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Recinos Y, Bao S, Wang X, Phillips BL, Yeh YT, Weyn-Vanhentenryck SM, Swanson MS, Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain. CELL GENOMICS 2024; 4:100563. [PMID: 38772368 PMCID: PMC11228892 DOI: 10.1016/j.xgen.2024.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/22/2024] [Accepted: 04/23/2024] [Indexed: 05/23/2024]
Abstract
Divergence of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is widespread in mammals, including primates, but the underlying mechanisms and functional impact are poorly understood. Here, we modeled cassette exon inclusion in primate brains as a quantitative trait and identified 1,170 (∼3%) exons with lineage-specific splicing shifts under stabilizing selection. Among them, microtubule-associated protein tau (MAPT) exons 2 and 10 underwent anticorrelated, two-step evolutionary shifts in the catarrhine and hominoid lineages, leading to their present inclusion levels in humans. The developmental-stage-specific divergence of exon 10 splicing, whose dysregulation can cause frontotemporal lobar degeneration (FTLD), is mediated by divergent distal intronic MBNL-binding sites. Competitive binding of these sites by CRISPR-dCas13d/gRNAs effectively reduces exon 10 inclusion, potentially providing a therapeutically compatible approach to modulate tau isoform expression. Our data suggest adaptation of MAPT function and, more generally, a role for AS in the evolutionary expansion of the primate brain.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Brittany L Phillips
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, FL 32610, USA; Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Burgardt R, Lambert D, Heuwieser C, Sack M, Wagner G, Weinberg Z, Wachter A. Positioning of pyrimidine motifs around cassette exons defines their PTB-dependent splicing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2202-2218. [PMID: 38578875 DOI: 10.1111/tpj.16739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Alternative splicing (AS) is a complex process that generates transcript variants from a single pre-mRNA and is involved in numerous biological functions. Many RNA-binding proteins are known to regulate AS; however, little is known about the underlying mechanisms, especially outside the mammalian clade. Here, we show that polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana regulate AS of cassette exons via pyrimidine (Py)-rich motifs close to the alternative splice sites. Mutational studies on three PTB-dependent cassette exon events revealed that only some of the Py motifs in this region are critical for AS. Moreover, in vitro binding of PTBs did not reflect a motif's impact on AS in vivo. Our mutational studies and bioinformatic investigation of all known PTB-regulated cassette exons from A. thaliana and human suggested that the binding position of PTBs relative to a cassette exon defines whether its inclusion or skipping is induced. Accordingly, exon skipping is associated with a higher frequency of Py stretches within the cassette exon, and in human also upstream of it, whereas exon inclusion is characterized by increased Py motif occurrence downstream of said exon. Enrichment of Py motifs downstream of PTB-activated 5' splice sites is also seen for PTB-dependent intron removal and alternative 5' splice site events from A. thaliana, suggesting this is a common step of exon definition. In conclusion, the position-dependent AS regulatory mechanism by PTB homologs has been conserved during the separate evolution of plants and mammals, while other critical features, in particular intron length, have considerably changed.
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Affiliation(s)
- Rica Burgardt
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Dorothee Lambert
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Christina Heuwieser
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Maximilian Sack
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Gabriele Wagner
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
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Wan X, Shi W, Ma L, Wang L, Zheng R, He J, Wang Y, Li X, Zha X, Wang J, Xu L. A 3'-pre-tRNA-derived small RNA tRF-1-Ser regulated by 25(OH)D promotes proliferation and stemness by inhibiting the function of MBNL1 in breast cancer. Clin Transl Med 2024; 14:e1681. [PMID: 38725048 PMCID: PMC11082093 DOI: 10.1002/ctm2.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We explored the potential novel anticancer mechanisms of 25-hydroxyvitamin D (25(OH)D), a vitamin D metabolite with antitumour effects in breast cancer. It is stable in serum and is used to assess vitamin D levels in clinical practice. Transfer RNA-derived small RNAs are small noncoding RNAs that generate various distinct biological functions, but more research is needed on their role in breast cancer. METHODS Small RNA microarrays were used to explore the novel regulatory mechanism of 25(OH)D. High-throughput RNA-sequencing technology was used to detect transcriptome changes after 25(OH)D treatment and tRF-1-Ser knockdown. RNA pull-down and high-performance liquid chromatography-mass spectrometry/mass spectrometry were used to explore the proteins bound to tRF-1-Ser. In vitro and in vivo functional experiments were conducted to assess the influence of 25(OH)D and tRF-1-Ser on breast cancer. Semi-quantitative PCR was performed to detect alternative splicing events. Western blot assay and qPCR were used to assess protein and mRNA expression. RESULTS The expression of tRF-1-Ser is negatively regulated by 25(OH)D. In our breast cancer (BRCA) clinical samples, we found that the expression of tRF-1-Ser was higher in cancer tissues than in paired normal tissues, and was significantly associated with tumour invasion. Moreover, tRF-1-Ser inhibits the function of MBNL1 by hindering its nuclear translocation. Functional experiments and transcriptome data revealed that the downregulation of tRF-1-Ser plays a vital role in the anticancer effect of 25(OH)D. CONCLUSIONS In brief, our research revealed a novel anticancer mechanism of 25(OH)D, unveiled the vital function of tRF-1-Ser in BRCA progression, and suggested that tRF-1-Ser could emerge as a new therapeutic target for BRCA.
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Affiliation(s)
- Xinyu Wan
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Wenjie Shi
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingjun Ma
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lexin Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ran Zheng
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinzhi He
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ye Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xuan Li
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaoming Zha
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jue Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Xu
- Department of NutritionThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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Nowzari ZR, Hale M, Ellis J, Biaesch S, Vangaveti S, Reddy K, Chen AA, Berglund JA. Mutation of two intronic nucleotides alters RNA structure and dynamics inhibiting MBNL1 and RBFOX1 regulated splicing of the Insulin Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574689. [PMID: 38260517 PMCID: PMC10802415 DOI: 10.1101/2024.01.08.574689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) of Exon 11 of the Insulin Receptor ( INSR ) is highly regulated and disrupted in several human disorders. To better understand INSR exon 11 AS regulation, splicing activity of an INSR exon 11 minigene reporter was measured across a gradient of the AS regulator muscleblind-like 1 protein (MBNL1). The RNA-binding protein Fox-1 (RBFOX1) was added to determine its impact on MBNL1-regulated splicing. The role of the RBFOX1 UGCAUG binding site within intron 11 was assessed across the MBNL1 gradient. Mutating the UGCAUG motif inhibited RBFOX1 regulation of exon 11 and had the unexpected effect of reducing MBNL1 regulation of this exon. Molecular dynamics simulations showed that exon 11 and the adjacent RNA adopts a dynamically stable conformation. Mutation of the RBFOX1 binding site altered RNA structure and dynamics, while a mutation that created an optimal MBNL1 binding site at the RBFOX1 site shifted the RNA back to wild type. An antisense oligonucleotide (ASO) was used to confirm the structure in this region of the pre-mRNA. This example of intronic mutations shifting pre-mRNA structure and dynamics to modulate splicing suggests RNA structure and dynamics should be taken into consideration for AS regulation and therapeutic interventions targeting pre-mRNA.
