Light-mediated control of Gene expression in mammalian cells

ADRIAN, 2017, A phytochrome-derived photoswitch for intracellular transport, ACS Synth. Biol., 6, 1248, 10.1021/acssynbio.6b00333 AHMARI, 2013, Repeated cortico-striatal stimulation generates persistent OCD-like behavior, Science, 340, 1234, 10.1126/science.1234733 AOKI, 2017, Propagating wave of ERK activation orients collective cell migration, Dev. Cell, 43, 305, 10.1016/j.devcel.2017.10.016 ATASOY, 2008, A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range circuit mapping, J. Neurosci., 28, 10.1523/JNEUROSCI.1954-08.2008 BERNDT, 2009, Bi-stable neural state switches, Nat. Neurosci., 12, 10.1038/nn.2247 BOYDEN, 2005, Millisecond-timescale, genetically targeted optical control of neural activity, Nat. Neurosci., 8, 10.1038/nn1525 BRAND, 1993, Targeted gene expression as a means of altering cell fates and generating dominant phenotypes, Development, 118, 10.1242/dev.118.2.401 BROWN, 1996, A cytokine mRNA-destabilizing element that is structurally and functionally distinct from A+U-rich elements, Proc Natl Acad Sci U S A, 93, 10.1073/pnas.93.24.13721 CAMBRIDGE, 2009, Doxycycline-dependent photoactivated gene expression in eukaryotic systems, Nat. Methods, 6, 10.1038/nmeth.1340 CARDIN, 2009, Driving fast-spiking cells induces gamma rhythm and controls sensory responses, Nature, 459, 10.1038/nature08002 CHEN, 2018, Near-infrared deep brain stimulation via upconversion nanoparticle-mediated optogenetics, Science, 359, 679, 10.1126/science.aaq1144 CHOI, 2002, The role of poly (A) tail stability in the ability of the woodchuck hepatitis virus posttranscriptional regulatory element to stimulate gene expression, Mol. Ther., 5, S143, 10.1016/S1525-0016(16)43269-7 CREFCOEUR, 2013, Ultraviolet-B-mediated induction of protein-protein interactions in mammalian cells, Nat. Commun., 4, 1779, 10.1038/ncomms2800 DAMGAARD, 2013, Regulation of ARE-mRNA stability by cellular signaling: implications for human Cancer, Cancer Treat. Res., 158, 10.1007/978-3-642-31659-3_7 DAS, 2016, Tet-on systems for doxycycline-inducible gene expression, Curr. Gene Ther., 16 DENARDO, 2019, Temporal evolution of cortical ensembles promoting remote memory retrieval, Nat. Neurosci., 22, 460, 10.1038/s41593-018-0318-7 DENNY, 2014, Hippocampal memory traces are differentially modulated by experience, time, and adult neurogenesis, Neuron, 83, 189, 10.1016/j.neuron.2014.05.018 DUAN, 2017, Understanding CRY2 interactions for optical control of intracellular signaling, Nat. Commun., 8, 547, 10.1038/s41467-017-00648-8 EBNER, 2019, Optically induced calcium-dependent gene activation and labeling of active neurons using CaMPARI and cal-light, Front. Synaptic Neurosci., 11, 16, 10.3389/fnsyn.2019.00016 GIORDANO, 2013, PI(4,5)P(2)-dependent and Ca(2+)-regulated ER-PM interactions mediated by the extended synaptotagmins, Cell, 153, 10.1016/j.cell.2013.05.026 GOMPF, 2015, Targeted genetic manipulations of neuronal subtypes using promoter-specific combinatorial AAVs in wild-type animals, Front. Behav. Neurosci., 9, 152, 10.3389/fnbeh.2015.00152 GOSSEN, 1992, Tight control of gene expression in mammalian cells by tetracycline-responsive promoters, Proc Natl Acad Sci U S A, 89, 10.1073/pnas.89.12.5547 GOSSEN, 1995, Transcriptional activation by tetracyclines in mammalian cells, Science, 268, 10.1126/science.7792603 GUENTHNER, 2013, Permanent genetic access to transiently active