May 4, 2024
Programmable RNA sensing for cell monitoring and manipulation – Nature

Programmable RNA sensing for cell monitoring and manipulation – Nature

  • Hu, B. C. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574, 187–192 (2019).

    ADS 
    Article 

    Google Scholar
     

  • BRAIN Initiative Cell Census Network (BICCN). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature 598, 86–102 (2021).

    Article 

    Google Scholar
     

  • Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744–757 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Baylis, F., Darnovsky, M., Hasson, K. & Krahn, T. M. Human germ line and heritable genome editing: the global policy landscape. CRISPR J. 3, 365–377 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Feng, G. et al. Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research. Proc. Natl Acad. Sci. USA 117, 24022–24031 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Mich, J. K. et al. Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. Cell Rep. 34, 108754 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hartl, D., Krebs, A. R., Juttner, J., Roska, B. & Schubeler, D. Cis-regulatory landscapes of four cell types of the retina. Nucleic Acids Res. 45, 11607–11621 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Juttner, J. et al. Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans. Nat. Neurosci. 22, 1345–1356 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Nair, R. R., Blankvoort, S., Lagartos, M. J. & Kentros, C. Enhancer-driven gene expression (EDGE) enables the generation of viral vectors specific to neuronal subtypes. iScience 23, 100888 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Vormstein-Schneider, D. et al. Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans. Nat. Neurosci. 23, 1629–1636 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Graybuck, L. T. et al. Enhancer viruses for combinatorial cell-subclass-specific labeling. Neuron 109, 1449–1464.e13 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dimidschstein, J. et al. A viral strategy for targeting and manipulating interneurons across vertebrate species. Nat. Neurosci. 19, 1743–1749 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Eisenberg, E. & Levanon, E. Y. A-to-I RNA editing—immune protector and transcriptome diversifier. Nat. Rev. Genet. 19, 473–490 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Nishikura, K. A-to-I editing of coding and non-coding RNAs by ADARs. Nat. Rev. Mol. Cell Biol. 17, 83–96 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Abudayyeh, O. O. et al. A cytosine deaminase for programmable single-base RNA editing. Science 365, 382–386 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Katrekar, D. et al. In vivo RNA editing of point mutations via RNA-guided adenosine deaminases. Nat. Methods 16, 239–242 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Merkle, T. et al. Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat. Biotechnol. 37, 133–138 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Qu, L. et al. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat. Biotechnol. 37, 1059–1069 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Rauch, S. et al. Programmable RNA-guided RNA effector proteins built from human parts. Cell 178, 122–134.e12 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tan, M. H. et al. Dynamic landscape and regulation of RNA editing in mammals. Nature 550, 249–254 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Beier, H. & Grimm, M. Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res. 29, 4767–4782 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Segel, M. et al. Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery. Science 373, 882–889 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Yang, C. F. et al. Sexually dimorphic neurons in the ventromedial hypothalamus govern mating in both sexes and aggression in males. Cell 153, 896–909 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chung, H. et al. Human ADAR1 prevents endogenous RNA from triggering translational shutdown. Cell 172, 811–824.e14 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Lamers, M. M., van den Hoogen, B. G. & Haagmans, B. L. ADAR1: “editor-in-chief” of cytoplasmic innate immunity. Front. Immunol. 10, 1763 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat. Protoc. 11, 1650–1667 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Lo Giudice, C., Tangaro, M. A., Pesole, G. & Picardi, E. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat. Protoc. 15, 1098–1131 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Lodato, S. et al. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat. Neurosci. 17, 1046–1054 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Matho, K. S. et al. Genetic dissection of the glutamatergic neuron system in cerebral cortex. Nature 598, 182–187 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Hodge, R. D. et al. Conserved cell types with divergent features in human versus mouse cortex. Nature 573, 61–68 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Eugene, E. et al. An organotypic brain slice preparation from adult patients with temporal lobe epilepsy. J. Neurosci. Methods 235, 234–244 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Mitric, M. et al. Layer- and subregion-specific electrophysiological and morphological changes of the medial prefrontal cortex in a mouse model of neuropathic pain. Sci Rep. 9, 9479 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Huang, Z. J. & Paul, A. The diversity of GABAergic neurons and neural communication elements. Nat. Rev. Neurosci. 20, 563–572 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Yi, Z. et al. Engineered circular ADAR-recruiting RNAs increase the efficiency and fidelity of RNA editing in vitro and in vivo. Nat. Biotechnol. 40, 946–955 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Katrekar, D. et al. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Nat. Biotechnol. 40, 938–945 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Monian, P. et al. Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides. Nat. Biotechnol. 40, 1093–1102 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Hou, X., Zaks, T., Langer, R. & Dong, Y. Lipid nanoparticles for mRNA delivery. Nat. Rev. Mater. 6, 1078–1094 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bedbrook, C. N., Deverman, B. E. & Gradinaru, V. Viral strategies for targeting the central and peripheral nervous systems. Annu. Rev. Neurosci. 41, 323–348 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Joyce, J. A. & Fearon, D. T. T cell exclusion, immune privilege, and the tumor microenvironment. Science 348, 74–80 (2015).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Aquino-Jarquin, G. Novel engineered programmable systems for ADAR-mediated RNA editing. Mol. Ther. Nucleic Acids 19, 1065–1072 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cox, D. B., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229–236 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kaiser, T., Zhou, Y. & Feng, G. Animal models for neuropsychiatric disorders: prospects for circuit intervention. Curr. Opin. Neurobiol. 45, 59–65 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • He, M. et al. Strategies and tools for combinatorial targeting of GABAergic neurons in mouse cerebral cortex. Neuron 92, 555 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Schwarz, N. et al. Human cerebrospinal fluid promotes long-term neuronal viability and network function in human neocortical organotypic brain slice cultures. Sci. Rep. 7, 12249 (2017).

    ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Schwarz, N. et al. Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease. eLife 8, e48417 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Source link