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González-Martínez I, Cerro-Herreros E, Moreno N, García-Rey A, Espinosa-Espinosa J, Carrascosa-Sàez M, Piqueras-Losilla D, Arzumanov A, Seoane-Miraz D, Jad Y, Raz R, Wood MJ, Varela MA, Llamusí B, Artero R. Peptide-conjugated antimiRs improve myotonic dystrophy type 1 phenotypes by promoting endogenous MBNL1 expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102024. [PMID: 37744174 PMCID: PMC10514136 DOI: 10.1016/j.omtn.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a rare neuromuscular disease caused by a CTG repeat expansion in the DMPK gene that generates toxic RNA with a myriad of downstream alterations in RNA metabolism. A key consequence is the sequestration of alternative splicing regulatory proteins MBNL1/2 by expanded transcripts in the affected tissues. MBNL1/2 depletion interferes with a developmental alternative splicing switch that causes the expression of fetal isoforms in adults. Boosting the endogenous expression of MBNL proteins by inhibiting the natural translational repressors miR-23b and miR-218 has previously been shown to be a promising therapeutic approach. We designed antimiRs against both miRNAs with a phosphorodiamidate morpholino oligonucleotide (PMO) chemistry conjugated to cell-penetrating peptides (CPPs) to improve delivery to affected tissues. In DM1 cells, CPP-PMOs significantly increased MBNL1 levels. In some candidates, this was achieved using concentrations less than two orders of magnitude below the median toxic concentration, with up to 5.38-fold better therapeutic window than previous antagomiRs. In HSALR mice, intravenous injections of CPP-PMOs improve molecular, histopathological, and functional phenotypes, without signs of toxicity. Our findings place CPP-PMOs as promising antimiR candidates to overcome the treatment delivery challenge in DM1 therapy.
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Affiliation(s)
- Irene González-Martínez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Estefanía Cerro-Herreros
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Nerea Moreno
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Andrea García-Rey
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
- Group of Emerging and Neglected Diseases, Ecoepidemiology and Biodiversity, Health Sciences Faculty, Universidad Internacional SEK, Quito 170521, Ecuador
| | - Marc Carrascosa-Sàez
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Diego Piqueras-Losilla
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Andrey Arzumanov
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - David Seoane-Miraz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Yahya Jad
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Richard Raz
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Matthew J. Wood
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Miguel A. Varela
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine (IDRM), University of Oxford, Roosevelt Dr, Oxford OX3 7TY, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
| | - Beatriz Llamusí
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Translational Genomics Group, INCLIVA Biomedical Research Institute, Avenue Menéndez Pelayo 4 acc, 46010 Valencia, Spain
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Verbeeren J, Teixeira J, Garcia SMDA. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism. PLoS Genet 2023; 19:e1011109. [PMID: 38134228 PMCID: PMC10773944 DOI: 10.1371/journal.pgen.1011109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/08/2024] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The Muscleblind-like (MBNL) family is a highly conserved set of RNA-binding proteins (RBPs) that regulate RNA metabolism during the differentiation of various animal tissues. Functional insufficiency of MBNL affects muscle and central nervous system development, and contributes to the myotonic dystrophies (DM), a set of incurable multisystemic disorders. Studies on the regulation of MBNL genes are essential to provide insight into the gene regulatory networks controlled by MBNL proteins and to understand how dysregulation within these networks causes disease. In this study, we demonstrate the evolutionary conservation of an autoregulatory mechanism that governs the function of MBNL proteins by generating two distinct protein isoform types through alternative splicing. Our aim was to further our understanding of the regulatory principles that underlie this conserved feedback loop in a whole-organismal context, and to address the biological significance of the respective isoforms. Using an alternative splicing reporter, our studies show that, during development of the Caenorhabditis elegans central nervous system, the orthologous mbl-1 gene shifts production from long protein isoforms that localize to the nucleus to short isoforms that also localize to the cytoplasm. Using isoform-specific CRISPR/Cas9-generated strains, we showed that expression of short MBL-1 protein isoforms is required for healthy neuromuscular function and neurodevelopment, while expression of long MBL-1 protein isoforms is dispensable, emphasizing a key role for cytoplasmic functionalities of the MBL-1 protein. Furthermore, RNA-seq and lifespan analyses indicated that short MBL-1 isoforms are crucial regulators of miRNA expression and, in consequence, required for normal lifespan. In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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Nutter CA, Kidd BM, Carter HA, Hamel JI, Mackie PM, Kumbkarni N, Davenport ML, Tuyn DM, Gopinath A, Creigh PD, Sznajder ŁJ, Wang ET, Ranum LPW, Khoshbouei H, Day JW, Sampson JB, Prokop S, Swanson MS. Choroid plexus mis-splicing and altered cerebrospinal fluid composition in myotonic dystrophy type 1. Brain 2023; 146:4217-4232. [PMID: 37143315 PMCID: PMC10545633 DOI: 10.1093/brain/awad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
Myotonic dystrophy type 1 is a dominantly inherited multisystemic disease caused by CTG tandem repeat expansions in the DMPK 3' untranslated region. These expanded repeats are transcribed and produce toxic CUG RNAs that sequester and inhibit activities of the MBNL family of developmental RNA processing factors. Although myotonic dystrophy is classified as a muscular dystrophy, the brain is also severely affected by an unusual cohort of symptoms, including hypersomnia, executive dysfunction, as well as early onsets of tau/MAPT pathology and cerebral atrophy. To address the molecular and cellular events that lead to these pathological outcomes, we recently generated a mouse Dmpk CTG expansion knock-in model and identified choroid plexus epithelial cells as particularly affected by the expression of toxic CUG expansion RNAs. To determine if toxic CUG RNAs perturb choroid plexus functions, alternative splicing analysis was performed on lateral and hindbrain choroid plexi from Dmpk CTG knock-in mice. Choroid plexus transcriptome-wide changes were evaluated in Mbnl2 knockout mice, a developmental-onset model of myotonic dystrophy brain dysfunction. To determine if transcriptome changes also occurred in the human disease, we obtained post-mortem choroid plexus for RNA-seq from neurologically unaffected (two females, three males; ages 50-70 years) and myotonic dystrophy type 1 (one female, three males; ages 50-70 years) donors. To test that choroid plexus transcriptome alterations resulted in altered CSF composition, we obtained CSF via lumbar puncture from patients with myotonic dystrophy type 1 (five females, five males; ages 35-55 years) and non-myotonic dystrophy patients (three females, four males; ages 26-51 years), and western blot and osmolarity analyses were used to test CSF alterations predicted by choroid plexus transcriptome analysis. We determined that CUG RNA induced toxicity was more robust in the lateral choroid plexus of Dmpk CTG knock-in mice due to comparatively higher Dmpk and lower Mbnl RNA levels. Impaired transitions to adult splicing patterns during choroid plexus development were identified in Mbnl2 knockout mice, including mis-splicing previously found in Dmpk CTG knock-in mice. Whole transcriptome analysis of myotonic dystrophy type 1 choroid plexus revealed disease-associated RNA expression and mis-splicing events. Based on these RNA changes, predicted alterations in ion homeostasis, secretory output and CSF composition were confirmed by analysis of myotonic dystrophy type 1 CSF. Our results implicate choroid plexus spliceopathy and concomitant alterations in CSF homeostasis as an unappreciated contributor to myotonic dystrophy type 1 CNS pathogenesis.
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Affiliation(s)
- Curtis A Nutter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Benjamin M Kidd
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Helmut A Carter
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Johanna I Hamel
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Philip M Mackie
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nayha Kumbkarni
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Mackenzie L Davenport
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Dana M Tuyn
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Adithya Gopinath
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Peter D Creigh
- Department of Neurology, University of Rochester, Rochester, NY 14642, USA
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Laura P W Ranum
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, McKnight Brain Institute and the Fixel Institute for Neurological Diseases, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Habibeh Khoshbouei
- Department of Neuroscience, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John W Day
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jacinda B Sampson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Stefan Prokop
- Department of Pathology, Immunology, and Laboratory Medicine, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute and the Fixel Institute for Neurological Diseases, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
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8
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Sznajder L, Khan M, Tadross M, Ciesiołka A, Nutter C, Taylor K, Pearson C, Sobczak K, Lewis M, Swanson M, Yuen R. Autistic traits in myotonic dystrophy type 1 due to MBNL inhibition and RNA mis-splicing. RESEARCH SQUARE 2023:rs.3.rs-3221704. [PMID: 37645891 PMCID: PMC10462192 DOI: 10.21203/rs.3.rs-3221704/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tandem repeat expansions are enriched in autism spectrum disorder, including CTG expansion in the DMPK gene that underlines myotonic muscular dystrophy type 1. Although the clinical connection of autism to myotonic dystrophy is corroborated, the molecular links remained unknown. Here, we show a mechanistic path of autism via repeat expansion in myotonic dystrophy. We found that inhibition of muscleblind-like (MBNL) splicing factors by expanded CUG RNAs alerts the splicing of autism-risk genes during brain development especially a class of autism-relevant microexons. To provide in vivo evidence that the CTG expansion and MBNL inhibition axis leads to the presentation of autistic traits, we demonstrate that CTG expansion and MBNL-null mouse models recapitulate autism-relevant mis-splicing profiles and demonstrate social deficits. Our findings indicate that DMPK CTG expansion-associated autism arises from developmental mis-splicing. Understanding this pathomechanistic connection provides an opportunity for greater in-depth investigations of mechanistic threads in autism.