neurons via TRAP: targeted recombination in active populations, Neuron, 78, 10.1016/j.neuron.2013.03.025 GUNTAS, 2015, Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins, Proc Natl Acad Sci U S A, 112, 10.1073/pnas.1417910112 HABETS, 2003, Cardiac expression of Gal4 causes cardiomyopathy in a dose-dependent manner, J. Muscle Res. Cell. Motil., 24, 10.1023/A:1026055612227 HALLETT, 2016, Correlating in vitro and in vivo activities of light-inducible dimers: a cellular optogenetics guide, ACS Synth. Biol., 5, 53, 10.1021/acssynbio.5b00119 HAN, 2019, Simultaneous visualization of multiple gene expression in single cells using an engineered multicolor reporter toolbox and approach of spectral crosstalk correction, ACS Synth. Biol., 10.1021/acssynbio.9b00223 HORNER, 2017, Light-responsive promoters, Methods Mol. Biol., 1651, 173, 10.1007/978-1-4939-7223-4_13 HOSOSHIMA, 2015, Near-infrared (NIR) up-conversion optogenetics, Sci. Rep., 5, 16533, 10.1038/srep16533 IMAYOSHI, 2013, Oscillatory control of factors determining multipotency and fate in mouse neural progenitors, Science, 342, 10.1126/science.1242366 IMAYOSHI, 2014, bHLH factors in self-renewal, multipotency, and fate choice of neural progenitor cells, Neuron, 82, 9, 10.1016/j.neuron.2014.03.018 ISOMURA, 2017, Optogenetic perturbation and bioluminescence imaging to analyze cell-to-cell transfer of oscillatory information, Genes Dev., 31, 524, 10.1101/gad.294546.116 JEONG, 2010, Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase, Proc Natl Acad Sci U S A, 107, 10.1073/pnas.1004529107 JUNG, 2019, Noninvasive optical activation of Flp recombinase for genetic manipulation in deep mouse brain regions, Nat. Commun., 10, 314, 10.1038/s41467-018-08282-8 KABERNIUK, 2016, A bacterial phytochrome-based optogenetic system controllable with near-infrared light, Nat. Methods, 13, 10.1038/nmeth.3864 KANTEVARI, 2010, Two-color, two-photon uncaging of glutamate and GABA, Nat. Methods, 7, 10.1038/nmeth.1413 KARIMOVA, 2018, A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination, Sci. Rep., 8, 14453, 10.1038/s41598-018-32802-7 KAWANO, 2016, A photoactivatable Cre-loxP recombination system for optogenetic genome engineering, Nat. Chem. Biol., 12, 1059, 10.1038/nchembio.2205 KAWANO, 2015, Engineered pairs of distinct photoswitches for optogenetic control of cellular proteins, Nat. Commun., 6, 6256, 10.1038/ncomms7256 KELLER, 2011, Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades, Plant J., 67, 195, 10.1111/j.1365-313X.2011.04598.x KENNEDY, 2010, Rapid blue-light-mediated induction of protein interactions in living cells, Nat. Methods, 7, 10.1038/nmeth.1524 KINJO, 2019, FRET-assisted photoactivation of flavoproteins for in vivo two-photon optogenetics, Nat. Methods, 16, 1029, 10.1038/s41592-019-0541-5 KITAMURA, 2014, Island cells control temporal association memory, Science, 343, 896, 10.1126/science.1244634 KOHARA, 2014, Cell type-specific genetic and optogenetic tools reveal hippocampal CA2 circuits, Nat. Neurosci., 17, 10.1038/nn.3614 KOHL, 2014, Ultrafast tissue staining with chemical tags, Proc Natl Acad Sci U S A, 111, 10.1073/pnas.1411087111 KONERMANN, 2013, Optical control of mammalian endogenous transcription and epigenetic states, Nature, 500, 472, 10.1038/nature12466 KUMAR, 2017, Understanding development and stem cells using single cell-based analyses of gene expression, Development, 144, 17, 10.1242/dev.133058 KYRIAKAKIS, 