VIDEO—Visual Integration of Drosophila Enhancer Organization: a tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes

Dissecting gene regulation today relies on many genomic assays—including transcriptional output from RNA-seq, chromatin accessibility from ATAC-seq, and transcription factor (TF) binding from ChIP-seq. Whereas numerous tools exist for each modality and some integrate data across modalities, few allow researchers to interactively explore and visualize how TF binding motifs intersect with transcriptional activity and chromatin accessibility in a tissue-specific context. Here we introduce VIDEO (Visual Integration of Drosophila Enhancer Organization), a web-based analysis tool that enables visualization of conserved TF binding motifs within proximal enhancers of genes differentially expressed in specific tissues. Starting with gene lists derived from in situ hybridization, microarray, and/or scRNA-seq studies of WT or mutant samples, one can identify the TFs expressed in each tissue and learn if and where the consensus binding motifs for those TFs are found within the proximal enhancers of a custom gene set. This pipeline also allows for coincident visualization of active chromatin, as determined from ATAC-seq data, and for the visualization of DNA binding data from ChIP-seq datasets for specific TFs. To demonstrate its utility, we apply VIDEO to the well-characterized regulatory system of CrebA and the secretory pathway in the Drosophila melanogaster salivary gland. We also explore a lesser-known system in the embryonic hindgut to show how utilization of this tool can serve to generate hypotheses regarding regulatory interactions.