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Giménez-Bejarano A, Alegre-Cortés E, Yakhine-Diop SMS, Gómez-Suaga P, Fuentes JM. Mitochondrial Dysfunction in Repeat Expansion Diseases. Antioxidants (Basel) 2023; 12:1593. [PMID: 37627588 PMCID: PMC10451345 DOI: 10.3390/antiox12081593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Repeat expansion diseases are a group of neuromuscular and neurodegenerative disorders characterized by expansions of several successive repeated DNA sequences. Currently, more than 50 repeat expansion diseases have been described. These disorders involve diverse pathogenic mechanisms, including loss-of-function mechanisms, toxicity associated with repeat RNA, or repeat-associated non-ATG (RAN) products, resulting in impairments of cellular processes and damaged organelles. Mitochondria, double membrane organelles, play a crucial role in cell energy production, metabolic processes, calcium regulation, redox balance, and apoptosis regulation. Its dysfunction has been implicated in the pathogenesis of repeat expansion diseases. In this review, we provide an overview of the signaling pathways or proteins involved in mitochondrial functioning described in these disorders. The focus of this review will be on the analysis of published data related to three representative repeat expansion diseases: Huntington's disease, C9orf72-frontotemporal dementia/amyotrophic lateral sclerosis, and myotonic dystrophy type 1. We will discuss the common effects observed in all three repeat expansion disorders and their differences. Additionally, we will address the current gaps in knowledge and propose possible new lines of research. Importantly, this group of disorders exhibit alterations in mitochondrial dynamics and biogenesis, with specific proteins involved in these processes having been identified. Understanding the underlying mechanisms of mitochondrial alterations in these disorders can potentially lead to the development of neuroprotective strategies.
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Affiliation(s)
- Alberto Giménez-Bejarano
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Eva Alegre-Cortés
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Sokhna M. S. Yakhine-Diop
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - Patricia Gómez-Suaga
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
| | - José M. Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Cáceres, Spain; (A.G.-B.); (E.A.-C.); (S.M.S.Y.-D.); (P.G.-S.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salus Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto de Investigación Biosanitaria de Extremadura (INUBE), 10003 Cáceres, Spain
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10
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Davey EE, Légaré C, Planco L, Shaughnessy S, Lennon CD, Roussel MP, Shorrock HK, Hung M, Cleary JD, Duchesne E, Berglund JA. Individual transcriptomic response to strength training for patients with myotonic dystrophy type 1. JCI Insight 2023; 8:e163856. [PMID: 37318869 PMCID: PMC10443797 DOI: 10.1172/jci.insight.163856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 06/13/2023] [Indexed: 06/17/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1), the most common form of adult-onset muscular dystrophy, is caused by a CTG expansion resulting in significant transcriptomic dysregulation that leads to muscle weakness and wasting. While strength training is clinically beneficial in DM1, molecular effects had not been studied. To determine whether training rescued transcriptomic defects, RNA-Seq was performed on vastus lateralis samples from 9 male patients with DM1 before and after a 12-week strength-training program and 6 male controls who did not undergo training. Differential gene expression and alternative splicing analysis were correlated with the one-repetition maximum strength evaluation method (leg extension, leg press, hip abduction, and squat). While training program-induced improvements in splicing were similar among most individuals, rescued splicing events varied considerably between individuals. Gene expression improvements were highly varied between individuals, and the percentage of differentially expressed genes rescued after training were strongly correlated with strength improvements. Evaluating transcriptome changes individually revealed responses to the training not evident from grouped analysis, likely due to disease heterogeneity and individual exercise response differences. Our analyses indicate that transcriptomic changes are associated with clinical outcomes in patients with DM1 undergoing training and that these changes are often specific to the individual and should be analyzed accordingly.
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Affiliation(s)
- Emily E. Davey
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Cécilia Légaré
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- Department of Health Sciences, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
- Groupe de Recherche Interdisciplinaire sur les Maladies Neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Quebec, Canada
- Centre de recherche Charles-Le Moyne Saguenay–Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Faculté de médecine et des sciences de la santé de l’Université de Sherbrooke, Site Saguenay, Saguenay, Quebec, Canada
| | - Lori Planco
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Sharon Shaughnessy
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Claudia D. Lennon
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Marie-Pier Roussel
- Groupe de Recherche Interdisciplinaire sur les Maladies Neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Quebec, Canada
- Centre de recherche Charles-Le Moyne Saguenay–Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Faculté de médecine et des sciences de la santé de l’Université de Sherbrooke, Site Saguenay, Saguenay, Quebec, Canada
- Department of Basic Sciences, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Hannah K. Shorrock
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Man Hung
- Department of Orthopaedic Surgery Operations, School of Medicine, University of Utah, Salt Lake City, Utah, USA
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, Utah, USA
| | - John Douglas Cleary
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
| | - Elise Duchesne
- Department of Health Sciences, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
- Groupe de Recherche Interdisciplinaire sur les Maladies Neuromusculaires (GRIMN), Centre intégré universitaire de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Quebec, Canada
- Centre de recherche Charles-Le Moyne Saguenay–Lac-Saint-Jean sur les innovations en santé (CR-CSIS), Faculté de médecine et des sciences de la santé de l’Université de Sherbrooke, Site Saguenay, Saguenay, Quebec, Canada
| | - J. Andrew Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, New York, USA
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11
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Porquet F, Weidong L, Jehasse K, Gazon H, Kondili M, Blacher S, Massotte L, Di Valentin E, Furling D, Gillet NA, Klein AF, Seutin V, Willems L. Specific DMPK-promoter targeting by CRISPRi reverses myotonic dystrophy type 1-associated defects in patient muscle cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:857-871. [PMID: 37273786 PMCID: PMC10238591 DOI: 10.1016/j.omtn.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 06/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a neuromuscular disease that originates from an expansion of CTG microsatellites in the 3' untranslated region of the DMPK gene, thus leading to the expression of transcripts containing expanded CUG repeats (CUGexp). The pathophysiology is explained by a toxic RNA gain of function where CUGexp RNAs form nuclear aggregates that sequester and alter the function of MBNL splicing factors, triggering splicing misregulation linked to the DM1 symptoms. There is currently no cure for DM1, and most therapeutic strategies aim at eliminating CUGexp-DMPK transcripts. Here, we investigate a DMPK-promoter silencing strategy using CRISPR interference as a new alternative approach. Different sgRNAs targeting the DMPK promoter are evaluated in DM1 patient muscle cells. The most effective guides allowed us to reduce the level of DMPK transcripts and CUGexp-RNA aggregates up to 80%. The CUGexp-DMPK repression corrects the overall transcriptome, including spliceopathy, and reverses a physiological parameter in DM1 muscle cells. Its action is specific and restricted to the DMPK gene, as confirmed by genome-wide expression analysis. Altogether, our findings highlight DMPK-promoter silencing by CRISPRi as a promising therapeutic approach for DM1.
