Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

When performing a computation, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to measure part function and identify the origins of failures. Here, we take “snapshots” of a large genetic circuit in different states. RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts are parameterized. The circuit behaves as designed; however, it is riddled with errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons and a failed gate. While serendipitously not impacting function, they reduce prediction accuracy and could lead to failures when used in other designs. Finally, the cellular power (RNAPs and ribosomes) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host. Overall design: Transcriptome and translatome of E.coli DH10b cells carrying a genetic circuit 0x41 at different induction states were generated