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Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

ABSTRACT: Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

PROVIDER: PRJNA640006 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12513910.fastq.gz	Fastqsanger.gz
	SRR12513911.fastq.gz	Fastqsanger.gz
	SRR12513912.fastq.gz	Fastqsanger.gz
	SRR12513913.fastq.gz	Fastqsanger.gz
	SRR12513914.fastq.gz	Fastqsanger.gz

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Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

Project description: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.

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Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage.

Project description:To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit 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 (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) 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.

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