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Affiliation(s)
- Florent Porquet
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Lin Weidong
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Kévin Jehasse
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Hélène Gazon
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Maria Kondili
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Silvia Blacher
- Laboratory of Biology of Tumor and Development, GIGA-Cancer, ULiège, 4000 Liège, Belgium
| | - Laurent Massotte
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | | | - Denis Furling
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Nicolas Albert Gillet
- Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, 5000 Namur, Belgium
| | - Arnaud François Klein
- Sorbonne Université, INSERM, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Vincent Seutin
- Laboratory of Neurophysiology, GIGA-Neurosciences, ULiège, 4000 Liège, Belgium
| | - Luc Willems
- Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, ULiège, 4000 Liège, Belgium
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12
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Ellis JA, Hale MA, Cleary JD, Wang E, Andrew Berglund J. Alternative splicing outcomes across an RNA-binding protein concentration gradient. J Mol Biol 2023:168156. [PMID: 37230319 DOI: 10.1016/j.jmb.2023.168156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered a MBNL1 and RBFOX1 inducible HEK-293 cell line. Modest induction of exogenous RBFOX1 in this cell line modulated MBNL1-dependent AS outcomes in 3 skipped exon events, despite significant levels of endogenous RBFOX1 and RBFOX2. Due to background RBFOX levels, we conducted a focused analysis of dose-dependent MBNL1 skipped exon AS outcomes and generated transcriptome wide dose-response curves. Analysis of this data demonstrates that MBNL1-regulated exclusion events may require higher concentrations of MBNL1 protein to properly regulate AS outcomes compared to inclusion events and that multiple arrangements of YGCY motifs can produce similar splicing outcomes. These results suggest that rather than a simple relationship between the organization of RBP binding sites and a specific splicing outcome, that complex interaction networks govern both AS inclusion and exclusion events across a RBP gradient.
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Affiliation(s)
- Joseph A Ellis
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Melissa A Hale
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - John D Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Eric Wang
- Department of Microbiology and Molecular Genetics & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - J Andrew Berglund
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; RNA Institute, State University of New York at Albany, LSRB-2033, 1400 Washington Avenue, Albany, New York, 12222.
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13
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Cognate RNA-Binding Modes by the Alternative-Splicing Regulator MBNL1 Inferred from Molecular Dynamics. Int J Mol Sci 2022; 23:ijms232416147. [PMID: 36555788 PMCID: PMC9780971 DOI: 10.3390/ijms232416147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The muscleblind-like protein family (MBNL) plays a prominent role in the regulation of alternative splicing. Consequently, the loss of MBNL function resulting from sequestration by RNA hairpins triggers the development of a neuromuscular disease called myotonic dystrophy (DM). Despite the sequence and structural similarities between the four zinc-finger domains that form MBNL1, recent studies have revealed that the four binding domains have differentiated splicing activity. The dynamic behaviors of MBNL1 ZnFs were simulated using conventional molecular dynamics (cMD) and steered molecular dynamics (sMD) simulations of a structural model of MBNL1 protein to provide insights into the binding selectivity of the four zinc-finger (ZnF) domains toward the GpC steps in YGCY RNA sequence. In accordance with previous studies, our results suggest that both global and local residue fluctuations on each domain have great impacts on triggering alternative splicing, indicating that local motions in RNA-binding domains could modulate their affinity and specificity. In addition, all four ZnF domains provide a distinct RNA-binding environment in terms of structural sampling and mobility that may be involved in the differentiated MBNL1 splicing events reported in the literature.
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14
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The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians. PLoS Biol 2022; 20:e3001615. [PMID: 35476669 PMCID: PMC9084524 DOI: 10.1371/journal.pbio.3001615] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 05/09/2022] [Accepted: 03/29/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process of evolutionary specialization in eutherian mammals resulting in the emergence of a novel placental function for the gene. Mbnl3 belongs to a family of RNA-binding proteins whose members regulate multiple aspects of RNA metabolism. We find that, in eutherians, while both Mbnl3 and its paralog Mbnl2 are strongly expressed in placenta, Mbnl3 expression has been lost from nonplacental tissues in association with the evolution of a novel promoter. Moreover, Mbnl3 has undergone accelerated protein sequence evolution leading to changes in its RNA-binding specificities and cellular localization. While Mbnl2 and Mbnl3 share partially redundant roles in regulating alternative splicing, polyadenylation site usage and, in turn, placenta maturation, Mbnl3 has also acquired novel biological functions. Specifically, Mbnl3 knockout (M3KO) alone results in increased placental growth associated with higher Myc expression. Furthermore, Mbnl3 loss increases fetal resource allocation during limiting conditions, suggesting that location of Mbnl3 on the X chromosome has led to its role in limiting placental growth, favoring the maternal side of the parental genetic conflict.
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15
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Pamudurti NR, Patop IL, Krishnamoorthy A, Bartok O, Maya R, Lerner N, Ashwall-Fluss R, Konakondla JVV, Beatus T, Kadener S. circMbl functions in cis and in trans to regulate gene expression and physiology in a tissue-specific fashion. Cell Rep 2022; 39:110740. [PMID: 35476987 PMCID: PMC9352392 DOI: 10.1016/j.celrep.2022.110740] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 11/03/2022] Open
Abstract
Muscleblind (mbl) is an essential muscle and neuronal splicing regulator. Mbl hosts multiple circular RNAs (circRNAs), including circMbl, which is conserved from flies to humans. Here, we show that mbl-derived circRNAs are key regulators of MBL by cis- and trans-acting mechanisms. By generating fly lines to specifically modulate the levels of all mbl RNA isoforms, including circMbl, we demonstrate that the two major mbl protein isoforms, MBL-O/P and MBL-C, buffer their own levels by producing different types of circRNA isoforms in the eye and fly brain, respectively. Moreover, we show that circMbl has unique functions in trans, as knockdown of circMbl results in specific morphological and physiological phenotypes. In addition, depletion of MBL-C or circMbl results in opposite behavioral phenotypes, showing that they also regulate each other in trans. Together, our results illuminate key aspects of mbl regulation and uncover cis and trans functions of circMbl in vivo.
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Affiliation(s)
| | | | | | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Roni Maya
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Noam Lerner
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Reut Ashwall-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Tsevi Beatus
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; Department of Neurobiology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sebastian Kadener
- Biology Department, Brandeis University, Waltham, MA 02454, USA; Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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16
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van Nijnatten J, Brandsma CA, Steiling K, Hiemstra PS, Timens W, van den Berge M, Faiz A. High miR203a-3p and miR-375 expression in the airways of smokers with and without COPD. Sci Rep 2022; 12:5610. [PMID: 35379844 PMCID: PMC8980043 DOI: 10.1038/s41598-022-09093-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Smoking is a leading cause of chronic obstructive pulmonary disease (COPD). It is known to have a significant impact on gene expression and (inflammatory) cell populations in the airways involved in COPD pathogenesis. In this study, we investigated the impact of smoking on the expression of miRNAs in healthy and COPD individuals. We aimed to elucidate the overall smoking-induced miRNA changes and those specific to COPD. In addition, we investigated the downstream effects on regulatory gene expression and the correlation to cellular composition. We performed a genome-wide miRNA expression analysis on a dataset of 40 current- and 22 ex-smoking COPD patients and a dataset of 35 current- and 38 non-smoking respiratory healthy controls and validated the results in an independent dataset. miRNA expression was then correlated with mRNA expression in the same patients to assess potential regulatory effects of the miRNAs. Finally, cellular deconvolution analysis was used to relate miRNAs changes to specific cell populations. Current smoking was associated with increased expression of three miRNAs in the COPD patients and 18 miRNAs in the asymptomatic smokers compared to respiratory healthy controls. In comparison, four miRNAs were lower expressed with current smoking in asymptomatic controls. Two of the three smoking-related miRNAs in COPD, miR-203a-3p and miR-375, were also higher expressed with current smoking in COPD patients and the asymptomatic controls. The other smoking-related miRNA in COPD patients, i.e. miR-31-3p, was not present in the respiratory healthy control dataset. miRNA-mRNA correlations demonstrated that miR-203a-3p, miR-375 and also miR-31-3p expression were negatively associated with genes involved in pro-inflammatory pathways and positively associated with genes involved in the xenobiotic pathway. Cellular deconvolution showed that higher levels of miR-203a-3p were associated with higher proportions of proliferating-basal cells and secretory (club and goblet) cells and lower levels of fibroblasts, luminal macrophages, endothelial cells, B-cells, amongst other cell types. MiR-375 expression was associated with lower levels of secretory cells, ionocytes and submucosal cells, but higher levels of endothelial cells, smooth muscle cells, and mast cells, amongst other cell types. In conclusion, we identified two smoking-induced miRNAs (miR-375 and miR-203a-3p) that play a role in regulating inflammation and detoxification pathways, regardless of the presence or absence of COPD. Additionally, in patients with COPD, we identified miR-31-3p as a miRNA induced by smoking. Our identified miRNAs should be studied further to unravel which smoking-induced inflammatory mechanisms are reactive and which are involved in COPD pathogenesis.
