Cell-specific regulation of gene expression using splicing-dependent frameshifting

Jonathan P. Ling, Alexei M. Bygrave, Clayton P. Santiago, Rogger P. Carmen-Orozco, Vickie T. Trinh, Minzhong Yu, Yini Li, Ying Liu, Kyra D. Bowden, Leighton H. Duncan, Jeong Han, Kamil Taneja, Rochinelle Dongmo, Travis A. Babola, Patrick Parker, Lizhi Jiang, Patrick J. Leavey, Jennifer J. Smith, Rachel Vistein, Megan Y. GimmenBenjamin Dubner, Eric Helmenstine, Patric Teodorescu, Theodoros Karantanos, Gabriel Ghiaur, Patrick O. Kanold, Dwight Bergles, Ben Langmead, Shuying Sun, Kristina J. Nielsen, Neal Peachey, Mandeep S. Singh, W. Brian Dalton, Fatemeh Rajaii, Richard L. Huganir, Seth Blackshaw

Research output: Contribution to journalArticlepeer-review

Abstract

Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length. This method, which we denote splicing-linked expression design (SLED), can be combined in a Boolean manner with existing techniques such as minipromoters and viral capsids. SLED can use strong constitutive promoters, without sacrificing precision, by decoupling the tradeoff between promoter strength and selectivity. AAV-packaged SLED vectors can selectively deliver fluorescent reporters and calcium indicators to various neuronal subtypes in vivo. We also demonstrate gene therapy utility by creating SLED vectors that can target PRPH2 and SF3B1 mutations. The flexibility of SLED technology enables creative avenues for basic and translational research.

Original languageEnglish (US)
Article number5773
JournalNature communications
Volume13
Issue number1
DOIs
StatePublished - Dec 2022

ASJC Scopus subject areas

  • General Physics and Astronomy
  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology

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