2018, Biosynthesis of orthogonal molecules using ferredoxin and Ferredoxin-NADP(+) reductase systems enables genetically encoded PhyB optogenetics, ACS Synth. Biol., 7, 706, 10.1021/acssynbio.7b00413 LEE, 2017, Temporally precise labeling and control of neuromodulatory circuits in the mammalian brain, Nat. Methods, 14, 495, 10.1038/nmeth.4234 LEE, 2017, A calcium- and light-gated switch to induce gene expression in activated neurons, Nat. Biotechnol., 35, 858, 10.1038/nbt.3902 LEVSKAYA, 2009, Spatiotemporal control of cell signalling using a light-switchable protein interaction, Nature, 461, 997, 10.1038/nature08446 LIN, 2016, Genetically encoded indicators of neuronal activity, Nat. Neurosci., 19, 1142, 10.1038/nn.4359 LIU, 2012, Optogenetic control of transcription in zebrafish, PLoS One, 7 LUNGU, 2012, Designing photoswitchable peptides using the AsLOV2 domain, Chem. Biol., 19, 10.1016/j.chembiol.2012.02.006 MAIURI, 2015, Actin flows mediate a universal coupling between cell speed and cell persistence, Cell, 161, 10.1016/j.cell.2015.01.056 MASAMIZU, 2006, Real-time imaging of the somite segmentation clock: revelation of unstable oscillators in the individual presomitic mesoderm cells, Proc Natl Acad Sci U S A, 103, 10.1073/pnas.0508658103 MIYAWAKI, 2011, Proteins on the move: insights gained from fluorescent protein technologies, Nat. Rev. Mol. Cell Biol., 12, 656, 10.1038/nrm3199 MIYAZAKI, 2019, Large timescale interrogation of neuronal function by fiberless optogenetics using lanthanide micro-particles, Cell Rep., 26, 10.1016/j.celrep.2019.01.001 MOTTA-MENA, 2014, An optogenetic gene expression system with rapid activation and deactivation kinetics, Nat. Chem. Biol., 10, 196, 10.1038/nchembio.1430 MULLER, 2013, A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells, Nucleic Acids Res., 41, e77, 10.1093/nar/gkt002 MULLER, 2013, Multi-chromatic control of mammalian gene expression and signaling, Nucleic Acids Res., 41, e124, 10.1093/nar/gkt340 MULLER, 2014, A red light-controlled synthetic gene expression switch for plant systems, Mol. Biosyst., 10, 1679, 10.1039/C3MB70579J NAGEL, 2003, Channelrhodopsin-2, a directly light-gated cation-selective membrane channel, Proc Natl Acad Sci U S A, 100, 10.1073/pnas.1936192100 NAGY, 2000, Cre recombinase: the universal reagent for genome tailoring, Genesis, 26, 99, 10.1002/(SICI)1526-968X(200002)26:2<99::AID-GENE1>3.0.CO;2-B NIHONGAKI, 2017, CRISPR-Cas9-based photoactivatable transcription systems to induce neuronal differentiation, Nat. Methods, 14, 963, 10.1038/nmeth.4430 NIHONGAKI, 2015, Photoactivatable CRISPR-Cas9 for optogenetic genome editing, Nat. Biotechnol., 33, 10.1038/nbt.3245 NIHONGAKI, 2019, A split CRISPR-Cpf1 platform for inducible genome editing and gene activation, Nat. Chem. Biol., 15, 882, 10.1038/s41589-019-0338-y NIHONGAKI, 2015, CRISPR-Cas9-based photoactivatable transcription system, Chem. Biol., 22, 10.1016/j.chembiol.2014.12.011 NODA, 2018, Light-controllable transcription system by nucleocytoplasmic shuttling of a truncated phytochrome B, Photochem. Photobiol., 94, 1071, 10.1111/php.12955 OKUMURA, 2018, Dynein-Dynactin-NuMA clusters generate cortical spindle-pulling forces as a multi-arm ensemble, Elife, 7 ORTH, 2000, Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system, Nat. Struct. Biol., 7, 215, 10.1038/73324 PARK, 2016, Stretchable multichannel antennas in soft wireless optoelectronic implants for optogenetics, Proc