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17
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Degener MJF, van Cruchten RTP, Otero BA, Wang E, Wansink DG, ‘t Hoen PAC. A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients. NAR Genom Bioinform 2022; 4:lqac016. [PMID: 35274098 PMCID: PMC8903011 DOI: 10.1093/nargab/lqac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/28/2022] [Accepted: 02/13/2022] [Indexed: 11/14/2022] Open
Abstract
In patients with myotonic dystrophy type 1 (DM1), dysregulation of RNA-binding proteins like MBNL and CELF1 leads to alternative splicing of exons and is thought to induce a return to fetal splicing patterns in adult tissues, including the central nervous system (CNS). To comprehensively evaluate this, we created an atlas of developmentally regulated splicing patterns in the frontal cortex of healthy individuals and DM1 patients, by combining RNA-seq data from BrainSpan, GTEx and DM1 patients. Thirty-four splice events displayed an inclusion pattern in DM1 patients that is typical for the fetal situation in healthy individuals. The regulation of DM1-relevant splicing patterns could partly be explained by changes in mRNA expression of the splice regulators MBNL1, MBNL2 and CELF1. On the contrary, interindividual differences in splicing patterns between healthy adults could not be explained by differential expression of these splice regulators. Our findings lend transcriptome-wide evidence to the previously noted shift to fetal splicing patterns in the adult DM1 brain as a consequence of an imbalance in antagonistic MBNL and CELF1 activities. Our atlas serves as a solid foundation for further study and understanding of the cognitive phenotype in patients.
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Affiliation(s)
- Max J F Degener
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Remco T P van Cruchten
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Brittney A Otero
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, FL 32610-0266 Gainesville, FL, USA
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, FL 32610-0266 Gainesville, FL, USA
| | - Derick G Wansink
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Peter A C ‘t Hoen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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18
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Wnt signaling and Hedgehog expression in basal cell carcinoma. EUROPEAN JOURNAL OF PLASTIC SURGERY 2021. [DOI: 10.1007/s00238-021-01920-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Hinman MN, Richardson JI, Sockol RA, Aronson ED, Stednitz SJ, Murray KN, Berglund JA, Guillemin K. Zebrafish mbnl mutants model physical and molecular phenotypes of myotonic dystrophy. Dis Model Mech 2021; 14:dmm045773. [PMID: 34125183 PMCID: PMC8246264 DOI: 10.1242/dmm.045773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
The muscleblind RNA-binding proteins (MBNL1, MBNL2 and MBNL3) are highly conserved across vertebrates and are important regulators of RNA alternative splicing. Loss of MBNL protein function through sequestration by CUG or CCUG RNA repeats is largely responsible for the phenotypes of the human genetic disorder myotonic dystrophy (DM). We generated the first stable zebrafish (Danio rerio) models of DM-associated MBNL loss of function through mutation of the three zebrafish mbnl genes. In contrast to mouse models, zebrafish double and triple homozygous mbnl mutants were viable to adulthood. Zebrafish mbnl mutants displayed disease-relevant physical phenotypes including decreased body size and impaired movement. They also exhibited widespread alternative splicing changes, including the misregulation of many DM-relevant exons. Physical and molecular phenotypes were more severe in compound mbnl mutants than in single mbnl mutants, suggesting partially redundant functions of Mbnl proteins. The high fecundity and larval optical transparency of this complete series of zebrafish mbnl mutants will make them useful for studying DM-related phenotypes and how individual Mbnl proteins contribute to them, and for testing potential therapeutics. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Melissa N. Hinman
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jared I. Richardson
- RNA Institute, State University of New York at Albany, Albany, NY 12222, USA
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, University of Florida, Gainesville, FL 32611, USA
| | - Rose A. Sockol
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eliza D. Aronson
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Sarah J. Stednitz
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Katrina N. Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403, USA
| | - J. Andrew Berglund
- RNA Institute, State University of New York at Albany, Albany, NY 12222, USA
- Department of Biochemistry and Molecular Biology, Center for NeuroGenetics, University of Florida, Gainesville, FL 32611, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
- Humans and the Microbiome Program, CIFAR, Toronto, ON M5G 1M1, Canada
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20
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Tanner MK, Tang Z, Thornton CA. Targeted splice sequencing reveals RNA toxicity and therapeutic response in myotonic dystrophy. Nucleic Acids Res 2021; 49:2240-2254. [PMID: 33503262 PMCID: PMC7913682 DOI: 10.1093/nar/gkab022] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
Biomarker-driven trials hold promise for therapeutic development in chronic diseases, such as muscular dystrophy. Myotonic dystrophy type 1 (DM1) involves RNA toxicity, where transcripts containing expanded CUG-repeats (CUGexp) accumulate in nuclear foci and sequester splicing factors in the Muscleblind-like (Mbnl) family. Oligonucleotide therapies to mitigate RNA toxicity have emerged but reliable measures of target engagement are needed. Here we examined muscle transcriptomes in mouse models of DM1 and found that CUGexp expression or Mbnl gene deletion cause similar dysregulation of alternative splicing. We selected 35 dysregulated exons for further study by targeted RNA sequencing. Across a spectrum of mouse models, the individual splice events and a composite index derived from all events showed a graded response to decrements of Mbnl or increments of CUGexp. Antisense oligonucleotides caused prompt reduction of CUGexp RNA and parallel correction of the splicing index, followed by subsequent elimination of myotonia. These results suggest that targeted splice sequencing may provide a sensitive and reliable way to assess therapeutic impact in DM1.
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Affiliation(s)
- Matthew K Tanner
- Medical Scientist Training Program, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Zhenzhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
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21
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Weskamp K, Olwin BB, Parker R. Post-Transcriptional Regulation in Skeletal Muscle Development, Repair, and Disease. Trends Mol Med 2020; 27:469-481. [PMID: 33384234 DOI: 10.1016/j.molmed.2020.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022]
Abstract
Skeletal muscle formation is a complex process that requires tight spatiotemporal control of key myogenic factors. Emerging evidence suggests that RNA processing is crucial for the regulation of these factors, and that multiple post-transcriptional regulatory pathways work dependently and independently of one another to enable precise control of transcripts throughout muscle development and repair. Moreover, disruption of these pathways is implicated in neuromuscular disease, and the recent development of RNA-mediated therapies shows enormous promise in the treatment of these disorders. We discuss the overlapping post-transcriptional regulatory pathways that mediate muscle development, how these pathways are disrupted in neuromuscular disorders, and advances in RNA-mediated therapies that present a novel approach to the treatment of these diseases.
