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

Jonathan P LingAlexei M BygraveClayton P SantiagoRogger P Carmen-OrozcoVickie T TrinhMinzhong YuYini LiYing LiuKyra D BowdenLeighton H DuncanJeong HanKamil TanejaRochinelle DongmoTravis A BabolaPatrick ParkerLizhi JiangPatrick J LeaveyJennifer J SmithRachel VisteinMegan Y GimmenBenjamin DubnerEric HelmenstinePatric TeodorescuTheodoros KarantanosGabriel GhiaurPatrick O KanoldDwight E BerglesBen LangmeadShuying SunKristina J NielsenNeal S PeacheyMandeep S SinghW Brian DaltonFatemeh RajaiiRichard L HuganirSeth Blackshaw
Published in: Nature communications (2022)
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.
Keyphrases
  • gene expression
  • single cell
  • gene therapy
  • cell therapy
  • dna methylation
  • rna seq
  • stem cells
  • sars cov
  • bone marrow
  • subarachnoid hemorrhage
  • long non coding rna
  • blood brain barrier
  • living cells