Natl Acad Sci U S A, 113, 10.1073/pnas.1611769113 PATHAK, 2017, Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2, Nucleic Acids Res., 45, e167, 10.1093/nar/gkx260 PATHAK, 2014, Benchmarking of optical dimerizer systems, ACS Synth. Biol., 3, 10.1021/sb500291r POLSTEIN, 2012, Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors, J. Am. Chem. Soc., 134, 10.1021/ja3065667 POLSTEIN, 2015, A light-inducible CRISPR-Cas9 system for control of endogenous gene activation, Nat. Chem. Biol., 11, 198, 10.1038/nchembio.1753 POTTER, 2011, Using the Q system in Drosophila melanogaster, Nat. Protoc., 6, 10.1038/nprot.2011.347 QUEJADA, 2017, Optimized light-inducible transcription in mammalian cells using Flavin Kelch-repeat F-box1/GIGANTEA and CRY2/CIB1, Nucleic Acids Res., 10.1093/nar/gkx804 RECHSTEINER, 1996, PEST sequences and regulation by proteolysis, Trends Biochem. Sci., 21, 10.1016/S0968-0004(96)10031-1 REDCHUK, 2018, Near-infrared light-controlled systems for gene transcription regulation, protein targeting and spectral multiplexing, Nat. Protoc., 13, 1121, 10.1038/nprot.2018.022 REDCHUK, 2018, Near-infrared light-controlled gene expression and protein targeting in neurons and non-neuronal cells, Chembiochem, 19, 1334, 10.1002/cbic.201700642 REDCHUK, 2017, Near-infrared optogenetic pair for protein regulation and spectral multiplexing, Nat. Chem. Biol., 13, 633, 10.1038/nchembio.2343 REPINA, 2017, At light speed: advances in optogenetic systems for regulating cell signaling and behavior, Annu. Rev. Chem. Biomol. Eng., 8, 13, 10.1146/annurev-chembioeng-060816-101254 RIABININA, 2015, Improved and expanded Q-system reagents for genetic manipulations, Nat. Methods, 12 RITTER, 2008, Monitoring light-induced structural changes of Channelrhodopsin-2 by UV-visible and Fourier transform infrared spectroscopy, J. Biol. Chem., 283, 10.1074/jbc.M806353200 RODRIQUES, 2019, Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution, Science, 363, 1463, 10.1126/science.aaw1219 RONZITTI, 2017, Recent advances in patterned photostimulation for optogenetics, J. Opt., 19, 1, 10.1088/2040-8986/aa8299 RUESS, 2015, Iterative experiment design guides the characterization of a light-inducible gene expression circuit, Proc Natl Acad Sci U S A, 112, 10.1073/pnas.1423947112 SAKAGUCHI, 2018, Bright multicolor labeling of neuronal circuits with fluorescent proteins and chemical tags, Elife, 7 SAKAUE-SAWANO, 2008, Visualizing spatiotemporal dynamics of multicellular cell-cycle progression, Cell, 132, 10.1016/j.cell.2007.12.033 SALINAS, 2018, Fungal light-oxygen-Voltage domains for optogenetic control of gene expression and flocculation in Yeast, MBio, 9 SCHERMELLEH, 2019, Super-resolution microscopy demystified, Nat. Cell Biol., 21, 72, 10.1038/s41556-018-0251-8 SCHINDLER, 2015, Photo-activatable Cre recombinase regulates gene expression in vivo, Sci. Rep., 5, 13627, 10.1038/srep13627 SCHWERDTFEGER, 2003, VIVID is a flavoprotein and serves as a fungal blue light photoreceptor for photoadaptation, EMBO J., 22, 10.1093/emboj/cdg451 SEIRIKI, 2017, High-speed and scalable whole-brain imaging in rodents and Primates, Neuron, 94, 10.1016/j.neuron.2017.05.017 SHAH, 2018, Single-cell transcriptomics and fate mapping of ependymal cells reveals an absence of neural stem cell function, Cell, 173, 10.1016/j.cell.2018.03.063 SHAO, 2018, Synthetic far-red light-mediated CRISPR-dCas9 device for inducing functional neuronal differentiation, Proc