A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle
The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing, including alternative splicing, which generates fiber-type specific isoforms of st...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/10/10/2505 |
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| author | Shao-Yen Kao Elena Nikonova Sabrina Chaabane Albiona Sabani Alexandra Martitz Anja Wittner Jakob Heemken Tobias Straub Maria L. Spletter |
| author_facet | Shao-Yen Kao Elena Nikonova Sabrina Chaabane Albiona Sabani Alexandra Martitz Anja Wittner Jakob Heemken Tobias Straub Maria L. Spletter |
| author_sort | Shao-Yen Kao |
| collection | DOAJ |
| description | The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing, including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently, only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here, we demonstrate the utility of <i>Drosophila</i> as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for <i>Doa</i>, <i>Rm62</i>, <i>mub</i>, <i>mbl</i>, <i>sbr</i>, and <i>clu</i>. Knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. <i>Drosophila</i> is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered. |
| first_indexed | 2024-03-10T06:40:29Z |
| format | Article |
| id | doaj.art-7445afa34a124946b4bbedc2a74c7185 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T06:40:29Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-7445afa34a124946b4bbedc2a74c71852023-11-22T17:44:43ZengMDPI AGCells2073-44092021-09-011010250510.3390/cells10102505A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight MuscleShao-Yen Kao0Elena Nikonova1Sabrina Chaabane2Albiona Sabani3Alexandra Martitz4Anja Wittner5Jakob Heemken6Tobias Straub7Maria L. Spletter8Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyBiomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyBiomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyDepartment of Biology, University of Wisconsin at Madison, 1117 W. Johnson St., Madison, WI 53706, USAMolecular Nutrition Medicine, Else Kröner-Fresenius Center, Technical University of Munich, 85354 Freising, GermanyBiomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyBiomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyBiomedical Center, Bioinformatics Core Facility, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyBiomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Martinsried-Planegg, GermanyThe proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing, including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently, only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here, we demonstrate the utility of <i>Drosophila</i> as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for <i>Doa</i>, <i>Rm62</i>, <i>mub</i>, <i>mbl</i>, <i>sbr</i>, and <i>clu</i>. Knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. <i>Drosophila</i> is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered.https://www.mdpi.com/2073-4409/10/10/2505RNA binding proteinsSF1Hrb87FBru1<i>Drosophila</i>flight muscle |
| spellingShingle | Shao-Yen Kao Elena Nikonova Sabrina Chaabane Albiona Sabani Alexandra Martitz Anja Wittner Jakob Heemken Tobias Straub Maria L. Spletter A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle Cells RNA binding proteins SF1 Hrb87F Bru1 <i>Drosophila</i> flight muscle |
| title | A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle |
| title_full | A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle |
| title_fullStr | A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle |
| title_full_unstemmed | A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle |
| title_short | A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in <i>Drosophila</i> Flight Muscle |
| title_sort | candidate rnai screen reveals diverse rna binding protein phenotypes in i drosophila i flight muscle |
| topic | RNA binding proteins SF1 Hrb87F Bru1 <i>Drosophila</i> flight muscle |
| url | https://www.mdpi.com/2073-4409/10/10/2505 |
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