Optical control of mammalian endogenous transcription and epigenetic states
Open accessAbstract
The dynamic nature of gene expression enables cellular programming, homeostasis and environmental adaptation in living systems. Dissection of causal gene functions in cellular and organismal processes therefore necessitates approaches that enable spatially and temporally precise modulation of gene expression. Recently, a variety of microbial and plant-derived light-sensitive proteins have been engineered as optogenetic actuators, enabling high-precision spatiotemporal control of many cellular functions. However, versatile and robust technologies that enable optical modulation of transcription in the mammalian endogenous genome remain elusive. Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana. LITEs do not require additional exogenous chemical cofactors, are easily customized to target many endogenous genomic loci, and can be activated within minutes with reversibility. LITEs can be packaged into viral vectors and genetically targeted to probe specific cell populations. We have applied this system in primary mouse neurons, as well as in the brain of freely behaving mice in vivo to mediate reversible modulation of mammalian endogenous gene expression as well as targeted epigenetic chromatin modifications. The LITE system establishes a novel mode of optogenetic control of endogenous cellular processes and enables direct testing of the causal roles of genetic and epigenetic regulation in normal biological processes and disease states.
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CRISPRi and CRISPRa technologies utilize catalytically inactive Cas9 (dCas9) fused to either a transcriptional repressor (e.g., KRAB) or a transcriptional activator (e.g., VPR).
“For example, CRISPRi (interference)23–25 and CRISPRa (activation)26–30 technologies utilize catalytically inactive Cas9 (dCas9) fused to either a transcriptional repressor (e.g., KRAB, Krüppel associated box) or a transcriptional activator (e.g., VPR, VP64-p65-Rta).”
From Large-scale CRISPR screening in primary human 3D gastric organoids enables comprehensive dissection of gene-drug interactions (2025) · cites this paper as [24]
The paper’s LITE-system description (section labeled Abstract; page unavailable) says that a nucleolytically inactive Cas9 domain could, in principle, replace its TALE genomic anchor, and that the modular system can use activating or repressing effectors. It does not describe CRISPRi or CRISPRa constructs with dCas9 fused to KRAB or VPR; its described activator is VP64, recruited through a light-responsive component. (LLM, conf=0.85)
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- Authors
- Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., Platt, R. J., Scott, D. A., Church, G. M., & Zhang, F.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Zhang, Feng
- ORCID
- Venue
- Nature
- Published
- 2013-08
- Volume
- 500
- Issue
- 7463
- Pages
- 472-476
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3856241
- OpenAlex
- W2111648798
- Cited by
- 803
- References
- 5
- Citations by year
- 2026: 15 · 2025: 26 · 2024: 34 · 2023: 26 · 2022: 42 · 2021: 46 · 2020: 44 · 2019: 52 · 2018: 60 · 2017: 88 · 2016: 114 · 2015: 106 · 2014: 126 · 2013: 23
- FWCI
- 60.37
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of Mental Health (DP1MH100706)
- National Human Genome Research Institute (P50HG005550)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK097768)
- National Institute of Neurological Disorders and Stroke (R01NS073124)
- National Center for Chronic Disease Prevention and Health Promotion (DP1‑MH100706)
- Topics
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Keywords
- optogenetics, CRY2, CIB1, chromatin modification, viral gene delivery, mouse neurons, freely moving mice, spatial and temporal gene regulation, chromatin accessibility
- MeSH terms
- Animals, Cells, Cultured, Chromatin, Gene Expression Regulation, Genetic Vectors, Light, Male, Mice, Inbred C57BL, Neurons, Time Factors, Transcription, Genetic, Wakefulness, Two-Hybrid System Techniques, Arabidopsis Proteins, Epigenesis, Genetic, Mice, Basic Helix-Loop-Helix Proteins, Basic Helix-Loop-Helix Transcription Factors, Cryptochromes, Optogenetics
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