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Affiliation(s)
- Kaitlin Weskamp
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
| | - Bradley B Olwin
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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22
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Chen YS, Liu CW, Lin YC, Tsai CY, Yang CH, Lin JC. The SRSF3-MBNL1-Acin1 circuit constitutes an emerging axis to lessen DNA fragmentation in colorectal cancer via an alternative splicing mechanism. Neoplasia 2020; 22:702-713. [PMID: 33142236 PMCID: PMC7586066 DOI: 10.1016/j.neo.2020.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023] Open
Abstract
Altered alternative splicing (AS) events are considered pervasive causes that result in the development of carcinogenesis. Herein, we identified reprogrammed expression and splicing profiles of Muscle blind-like protein 1 (MBNL1) transcripts in tumorous tissues compared to those of adjacent normal tissues dissected from individual colorectal cancer (CRC) patients using whole-transcriptome analyses. MBNL1 transcript 8 (MBNL18) containing exons 5 and 7 was majorly generated by cancerous tissues and CRC-derived cell lines compared with those of the normal counterparts. Interplay between the exonic CA-rich element and upregulated SRSF3 facilitated the inclusion of MBNL1 exons 5 and 7, which encode a bipartite nuclear localization signal (NLS) and conformational NLS. Moreover, abundant SRSF3 interfered with the autoregulatory mechanism involved in utilization of MBNL1 exons 5 and 7, resulting in enrichment of the MBNL18 isoform in cultured CRC cell lines. Subsequently, an increase in the MBNL18 isoform drove a shift in the apoptotic chromatin condensation inducer in nucleus 1-S (Acin1-S) isoform to the Acin1-L isoform, leading to diminished DNA fragmentation in cultured CRC cells under oxidative stress. Taken together, SRSF3-MBNL1-Acin1 was demonstrated to constitute an emerging axis which is relevant to proapoptotic signatures and post-transcriptional events of CRC cells.
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Affiliation(s)
- Yi-Su Chen
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Chao-Wei Liu
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Department of Laboratory Science, National Taiwan University Hospital, Taipei, Taiwan
| | - Ying-Chin Lin
- Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chia-Ying Tsai
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ching-Hui Yang
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chun Lin
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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23
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An Overview of Alternative Splicing Defects Implicated in Myotonic Dystrophy Type I. Genes (Basel) 2020; 11:genes11091109. [PMID: 32971903 PMCID: PMC7564762 DOI: 10.3390/genes11091109] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy, caused by expansion of a CTG triplet repeat in the 3′ untranslated region (3′UTR) of the myotonic dystrophy protein kinase (DMPK) gene. The pathological CTG repeats result in protein trapping by expanded transcripts, a decreased DMPK translation and the disruption of the chromatin structure, affecting neighboring genes expression. The muscleblind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) are two families of tissue-specific regulators of developmentally programmed alternative splicing that act as antagonist regulators of several pre-mRNA targets, including troponin 2 (TNNT2), insulin receptor (INSR), chloride channel 1 (CLCN1) and MBNL2. Sequestration of MBNL proteins and up-regulation of CELF1 are key to DM1 pathology, inducing a spliceopathy that leads to a developmental remodelling of the transcriptome due to an adult-to-foetal splicing switch, which results in the loss of cell function and viability. Moreover, recent studies indicate that additional pathogenic mechanisms may also contribute to disease pathology, including a misregulation of cellular mRNA translation, localization and stability. This review focuses on the cause and effects of MBNL and CELF1 deregulation in DM1, describing the molecular mechanisms underlying alternative splicing misregulation for a deeper understanding of DM1 complexity. To contribute to this analysis, we have prepared a comprehensive list of transcript alterations involved in DM1 pathogenesis, as well as other deregulated mRNA processing pathways implications.
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24
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Park B, Han K. Discovering protein-binding RNA motifs with a generative model of RNA sequences. Comput Biol Chem 2020; 84:107171. [DOI: 10.1016/j.compbiolchem.2019.107171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/19/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023]
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25
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Abstract
BACKGROUND Interactions between protein and nucleic acid molecules are essential to a variety of cellular processes. A large amount of interaction data generated by high-throughput technologies have triggered the development of several computational methods either to predict binding sites in a sequence or to determine whether a pair of sequences interacts or not. Most of these methods treat the problem of the interaction of nucleic acids with proteins as a classification problem rather than a generation problem. RESULTS We developed a generative model for constructing single-stranded nucleic acids binding to a target protein using a long short-term memory (LSTM) neural network. Experimental results of the generative model are promising in the sense that DNA and RNA sequences generated by the model for several target proteins show high specificity and that motifs present in the generated sequences are similar to known protein-binding motifs. CONCLUSIONS Although these are preliminary results of our ongoing research, our approach can be used to generate nucleic acid sequences binding to a target protein. In particular, it will help design efficient in vitro experiments by constructing an initial pool of potential aptamers that bind to a target protein with high affinity and specificity.
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Affiliation(s)
- Jinho Im
- Department of Computer Engineering, Inha University, Incheon, 22212, South Korea
| | - Byungkyu Park
- Department of Computer Engineering, Inha University, Incheon, 22212, South Korea
| | - Kyungsook Han
- Department of Computer Engineering, Inha University, Incheon, 22212, South Korea.
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26
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Hung CS, Lin JC. Alternatively spliced MBNL1 isoforms exhibit differential influence on enhancing brown adipogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194437. [PMID: 31730826 DOI: 10.1016/j.bbagrm.2019.194437] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 01/15/2023]
Abstract
Browning of white adipocytes (WAs) (also referred as beige cells) was demonstrated to execute thermogenesis by consuming stored lipids as do brown adipocytes (BAs), and this is highly related to metabolic homeostasis. Alternative splicing (AS) constitutes a pivotal mechanism for defining cellular fates and functional specifications. Nevertheless, the impacts of AS regulation on the browning of WAs have not been comprehensively investigated. In this study, we first identified the discriminative expression and splicing profiles of the muscleblind-like 1 (MBNL1) gene in postnatal brown adipose tissues (BATs) compared to those of embryonic BATs. A shift in the MBNL1+ex 5 isoform 7 (MBNL17) to MBNL1-ex 5 isoform 1 (MBNL11) was characterized throughout BAT development or during the in vitro browning of pre-WAs, 3T3-L1 cells. The interplay between MBNL1 and the exonic CCUG motif constitutes an autoregulatory mechanism for excluding MBNL1 exon 5. The simultaneous association of RNA-binding motif protein 4a (RBM4a) with exonic and intronic CU elements collaboratively mediates the skipping of MBNL1 exon 5. Overexpressing the MBNL11 isoform exhibited a more-prominent effect than that of the MBNL17 isoform on programming its own transcripts and beige cell-related splicing events in a CCUG motif-mediated manner. In addition to splicing regulation, overexpression of the MBNL11 and MBNL17 isoforms differentially enhanced beige adipogenic signatures of 3T3-L1 cells. Our findings demonstrated that MBNL1 constitutes an emerging and autoregulatory mechanism involved in development of beige cells.
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Affiliation(s)
- Ching-Sheng Hung
- PhD Program in Medicine Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chun Lin
- PhD Program in Medicine Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
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27
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Taylor K, Sznajder LJ, Cywoniuk P, Thomas JD, Swanson MS, Sobczak K. MBNL splicing activity depends on RNA binding site structural context. Nucleic Acids Res 2019; 46:9119-9133. [PMID: 29955876 PMCID: PMC6158504 DOI: 10.1093/nar/gky565] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/16/2018] [Indexed: 02/02/2023] Open
Abstract
Muscleblind-like (MBNL) proteins are conserved RNA-binding factors involved in alternative splicing (AS) regulation during development. While AS is controlled by distribution of MBNL paralogs and isoforms, the affinity of these proteins for specific RNA-binding regions and their location within transcripts, it is currently unclear how RNA structure impacts MBNL-mediated AS regulation. Here, we defined the RNA structural determinants affecting MBNL-dependent AS activity using both cellular and biochemical assays. While enhanced inclusion of MBNL-regulated alternative exons is controlled by the arrangement and number of MBNL binding sites within unstructured RNA, when these sites are embedded in a RNA hairpin MBNL binds preferentially to one side of stem region. Surprisingly, binding of MBNL proteins to RNA targets did not entirely correlate with AS efficiency. Moreover, comparison of MBNL proteins revealed structure-dependent competitive behavior between the paralogs. Our results showed that the structure of targeted RNAs is a prevalent component of the mechanism of alternative splicing regulation by MBNLs.
