Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarray-...
| Main Authors: | , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2012
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| Online Access: | http://hdl.handle.net/1721.1/74097 https://orcid.org/0000-0002-0964-0616 |
| _version_ | 1826193845979709440 |
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| author | Melnikov, Alexandre Murugan, Anand Zhang, Xiaolan Tesileanu, Tiberiu Wang, Li Rogov, Peter Feizi-Khankandi, Soheil Gnirke, Andreas Callan Jr, Curtis G. Kinney, Justin B. Kellis, Manolis Lander, Eric S. Mikkelsen, Tarjei Sigurd, 1978- |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Melnikov, Alexandre Murugan, Anand Zhang, Xiaolan Tesileanu, Tiberiu Wang, Li Rogov, Peter Feizi-Khankandi, Soheil Gnirke, Andreas Callan Jr, Curtis G. Kinney, Justin B. Kellis, Manolis Lander, Eric S. Mikkelsen, Tarjei Sigurd, 1978- |
| author_sort | Melnikov, Alexandre |
| collection | MIT |
| description | Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarray-synthesized DNA regulatory elements and unique sequence tags are cloned into plasmids to generate a library of reporter constructs. These constructs are transfected into cells and tag expression is assayed by high-throughput sequencing. We apply MPRA to compare >27,000 variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon-β enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution. We then use the data to train quantitative sequence-activity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to design enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity. |
| first_indexed | 2024-09-23T09:46:18Z |
| format | Article |
| id | mit-1721.1/74097 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T09:46:18Z |
| publishDate | 2012 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/740972022-09-26T13:35:42Z Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay Melnikov, Alexandre Murugan, Anand Zhang, Xiaolan Tesileanu, Tiberiu Wang, Li Rogov, Peter Feizi-Khankandi, Soheil Gnirke, Andreas Callan Jr, Curtis G. Kinney, Justin B. Kellis, Manolis Lander, Eric S. Mikkelsen, Tarjei Sigurd, 1978- Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Lander, Eric S. Kellis, Manolis Feizi-Khankandi, Soheil Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarray-synthesized DNA regulatory elements and unique sequence tags are cloned into plasmids to generate a library of reporter constructs. These constructs are transfected into cells and tag expression is assayed by high-throughput sequencing. We apply MPRA to compare >27,000 variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon-β enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution. We then use the data to train quantitative sequence-activity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to design enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity. National Human Genome Research Institute (U.S.) (grant R01HG004037) National Science Foundation (U.S.) ((NSF) grant PHY-0957573) National Science Foundation (U.S.) (NSF grant PHY-1022140) Broad Institute 2012-10-18T18:32:29Z 2012-10-18T18:32:29Z 2012-02 2011-08 Article http://purl.org/eprint/type/JournalArticle 1087-0156 1546-1696 http://hdl.handle.net/1721.1/74097 Melnikov, Alexandre et al. “Systematic Dissection and Optimization of Inducible Enhancers in Human Cells Using a Massively Parallel Reporter Assay.” Nature Biotechnology 30.3 (2012): 271–277. Web. https://orcid.org/0000-0002-0964-0616 en_US http://dx.doi.org/10.1038/nbt.2137 Nature Biotechnology Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Nature Publishing Group PMC |
| spellingShingle | Melnikov, Alexandre Murugan, Anand Zhang, Xiaolan Tesileanu, Tiberiu Wang, Li Rogov, Peter Feizi-Khankandi, Soheil Gnirke, Andreas Callan Jr, Curtis G. Kinney, Justin B. Kellis, Manolis Lander, Eric S. Mikkelsen, Tarjei Sigurd, 1978- Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title | Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title_full | Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title_fullStr | Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title_full_unstemmed | Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title_short | Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| title_sort | rapid dissection and model based optimization of inducible enhancers in human cells using a massively parallel reporter assay |
| url | http://hdl.handle.net/1721.1/74097 https://orcid.org/0000-0002-0964-0616 |
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