A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

Transcription factor (TF)-mediated gene regulation is critical to cellular development and function, an understanding of which has been promoted by the advent of genome-wide TF profiling methodologies. While traditional TF profiling methods in a variety of cell lines have made clear that TF binding is highly diverse amongst cell types, these techniques become challenging to interpret in vivo in complex tissues, such as the brain, which are composed of numerous, distinct cell types. Here we present FLEX calling cards, a virally-mediated system for genome-wide, longitudinal, cell type-specific recording of TF occupancy. We generated cell type-specific TF occupancy profiles in multiple cell types of the mouse brain and demonstrated the ability of this system to record and integrate historical TF binding events across time. FLEX calling cards is now ready for adaptation to any AAV-tractable animal model to investigate cell type-specific, TF-mediated gene regulation in vivo. C57bl6J injected with Cre-independent viruses. Cre lines and replicate numbers indicated in sample names. For SRT libraries, 10 "barcodes" per replicate were pooled and used in creation of .ccf files. Each barcode is listed as a separate sample, each with a unique .combination of .fastq file and 5' primer.