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Affiliation(s)
- Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Piotr Cywoniuk
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - James D Thomas
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA.,Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Maurice S Swanson
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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28
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Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA. An engineered RNA binding protein with improved splicing regulation. Nucleic Acids Res 2019; 46:3152-3168. [PMID: 29309648 PMCID: PMC5888374 DOI: 10.1093/nar/gkx1304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
The muscleblind-like (MBNL) family of proteins are key developmental regulators of alternative splicing. Sequestration of MBNL proteins by expanded CUG/CCUG repeat RNA transcripts is a major pathogenic mechanism in the neuromuscular disorder myotonic dystrophy (DM). MBNL1 contains four zinc finger (ZF) motifs that form two tandem RNA binding domains (ZF1-2 and ZF3-4) which each bind YGCY RNA motifs. In an effort to determine the differences in function between these domains, we designed and characterized synthetic MBNL proteins with duplicate ZF1-2 or ZF3-4 domains, referred to as MBNL-AA and MBNL-BB, respectively. Analysis of splicing regulation revealed that MBNL-AA had up to 5-fold increased splicing activity while MBNL-BB had 4-fold decreased activity compared to a MBNL protein with the canonical arrangement of zinc finger domains. RNA binding analysis revealed that the variations in splicing activity are due to differences in RNA binding specificities between the two ZF domains rather than binding affinity. Our findings indicate that ZF1-2 drives splicing regulation via recognition of YGCY RNA motifs while ZF3-4 acts as a general RNA binding domain. Our studies suggest that synthetic MBNL proteins with improved or altered splicing activity have the potential to be used as both tools for investigating splicing regulation and protein therapeutics for DM and other microsatellite diseases.
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Affiliation(s)
- Melissa A Hale
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Jared I Richardson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ryan C Day
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ona L McConnell
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Juan Arboleda
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Eric T Wang
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - J Andrew Berglund
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
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29
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Czubak K, Taylor K, Piasecka A, Sobczak K, Kozlowska K, Philips A, Sedehizadeh S, Brook JD, Wojciechowska M, Kozlowski P. Global Increase in Circular RNA Levels in Myotonic Dystrophy. Front Genet 2019; 10:649. [PMID: 31428124 PMCID: PMC6689976 DOI: 10.3389/fgene.2019.00649] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022] Open
Abstract
Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.
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Affiliation(s)
- Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Kozlowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Saam Sedehizadeh
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J. David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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30
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Hale MA, Johnson NE, Berglund JA. Repeat-associated RNA structure and aberrant splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194405. [PMID: 31323433 DOI: 10.1016/j.bbagrm.2019.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Over 30 hereditary disorders attributed to the expansion of microsatellite repeats have been identified. Despite variant nucleotide content, number of consecutive repeats, and different locations in the genome, many of these diseases have pathogenic RNA gain-of-function mechanisms. The repeat-containing RNAs can form structures in vitro predicted to contribute to the disease through assembly of intracellular RNA aggregates termed foci. The expanded repeat RNAs within these foci sequester RNA binding proteins (RBPs) with important roles in the regulation of RNA metabolism, most notably alternative splicing (AS). These deleterious interactions lead to downstream alterations in transcriptome-wide AS directly linked with disease symptoms. This review summarizes existing knowledge about the association between the repeat RNA structures and RBPs as well as the resulting aberrant AS patterns, specifically in the context of myotonic dystrophy. The connection between toxic, structured RNAs and dysregulation of AS in other repeat expansion diseases is also discussed. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Melissa A Hale
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nicholas E Johnson
- Department of Neurology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J Andrew Berglund
- The RNA Institute, Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA.
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31
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Sznajder ŁJ, Swanson MS. Short Tandem Repeat Expansions and RNA-Mediated Pathogenesis in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20133365. [PMID: 31323950 PMCID: PMC6651174 DOI: 10.3390/ijms20133365] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/23/2022] Open
Abstract
Short tandem repeat (STR) or microsatellite, expansions underlie more than 50 hereditary neurological, neuromuscular and other diseases, including myotonic dystrophy types 1 (DM1) and 2 (DM2). Current disease models for DM1 and DM2 propose a common pathomechanism, whereby the transcription of mutant DMPK (DM1) and CNBP (DM2) genes results in the synthesis of CUG and CCUG repeat expansion (CUGexp, CCUGexp) RNAs, respectively. These CUGexp and CCUGexp RNAs are toxic since they promote the assembly of ribonucleoprotein (RNP) complexes or RNA foci, leading to sequestration of Muscleblind-like (MBNL) proteins in the nucleus and global dysregulation of the processing, localization and stability of MBNL target RNAs. STR expansion RNAs also form phase-separated gel-like droplets both in vitro and in transiently transfected cells, implicating RNA-RNA multivalent interactions as drivers of RNA foci formation. Importantly, the nucleation and growth of these nuclear foci and transcript misprocessing are reversible processes and thus amenable to therapeutic intervention. In this review, we provide an overview of potential DM1 and DM2 pathomechanisms, followed by a discussion of MBNL functions in RNA processing and how multivalent interactions between expanded STR RNAs and RNA-binding proteins (RBPs) promote RNA foci assembly.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA.
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
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32
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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33
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Wang ET, Treacy D, Eichinger K, Struck A, Estabrook J, Olafson H, Wang TT, Bhatt K, Westbrook T, Sedehizadeh S, Ward A, Day J, Brook D, Berglund JA, Cooper T, Housman D, Thornton C, Burge C. Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Hum Mol Genet 2019; 28:1312-1321. [PMID: 30561649 DOI: 10.1093/hmg/ddy432] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 11/12/2022] Open
Abstract
Myotonic dystrophy (dystrophia myotonica, DM) is a multi-systemic disease caused by expanded CTG or CCTG microsatellite repeats. Characterized by symptoms in muscle, heart and central nervous system, among others, it is one of the most variable diseases known. A major pathogenic event in DM is the sequestration of muscleblind-like proteins by CUG or CCUG repeat-containing RNAs transcribed from expanded repeats, and differences in the extent of MBNL sequestration dependent on repeat length and expression level may account for some portion of the variability. However, many other cellular pathways are reported to be perturbed in DM, and the severity of specific disease symptoms varies among individuals. To help understand this variability and facilitate research into DM, we generated 120 RNASeq transcriptomes from skeletal and heart muscle derived from healthy and DM1 biopsies and autopsies. A limited number of DM2 and Duchenne muscular dystrophy samples were also sequenced. We analyzed splicing and gene expression, identified tissue-specific changes in RNA processing and uncovered transcriptome changes strongly correlating with muscle strength. We created a web resource at http://DMseq.org that hosts raw and processed transcriptome data and provides a lightweight, responsive interface that enables browsing of processed data across the genome.
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Affiliation(s)
- Eric T Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Daniel Treacy
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katy Eichinger
- Department of Neurology, University of Rochester, Rochester, NY, USA
| | - Adam Struck
- Department of Biochemistry, University of Oregon, Eugene, OR, USA
| | - Joseph Estabrook
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Hailey Olafson
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Thomas T Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kirti Bhatt
- Department of Neurology, University of Rochester, Rochester, NY, USA
| | - Tony Westbrook
- School of Life Sciences, Queen's Medical Center, University of Nottingham, Nottingham, UK
| | - Sam Sedehizadeh
- School of Life Sciences, Queen's Medical Center, University of Nottingham, Nottingham, UK
| | - Amanda Ward
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - John Day
- Department of Neurology, Stanford University, Palo Alto, CA, USA
| | - David Brook
- School of Life Sciences, Queen's Medical Center, University of Nottingham, Nottingham, UK
| | - J Andrew Berglund
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA.,Department of Biochemistry, University of Oregon, Eugene, OR, USA
| | - Thomas Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David Housman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles Thornton
- Department of Neurology, University of Rochester, Rochester, NY, USA
| | - Christopher Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
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Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model. Proc Natl Acad Sci U S A 2019; 116:7799-7804. [PMID: 30926669 PMCID: PMC6475439 DOI: 10.1073/pnas.1901484116] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Development of small-molecule lead medicines that potently and specifically modulate RNA function is challenging. We designed a small molecule that cleaves r(CUG)exp, the RNA repeat expansion that causes myotonic dystrophy type 1. In cells and in an animal model, the small-molecule cleaver specifically recognizes the 3-dimensional structure of r(CUG)exp, cleaving it more selectively among transcripts containing short, nonpathogenic r(CUG) repeats than an oligonucleotide that recognizes RNA sequence via Watson-Crick base pairing. The small molecule broadly relieves disease-associated phenotype in a mouse model. Thus, small molecules that recognize and cleave RNA structures should be considered a therapeutic strategy for targeting RNA in vivo. Myotonic dystrophy type 1 (DM1) is an incurable neuromuscular disorder caused by an expanded CTG repeat that is transcribed into r(CUG)exp. The RNA repeat expansion sequesters regulatory proteins such as Muscleblind-like protein 1 (MBNL1), which causes pre-mRNA splicing defects. The disease-causing r(CUG)exp has been targeted by antisense oligonucleotides, CRISPR-based approaches, and RNA-targeting small molecules. Herein, we describe a designer small molecule, Cugamycin, that recognizes the structure of r(CUG)exp and cleaves it in both DM1 patient-derived myotubes and a DM1 mouse model, leaving short repeats of r(CUG) untouched. In contrast, oligonucleotides that recognize r(CUG) sequence rather than structure cleave both long and short r(CUG)-containing transcripts. Transcriptomic, histological, and phenotypic studies demonstrate that Cugamycin broadly and specifically relieves DM1-associated defects in vivo without detectable off-targets. Thus, small molecules that bind and cleave RNA have utility as lead chemical probes and medicines and can selectively target disease-causing RNA structures to broadly improve defects in preclinical animal models.
