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A Neuron-Optimized CRISPR/dCas9 Activation System for Robust and Specific Gene Regulation

Katherine E. Savell, Svitlana V. Bach, Morgan E. Zipperly and 9 more

eneuro · 2019 · CC BY-NC-SA

doi:10.1523/eneuro.0495-18.2019

Abstract

CRISPR-based technology has provided new avenues to interrogate gene function, but difficulties in transgene expression in post-mitotic neurons has delayed incorporation of these tools in the central nervous system (CNS). Here, we demonstrate a highly efficient, neuron-optimized dual lentiviral CRISPR-based transcriptional activation (CRISPRa) system capable of robust, modular, and tunable gene induction and multiplexed gene regulation across several primary rodent neuron culture systems. CRISPRa targeting unique promoters in the complex multi-transcript gene brain-derived neurotrophic factor ( Bdnf ) revealed both transcript- and genome-level selectivity of this approach, in addition to highlighting downstream transcriptional and physiological consequences of Bdnf regulation. Finally, we illustrate that CRISPRa is highly efficient in vivo , resulting in increased protein levels of a target gene in diverse brain structures. Taken together, these results demonstrate that CRISPRa is an efficient and selective method to study gene expression programs in brain health and disease.

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References 65

  1. 1.
  2. 2.

    An JJ, Gharami K, Liao GY, Woo NH, Lau AG, Vanevski F, Torre ER, Jones KR, Feng Y, Lu B, Xu B (2008 ) Distinct role of long 3′ UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. Cell 134:175–187.

    Not in our library10.1016/j.cell.2008.05.045

  3. 3.

    Autry AE, Monteggia LM (2012 ) Brain-derived neurotrophic factor and neuropsychiatric disorders. Pharmacol Rev 64:238–258.

    Not in our library10.1124/pr.111.005108

  4. 4.

    Bae S, Park J, Kim JS (2014 ) Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 30:1473–1475.

    Not in our library10.1093/bioinformatics/btu048

  5. 5.

    Baj G, Leone E, Chao MV, Tongiorgi E (2011 ) Spatial segregation of BDNF transcripts enables BDNF to differentially shape distinct dendritic compartments. Proc Natl Acad Sci USA 108:16813–16818.

    Not in our library10.1073/pnas.1014168108

  6. 6.

    Benito E, Barco A (2015 ) The neuronal activity-driven transcriptome. Mol Neurobiol 51:1071–1088.

    Not in our library10.1007/s12035-014-8772-z

  7. 7.

    Bramham CR, Messaoudi E (2005 ) BDNF function in adult synaptic plasticity: the synaptic consolidation hypothesis. Prog Neurobiol 76:99–125.

    Not in our library10.1016/j.pneurobio.2005.06.003

  8. 8.

    Bredy TW, Wu H, Crego C, Zellhoefer J, Sun YE, Barad M (2007 ) Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear. Learn Mem 14:268–276.

    Not in our library10.1101/lm.500907

  9. 9.
  10. 10.

    Chameau P, Inta D, Vitalis T, Monyer H, Wadman WJ, van Hooft JA (2009 ) The N-terminal region of reelin regulates postnatal dendritic maturation of cortical pyramidal neurons. Proc Natl Acad Sci USA 106:7227–7232.

    Not in our library10.1073/pnas.0810764106

  11. 11.

    Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM (2015 ) Highly efficient Cas9-mediated transcriptional programming. Nat Methods 12:326–328.

    Not in our library10.1038/nmeth.3312

  12. 12.

    Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJK, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G (2016 ) Comparison of Cas9 activators in multiple species. Nat Methods 13:563–567.

    Not in our library10.1038/nmeth.3871

  13. 13.

    Cortés-Mendoza J, Díaz de León-Guerrero S, Pedraza-Alva G, Pérez-Martínez L (2013 ) Shaping synaptic plasticity: the role of activity-mediated epigenetic regulation on gene transcription. Int J Dev Neurosci 31:359–369.

    Not in our library10.1016/j.ijdevneu.2013.04.003

  14. 14.

    Cunha C, Brambilla R, Thomas KL (2010 ) A simple role for BDNF in learning and memory? Front Mol Neurosci 3:1.

    Not in our library10.3389/neuro.02.001.2010

  15. 15.

    Day JJ, Childs D, Guzman-Karlsson MC, Kibe M, Moulden J, Song E, Tahir A, Sweatt JD (2013 ) DNA methylation regulates associative reward learning. Nat Neurosci 16:1445–1452.

    Not in our library10.1038/nn.3504

  16. 16.

    Desai NS, Rutherford LC, Turrigiano GG (1999 ) BDNF regulates the intrinsic excitability of cortical neurons. Learn Mem 6:284–291.

