Autocatalytic base editing for RNA-responsive translational control

Raphaël V Gayet; Katherine Ilia; Shiva Razavi; Nathaniel D Tippens; Makoto A Lalwani; Kehan Zhang; Jack X Chen; Jonathan C Chen; Jose Vargas-Asencio; James J Collins

doi:10.1038/s41467-023-36851-z

Autocatalytic base editing for RNA-responsive translational control

Nat Commun. 2023 Mar 11;14(1):1339. doi: 10.1038/s41467-023-36851-z.

Authors

Raphaël V Gayet^#^{1

2

3

4}, Katherine Ilia^#^{1

2}, Shiva Razavi^#^{1

2

4

5}, Nathaniel D Tippens^#^{1

2

4}, Makoto A Lalwani^{2

4}, Kehan Zhang^{2

4}, Jack X Chen^{1

2

4}, Jonathan C Chen^{1

2

5}, Jose Vargas-Asencio⁶, James J Collins^{7

8

9

10}

Affiliations

¹ Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
² Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA.
³ Microbiology Graduate Program, MIT, Cambridge, MA, USA.
⁴ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
⁵ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
⁷ Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA. jimjc@mit.edu.
⁸ Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. jimjc@mit.edu.
⁹ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. jimjc@mit.edu.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA, USA. jimjc@mit.edu.

^# Contributed equally.

Abstract

Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. We leverage DART VADAR to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Adenosine Deaminase / genetics
Animals
Gene Editing*
Gene Expression Regulation
Gene Regulatory Networks
Mammals / genetics
RNA / metabolism
RNA Editing*

Substances

RNA
Adenosine Deaminase

Abstract

Publication types

MeSH terms

Substances

Grants and funding