Author ORCID Identifier

Date of Award

Spring 3-1-2023

Document Type

Thesis (Ph.D.)

Department or Program

Molecular and Systems Biology

First Advisor

Aaron McKenna

Second Advisor

Yina Huang

Third Advisor

Xiaofeng Wang


Current approaches to study cellular transcriptional states offer only a single frame in the life of a cell, often in a destructive fashion. This means that our state snapshot neither has the context of the past, nor the ability to be traced into the future. To overcome this, we present a technology that can permanently encode gene expression for later recovery. Our technology uses transcriptional responses to guide CRISPR/AsCas12a to ‘write’ information into the cell’s own genome, creating a permanent and heritable record of this response. By placing a set of AsCas12a guides under the control of a Wnt-responsive TCF/LEF reporter we show that we can faithfully record Wnt responses. Whereas by placing guides within endogenous genes we can record their transcription. We go on to show that our system can be multiplexed with constitutive lineage recording, with implications for creating future annotated lineage trees that are able to describe the decision points in a cell’s past. We think this method will be widely applicable in the study of development, regenerative biology, and cancer evolution.

Original Citation

Emiliani, Francesco E., Ian Hsu, and Aaron McKenna. "Multiplexed assembly and annotation of synthetic biology constructs using long-read Nanopore sequencing." ACS Synthetic Biology 11.7 (2022): 2238-2246.

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Biotechnology Commons