    Not in our library

  17. 17.

    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013 ) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21.

    Not in our library10.1093/bioinformatics/bts635

  18. 18.

    Duke CG, Kennedy AJ, Gavin CF, Day JJ, Sweatt JD (2017 ) Experience-dependent epigenomic reorganization in the hippocampus. Learn Mem 24:278–288.

    Not in our library10.1101/lm.045112.117

  19. 19.
  20. 20.

    Ericsson AC, Crim MJ, Franklin CL (2013 ) A brief history of animal modeling. Missouri Med 110:201–205.

    Not in our library

  21. 21.

    Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998 ) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811.

    Not in our library10.1038/35888

  22. 22.

    Frank CL, Liu F, Wijayatunge R, Song L, Biegler MT, Yang MG, Vockley CM, Safi A, Gersbach CA, Crawford GE, West AE (2015 ) Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum. Nat Neurosci 18:647–656.

    Not in our library10.1038/nn.3995

  23. 23.

    Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS (2013 ) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442–451.

    Not in our library10.1016/j.cell.2013.06.044

  24. 24.

    Graves AR, Moore SJ, Spruston N, Tryba AK, Kaczorowski CC (2016 ) Brain-derived neurotrophic factor differentially modulates excitability of two classes of hippocampal output neurons. J Neurophysiol 116:466–471.

    Not in our library10.1152/jn.00186.2016

  25. 25.

    Harrison PJ, Weinberger DR (2005 ) Schizophrenia genes, gene expression, and neuropathology: on the matter of their convergence. Mol Psychiatry 10:40–68.

    Not in our library10.1038/sj.mp.4001558

  26. 26.

    Hermey G, Mahlke C, Gutzmann JJ, Schreiber J, Blüthgen N, Kuhl D (2013 ) Genome-wide profiling of the activity-dependent hippocampal transcriptome. PLoS One 8:e76903.

    Not in our library10.1371/journal.pone.0076903

  27. 27.

    Jackson KL, Dayton RD, Deverman BE, Klein RL (2016 ) Better targeting, better efficiency for wide-scale neuronal transduction with the synapsin promoter and AAV-PHP.B. Front Mol Neurosci 9:116.

    Not in our library10.3389/fnmol.2016.00116

  28. 28.

    Jansen R, Penninx BW, Madar V, Xia K, Milaneschi Y, Hottenga JJ, Hammerschlag AR, Beekman A, van der Wee N, Smit JH, Brooks AI, Tischfield J, Posthuma D, Schoevers R, van Grootheest G, Willemsen G, de Geus EJ, Boomsma DI, Wright FA, Zou F, et al. (2016 ) Gene expression in major depressive disorder. Mol Psychiatry 21:339–347.

    Not in our library10.1038/mp.2015.57

  29. 29.

    Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012 ) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821.

    Not in our library10.1126/science.1225829

  30. 30.

    Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO, Barcena C, Hsu PD, Habib N, Gootenberg JS, Nishimasu H, Nureki O, Zhang F (2015 ) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517:583–588.

    Not in our library10.1038/nature14136

  31. 31.

    Köster J, Rahmann S (2018 ) Snakemake-a scalable bioinformatics workflow engine. Bioinformatics 34:3600.

    Not in our library10.1093/bioinformatics/bty350

  32. 32.
  33. 33.

    Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, et al. (2007 ) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445:168–176.

    Not in our library10.1038/nature05453

  34. 34.

    Lentz TB, Gray SJ, Samulski RJ (2012 ) Viral vectors for gene delivery to the central nervous system. Neurobiol Dis 48:179–188.

    Not in our library10.1016/j.nbd.2011.09.014

  35. 35.

    Liao Y, Liao Y, Smyth GK, Smyth GK, Shi W, Shi W (2014 ) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923–930.

    Not in our library10.1093/bioinformatics/btt656

  36. 36.

    Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R (2016 ) Editing DNA methylation in the mammalian genome. Cell 167:233–235.e17.

    Not in our library10.1016/j.cell.2016.08.056

  37. 37.
  38. 38.

    Lu Y, Christian K, Lu B (2008 ) BDNF: a key regulator for protein synthesis-dependent LTP and long-term memory? Neurobiol Learn Mem 89:312–323.

    Not in our library10.1016/j.nlm.2007.08.018

  39. 39.

    Lubin FD, Roth TL, Sweatt JD (2008 ) Epigenetic regulation of BDNF gene transcription in the consolidation of fear memory. J Neurosci 28:10576–10586.

    Not in our library10.1523/jneurosci.1786-08.2008

  40. 40.

    Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK (2013 ) CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10:977–979.

    Not in our library10.1038/nmeth.2598

All 65 references

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