RNA and CRISPR-based Genome Engineering of Synthetic and Endogenous Networks in Eukaryotic Cells

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RNA and CRISPR-based genome engineering of synthetic and endogenous networks in eukaryotic cells
Professor Timothy Lu
Department of Biological Engineering, MIT
External Link (be.mit.edu)
Lior Nissim
Department of Biological Engineering, MIT
Samuel Perli
Department of Electrical Engineering and Computer Science, MIT
Managed By
Jon Gilbert
MIT Technology Licensing Officer
Patent Protection

Methods and compositions for the production of guide RNA

US Patent Pending US 2017-0022499
Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells
Molecular Cell, http://dx.doi.org/10.1016/j.molcel.2014.04.022


The generation of robust, scalable gene networks that interfere minimally with endogenous cellular processes is fundamental to synthetic biology. The use of RNA regulatory strategies in combination with CRISPR/Cas transcription factors (CRISPR-TFs) allows for the conditional regulation of large-scale synthetic and endogenous gene networks in eukaryotic cells. The system is uniquely suited to build sophisticated circuits and transcriptional cascades that could be linked to specific events (e.g., cell cycle) or environments (e.g., chemical gradients). 

Problem Addressed

Current methods for genome editing (e.g., CRISPR/Cas) have the potential to modulate gene expression in a tunable manner but are often limited by a combination of scalability, lack of conditional regulation, and inefficient regulation of endogenous promoters. This genome engineering toolkit provides the means to regulate and synchronize multiplexed, large-scale synthetic gene networks in addition to modulating endogenous gene expression.  


Here we describe a genome editing toolkit for the generation of robust, scalable synthetic gene networks and native gene modulation in eukaryotic cells. Existing CRISPR/Cas methodology cannot be used for conditional gene regulation, as the guide RNAs (gRNAs) used to target DNA sites can only be expressed from RNA polymerase III (RNAP III) promoters, most of which are constitutively active. This technology produces gRNAs from RNA polymerase II (RNAP II) promoters, allowing for conditional gene expression and tunable responses to external inputs. The system integrates CRISPR-TFs with RNA regulatory machinery (e.g., Csy4 endonuclease, RNA triple helix) to produce functional gRNAs from RNAP II promoters while preserving downstream translation and expression of the harboring gene. The system is capable of multiplexed gRNA expression from one individual transcript, thus modulating multiple nodes from a single one and enabling sophisticated regulatory circuits with a large number of interconnections. 


  • Multiplexed, large-scale genome engineering
  • Synthesize multi-stage transcriptional cascades
  • Regulate synthetic and endogenous networks