Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome.
Enhancer-driven genomic recording of transcriptional activity in multiplex is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities.
Overall there remains a need for a biologically conditional recording system that is at once quantitative, reproducible, temporally resolved, applicable to opaque systems and expansible to the concurrent measurement of thousands of biological signals. Here we describe a new framework, enhancer-driven genomic recording of transcriptional activity in multiplex , that aims to meet these criteria. We reasoned that a signal-responsive CRE positioned upstream of a minimal promoter ).
We observed minimal background recording in the absence of stimulus with signal-responsive ENGRAM recorders after 7 or 14 days. This background did not accumulate over time, consistent with the hypothesis that it primarily accumulates shortly after transfection, potentially due to ORI-driven, plasmid-mediated transcription. Plotted points correspond to three integration replicates.
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