Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells
RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human ce...
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| Format: | Article |
| Language: | en_US |
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Elsevier
2016
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| Online Access: | http://hdl.handle.net/1721.1/100849 https://orcid.org/0000-0002-8346-2184 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0001-6495-4741 |
| _version_ | 1826217300425965568 |
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| author | Nissim, Lior Fridkin, Alexandra Perez-Pinera, Pablo Lu, Timothy K. Perli, Samuel |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Nissim, Lior Fridkin, Alexandra Perez-Pinera, Pablo Lu, Timothy K. Perli, Samuel |
| author_sort | Nissim, Lior |
| collection | MIT |
| description | RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human cells, limiting their use for conditional gene regulation. We present new strategies that enable expression of functional gRNAs from RNA polymerase II promoters and multiplexed production of proteins and gRNAs from a single transcript in human cells. We use multiple RNA regulatory strategies, including RNA-triple-helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing. Using these tools, we efficiently modulate endogenous promoters and implement tunable synthetic circuits, including multistage cascades and RNA-dependent networks that can be rewired with Csy4 to achieve complex behaviors. This toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for biology, therapeutic, and synthetic biology applications. |
| first_indexed | 2024-09-23T17:01:14Z |
| format | Article |
| id | mit-1721.1/100849 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T17:01:14Z |
| publishDate | 2016 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1008492022-10-03T09:52:25Z Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells Nissim, Lior Fridkin, Alexandra Perez-Pinera, Pablo Lu, Timothy K. Perli, Samuel Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology. Research Laboratory of Electronics Massachusetts Institute of Technology. Synthetic Biology Center Nissim, Lior Perli, Samuel Fridkin, Alexandra Perez-Pinera, Pablo Lu, Timothy K. RNA-based regulation and CRISPR/Cas transcription factors (CRISPR-TFs) have the potential to be integrated for the tunable modulation of gene networks. A major limitation of this methodology is that guide RNAs (gRNAs) for CRISPR-TFs can only be expressed from RNA polymerase III promoters in human cells, limiting their use for conditional gene regulation. We present new strategies that enable expression of functional gRNAs from RNA polymerase II promoters and multiplexed production of proteins and gRNAs from a single transcript in human cells. We use multiple RNA regulatory strategies, including RNA-triple-helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing. Using these tools, we efficiently modulate endogenous promoters and implement tunable synthetic circuits, including multistage cascades and RNA-dependent networks that can be rewired with Csy4 to achieve complex behaviors. This toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for biology, therapeutic, and synthetic biology applications. United States. Defense Advanced Research Projects Agency National Institutes of Health (U.S.) (DP2 OD008435) National Institutes of Health (U.S.) (P50 GM098792) 2016-01-15T04:00:10Z 2016-01-15T04:00:10Z 2014-05 2014-04 Article http://purl.org/eprint/type/JournalArticle 10972765 1097-4164 http://hdl.handle.net/1721.1/100849 Nissim, Lior, Samuel D. Perli, Alexandra Fridkin, Pablo Perez-Pinera, and Timothy K. Lu. “Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells.” Molecular Cell 54, no. 4 (May 2014): 698–710. https://orcid.org/0000-0002-8346-2184 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0001-6495-4741 en_US http://dx.doi.org/10.1016/j.molcel.2014.04.022 Molecular Cell Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier PMC |
| spellingShingle | Nissim, Lior Fridkin, Alexandra Perez-Pinera, Pablo Lu, Timothy K. Perli, Samuel Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title | Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title_full | Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title_fullStr | Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title_full_unstemmed | Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title_short | Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells |
| title_sort | multiplexed and programmable regulation of gene networks with an integrated rna and crispr cas toolkit in human cells |
| url | http://hdl.handle.net/1721.1/100849 https://orcid.org/0000-0002-8346-2184 https://orcid.org/0000-0002-9999-6690 https://orcid.org/0000-0001-6495-4741 |
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