We propose to develop and apply a paradigm-shifting technological platform that uses a series of Light- Inducible Transcriptional Effectors (LITEs) to orchestrate the temporal regulation of multiple genes in both individual cells in vitro and in the intact organism. The technology we propose to develop will be very broadly applicable and has the potential to radically transform the scale and rate of discovery across different biomedical fields. Application of this novel technology will enable high throughput discovery of the upstream transcriptional regulatory elements of any endogenous gene, as well as temporally precise modulation of gene expression in the native genome. Precise temporal and spatial patterns of gene expression are observed in different tissue and cell types, and are orchestrated and maintained by complex transcriptionally regulated circuits involving multiple genes. Due to the lack of integrated control and readout technologies that enable simultaneous perturbation and """"""""fast"""""""" tuning of multiple genes, our ability to causally link transcriptional network dynamics with physiology and development remains at the infancy stage. The LITEs platform will enable modification and regulation of gene expression on the time-scale of hours using a non-invasive, light-mediated inductive strategy, thereby enabling a new generation of interactive genetic studies currently inaccessible with conventional techniques. Our proposal consists of two main components: 1) Novel technology development of light sensitive designer zinc finger (ZF) transcriptional modulators (LITEs-ZF). Genomic, synthetic biology, and protein engineering approaches will be used to develop a suite of novel light-inducible transcriptional regulators targeted at specific genes in the native genome of mammalian cells. Since ZF DNA binding domains can be engineered to target any DNA sequence, ZF-LITEs are applicable to a broad range of biological research studies in a variety of different organisms and cells types. 2) Application of the technology toward high-throughput in vitro and in vivo interrogation of transcriptional network dynamics in the central nervous system. In vitro application will be aimed at identification of upstream effectors of gene expression critical to the differentiation of corticospinal motor neurons (CSMN), a clinically relevant neuronal population that degenerates in amyotrophic lateral sclerosis (ALS) and is injured in spinal cord injury. In vivo application will be focused on directing the regeneration of CSMN by mimicking specific temporal sequences of CSMN-specific developmental cues within the adult brain. Given the broad applicability of this technology, the impact of this proposed work will be far reaching and will radically transform existing experimental approaches for studying gene interactions in all fields of life science and medicine.

Public Health Relevance

Understanding the transcriptional networks that drive cellular development and repair has landscape- shifting impacts in the field of regenerative medicine. Here we develop a non-invasive, optical technology to enable genome-wide tuning of gene expression dynamics toward regeneration of corticospinal motor neurons.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-A (51))
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Mamounas, Laura
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Massachusetts General Hospital
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Quadrato, Giorgia; Nguyen, Tuan; Macosko, Evan Z et al. (2017) Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545:48-53
Molyneaux, Bradley J; Goff, Loyal A; Brettler, Andrea C et al. (2015) DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 85:275-288
Konermann, Silvana; Brigham, Mark D; Trevino, Alexandro E et al. (2015) Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517:583-8
Ramanan, Vyas; Shlomai, Amir; Cox, David B T et al. (2015) CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. Sci Rep 5:10833
Swiech, Lukasz; Heidenreich, Matthias; Banerjee, Abhishek et al. (2015) In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat Biotechnol 33:102-6
Cox, David Benjamin Turitz; Platt, Randall Jeffrey; Zhang, Feng (2015) Therapeutic genome editing: prospects and challenges. Nat Med 21:121-31
Hsu, Patrick D; Lander, Eric S; Zhang, Feng (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell 157:1262-78
Pyzocha, Neena K; Ran, F Ann; Hsu, Patrick D et al. (2014) RNA-guided genome editing of mammalian cells. Methods Mol Biol 1114:269-77
Cong, Le; Ran, F Ann; Cox, David et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-23
Konermann, Silvana; Brigham, Mark D; Trevino, Alexandro et al. (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature 500:472-476

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