Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity
© 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart and muscle. Rbfox proteins have long been known to bi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Springer Science and Business Media LLC
2021
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| Online Access: | https://hdl.handle.net/1721.1/133385 |
| _version_ | 1811068791895883776 |
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| author | Begg, Bridget E Jens, Marvin Wang, Peter Y Minor, Christine M Burge, Christopher B |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Begg, Bridget E Jens, Marvin Wang, Peter Y Minor, Christine M Burge, Christopher B |
| author_sort | Begg, Bridget E |
| collection | MIT |
| description | © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity and specificity, but just half of Rbfox binding sites contain a GCAUG motif in vivo. We incubated recombinant RBFOX2 with over 60,000 mouse and human transcriptomic sequences to reveal substantial binding to several moderate-affinity, non-GCAYG sites at a physiologically relevant range of RBFOX2 concentrations. We find that these ‘secondary motifs’ bind Rbfox robustly in cells and that several together can exert regulation comparable to GCAUG in a trichromatic splicing reporter assay. Furthermore, secondary motifs regulate RNA splicing in neuronal development and in neuronal subtypes where cellular Rbfox concentrations are highest, enabling a second wave of splicing changes as Rbfox levels increase. |
| first_indexed | 2024-09-23T08:01:14Z |
| format | Article |
| id | mit-1721.1/133385 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:01:14Z |
| publishDate | 2021 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1333852023-12-08T21:19:55Z Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity Begg, Bridget E Jens, Marvin Wang, Peter Y Minor, Christine M Burge, Christopher B Massachusetts Institute of Technology. Department of Biology © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity and specificity, but just half of Rbfox binding sites contain a GCAUG motif in vivo. We incubated recombinant RBFOX2 with over 60,000 mouse and human transcriptomic sequences to reveal substantial binding to several moderate-affinity, non-GCAYG sites at a physiologically relevant range of RBFOX2 concentrations. We find that these ‘secondary motifs’ bind Rbfox robustly in cells and that several together can exert regulation comparable to GCAUG in a trichromatic splicing reporter assay. Furthermore, secondary motifs regulate RNA splicing in neuronal development and in neuronal subtypes where cellular Rbfox concentrations are highest, enabling a second wave of splicing changes as Rbfox levels increase. 2021-10-27T19:52:32Z 2021-10-27T19:52:32Z 2020 2021-07-14T16:42:57Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/133385 en 10.1038/S41594-020-0475-8 Nature Structural and Molecular Biology Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Springer Science and Business Media LLC PMC |
| spellingShingle | Begg, Bridget E Jens, Marvin Wang, Peter Y Minor, Christine M Burge, Christopher B Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title | Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title_full | Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title_fullStr | Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title_full_unstemmed | Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title_short | Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity |
| title_sort | concentration dependent splicing is enabled by rbfox motifs of intermediate affinity |
| url | https://hdl.handle.net/1721.1/133385 |
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