genes to specify cardiac cell subtypes

“…Yet other such potential TF candidates necessary for producing wild-type levels of PC gene expression include PAR-domain protein 1 (Pdp1), and the Drosophila orthologs (CG17385, CG10321, and CG44002) of Zinc finger and BTB domain containing 14 (ZBTB14)—binding site motifs for these TFs were identified as positively weighted sequence features in machine learning-mediated discrimination of PC enhancers and subsequently validated empirically [ 57 ]. In this context, it is worth noting that, based on protein binding microarray data, putative binding sites for both Pnt and Pdp1 are present on both the Him and zfh1 PC enhancers ( S1 and S2 Files) [ 58 , 59 ].…”

“…Furthermore, in anterior corner cell (aCC) motor neurons, Eve transcriptionally activates the GATA TF Grain (Grn), and both Eve and Grn activate zfh1 expression [ 68 ]. Finally, based on protein binding microarray data, putative binding sites for both Eve and Grn are present on the zfh1 PC enhancer sequence ( S2 File ) [ 58 , 59 , 69 ]. However, since we were unsuccessful in completely eliminating Eve in Eve-PCs via RNAi knockdown as determined by immunohistochemical staining, we are unable to assess at present if Eve is indeed the TF driving the Eve-PC-specific Notch-independent zfh1 expression.…”