Natl Acad Sci U S A, 115, 10.1073/pnas.1802448115 SHIMIZU-SATO, 2002, A light-switchable gene promoter system, Nat. Biotechnol., 20, 10.1038/nbt734 SHIMOJO, 2016, Oscillatory control of Delta-like1 in cell interactions regulates dynamic gene expression and tissue morphogenesis, Genes Dev., 30, 102, 10.1101/gad.270785.115 SHIMOJO, 2008, Oscillations in notch signaling regulate maintenance of neural progenitors, Neuron, 58, 52, 10.1016/j.neuron.2008.02.014 SHIN, 2017, Flexible near-field wireless optoelectronics as subdermal implants for broad applications in optogenetics, Neuron, 93, 10.1016/j.neuron.2016.12.031 SHIN, 2015, Single-cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis, Cell Stem Cell, 17, 10.1016/j.stem.2015.07.013 STEHFEST, 2010, The branched photocycle of the slow-cycling channelrhodopsin-2 mutant C128T, J. Mol. Biol., 398, 690, 10.1016/j.jmb.2010.03.031 STRICKLAND, 2012, TULIPs: tunable, light-controlled interacting protein tags for cell biology, Nat. Methods, 9, 10.1038/nmeth.1904 SUEDA, 2019, High Hes1 expression and resultant Ascl1 suppression regulate quiescent vs. Active neural stem cells in the adult mouse brain, Genes Dev., 33, 511, 10.1101/gad.323196.118 SUZUKI, 2017, Recent progress in expanding the chemiluminescent toolbox for bioimaging, Curr. Opin. Biotechnol., 48, 135, 10.1016/j.copbio.2017.04.001 TASIC, 2018, Shared and distinct transcriptomic cell types across neocortical areas, Nature, 563, 72, 10.1038/s41586-018-0654-5 TASLIMI, 2016, Optimized second-generation CRY2-CIB dimerizers and photoactivatable Cre recombinase, Nat. Chem. Biol., 12, 10.1038/nchembio.2063 TEPE, 2018, Single-cell RNA-Seq of mouse olfactory bulb reveals cellular heterogeneity and activity-dependent molecular census of adult-born neurons, Cell Rep., 25, 10.1016/j.celrep.2018.11.034 UDA, 2017, Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling, Proc Natl Acad Sci U S A, 114, 11962, 10.1073/pnas.1707190114 WANG, 2012, Spatiotemporal control of gene expression by a light-switchable transgene system, Nat. Methods, 9, 266, 10.1038/nmeth.1892 WANG, 2017, Tetherless near-infrared control of brain activity in behaving animals using fully implantable upconversion microdevices, Biomaterials, 142, 136, 10.1016/j.biomaterials.2017.07.017 WEISSLEDER, 2003, Shedding light onto live molecular targets, Nat. Med., 9, 123, 10.1038/nm0103-123 WINNUBST, 2019, Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain, Cell, 179, 10.1016/j.cell.2019.07.042 WU, 2010, CRYPTOCHROME 1 is implicated in promoting R protein-mediated plant resistance to Pseudomonas syringae in Arabidopsis, Mol. Plant, 3, 10.1093/mp/ssp107 YAMADA, 2018, Light control of the tet gene expression system in mammalian cells, Cell Rep., 25, 10.1016/j.celrep.2018.09.026 YAO, 2019, RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations, bioRxiv YAZAWA, 2009, Induction of protein-protein interactions in live cells using light, Nat. Biotechnol., 27, 941, 10.1038/nbt.1569 YU, 2010, The cryptochrome blue light receptors, Arabidopsis Book, 8, e0135, 10.1199/tab.0135 YUZ, 2018, Independent control over multiple cell types in space and time using orthogonal blue and red light switchable cell interactions, Adv. Sci. Weinh. (Weinh), 5 ZHANG, 2009, Ectopic expression of multiple microbial rhodopsins restores ON and OFF light responses in retinas with photoreceptor degeneration, J. Neurosci., 29, 9186, 10.1523/JNEUROSCI.0184-09.2009