In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe geno...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Published: |
Springer Nature
2017
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| _version_ | 1826288844599721984 |
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| author | Wu, Q Ferry, Q Baeumler, T Michaels, Y Vitsios, D Habib, O Arnold, R Jiang, X Maio, S Steinkraus, B Tapia, M Piazza, P Xu, N Holländer, G Milne, T Kim, J Enright, A Bassett, A Fulga, T |
| author_facet | Wu, Q Ferry, Q Baeumler, T Michaels, Y Vitsios, D Habib, O Arnold, R Jiang, X Maio, S Steinkraus, B Tapia, M Piazza, P Xu, N Holländer, G Milne, T Kim, J Enright, A Bassett, A Fulga, T |
| author_sort | Wu, Q |
| collection | OXFORD |
| description | RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a CRISPR-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3’UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment. |
| first_indexed | 2024-03-07T02:19:51Z |
| format | Journal article |
| id | oxford-uuid:a38965cf-7752-4775-86eb-71424c193fb6 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T02:19:51Z |
| publishDate | 2017 |
| publisher | Springer Nature |
| record_format | dspace |
| spelling | oxford-uuid:a38965cf-7752-4775-86eb-71424c193fb62022-03-27T02:27:46ZIn situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineeringJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a38965cf-7752-4775-86eb-71424c193fb6Symplectic Elements at OxfordSpringer Nature2017Wu, QFerry, QBaeumler, TMichaels, YVitsios, DHabib, OArnold, RJiang, XMaio, SSteinkraus, BTapia, MPiazza, PXu, NHolländer, GMilne, TKim, JEnright, ABassett, AFulga, TRNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a CRISPR-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3’UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment. |
| spellingShingle | Wu, Q Ferry, Q Baeumler, T Michaels, Y Vitsios, D Habib, O Arnold, R Jiang, X Maio, S Steinkraus, B Tapia, M Piazza, P Xu, N Holländer, G Milne, T Kim, J Enright, A Bassett, A Fulga, T In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title | In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title_full | In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title_fullStr | In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title_full_unstemmed | In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title_short | In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering |
| title_sort | in situ functional dissection of rna cis regulatory elements by multiplex crispr cas9 genome engineering |
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