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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36
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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37
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Urbanek-Trzeciak MO, Jaworska E, Krzyzosiak WJ. miRNAmotif-A Tool for the Prediction of Pre-miRNA⁻Protein Interactions. Int J Mol Sci 2018; 19:ijms19124075. [PMID: 30562930 PMCID: PMC6321451 DOI: 10.3390/ijms19124075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding post-transcriptional gene regulators. In mammalian cells, mature miRNAs are produced from primary precursors (pri-miRNAs) using canonical protein machinery, which includes Drosha/DGCR8 and Dicer, or the non-canonical mirtron pathway. In plant cells, mature miRNAs are excised from pri-miRNAs by the DICER-LIKE1 (DCL1) protein complex. The involvement of multiple regulatory proteins that bind directly to distinct miRNA precursors in a sequence- or structure-dependent manner adds to the complexity of the miRNA maturation process. Here, we present a web server that enables searches for miRNA precursors that can be recognized by diverse RNA-binding proteins based on known sequence motifs to facilitate the identification of other proteins involved in miRNA biogenesis. The database used by the web server contains known human, murine, and Arabidopsis thaliana pre-miRNAs. The web server can also be used to predict new RNA-binding protein motifs based on a list of user-provided sequences. We show examples of miRNAmotif applications, presenting precursors that contain motifs recognized by Lin28, MCPIP1, and DGCR8 and predicting motifs within pre-miRNA precursors that are recognized by two DEAD-box helicases—DDX1 and DDX17. miRNAmotif is released as an open-source software under the MIT License. The code is available at GitHub (www.github.com/martynaut/mirnamotif). The webserver is freely available at http://mirnamotif.ibch.poznan.pl.
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Affiliation(s)
- Martyna O Urbanek-Trzeciak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Edyta Jaworska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Wlodzimierz J Krzyzosiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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38
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Li J, Nakamori M, Matsumoto J, Murata A, Dohno C, Kiliszek A, Taylor K, Sobczak K, Nakatani K. A Dimeric 2,9‐Diamino‐1,10‐phenanthroline Derivative Improves Alternative Splicing in Myotonic Dystrophy Type 1 Cell and Mouse Models. Chemistry 2018; 24:18115-18122. [DOI: 10.1002/chem.201804368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Jinxing Li
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Masayuki Nakamori
- Department of NeurologyGraduate School of MedicineOsaka University 2-2 Yamadaoka Suita 565-0871 Japan
| | - Jun Matsumoto
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Asako Murata
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Agnieszka Kiliszek
- Department of Structure and Function of BiomoleculesThe Institute of Bioorganic ChemistryPolish Academy of Sciences Z. Noskowskiego 12/14 61-704 Poznan Poland
| | - Katarzyna Taylor
- Department of Gene ExpressionLaboratory of Gene TherapyInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz University Umultowska 89 61-614 Poznań Poland
| | - Krzysztof Sobczak
- Department of Gene ExpressionLaboratory of Gene TherapyInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz University Umultowska 89 61-614 Poznań Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic ChemistryThe Institute of Scientific and Industrial ResearchOsaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
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39
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Tabaglio T, Low DH, Teo WKL, Goy PA, Cywoniuk P, Wollmann H, Ho J, Tan D, Aw J, Pavesi A, Sobczak K, Wee DKB, Guccione E. MBNL1 alternative splicing isoforms play opposing roles in cancer. Life Sci Alliance 2018; 1:e201800157. [PMID: 30456384 PMCID: PMC6238595 DOI: 10.26508/lsa.201800157] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Abstract
MBNL1 proteins lacking exon 7 (−ex7) are antisurvival factors with tumor suppressive role that cancer cells tend to down-regulate in favor of MBNL +ex7 isoforms. The extent of and the oncogenic role played by alternative splicing (AS) in cancer are well documented. Nonetheless, only few studies have attempted to dissect individual gene function at an isoform level. Here, we focus on the AS of splicing factors during prostate cancer progression, as these factors are known to undergo extensive AS and have the potential to affect hundreds of downstream genes. We identified exon 7 (ex7) in the MBNL1 (Muscleblind-like 1) transcript as being the most differentially included exon in cancer, both in cell lines and in patients' samples. In contrast, MBNL1 overall expression was down-regulated, consistently with its described role as a tumor suppressor. This observation holds true in the majority of cancer types analyzed. We first identified components associated to the U2 splicing complex (SF3B1, SF3A1, and PHF5A) as required for efficient ex7 inclusion and we confirmed that this exon is fundamental for MBNL1 protein homodimerization. We next used splice-switching antisense oligonucleotides (AONs) or siRNAs to compare the effect of MBNL1 splicing isoform switching with knockdown. We report that whereas the absence of MBNL1 is tolerated in cancer cells, the expression of isoforms lacking ex7 (MBNL1 Δex7) induces DNA damage and inhibits cell viability and migration, acting as dominant negative proteins. Our data demonstrate the importance of studying gene function at the level of alternative spliced isoforms and support our conclusion that MBNL1 Δex7 proteins are antisurvival factors with a defined tumor suppressive role that cancer cells tend to down-regulate in favor of MBNL +ex7 isoforms.
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Affiliation(s)
- Tommaso Tabaglio
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Diana Hp Low
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Cancer Science Institute, Singapore
| | - Winnie Koon Lay Teo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Pierre Alexis Goy
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Heike Wollmann
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Jessica Ho
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Damien Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Joey Aw
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Andrea Pavesi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dave Keng Boon Wee
- Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute, Singapore.,National Cancer Centre Singapore, Singapore.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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40
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Nakka K, Ghigna C, Gabellini D, Dilworth FJ. Diversification of the muscle proteome through alternative splicing. Skelet Muscle 2018; 8:8. [PMID: 29510724 PMCID: PMC5840707 DOI: 10.1186/s13395-018-0152-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/15/2018] [Indexed: 12/16/2022] Open
Abstract
Background Skeletal muscles express a highly specialized proteome that allows the metabolism of energy sources to mediate myofiber contraction. This muscle-specific proteome is partially derived through the muscle-specific transcription of a subset of genes. Surprisingly, RNA sequencing technologies have also revealed a significant role for muscle-specific alternative splicing in generating protein isoforms that give specialized function to the muscle proteome. Main body In this review, we discuss the current knowledge with respect to the mechanisms that allow pre-mRNA transcripts to undergo muscle-specific alternative splicing while identifying some of the key trans-acting splicing factors essential to the process. The importance of specific splicing events to specialized muscle function is presented along with examples in which dysregulated splicing contributes to myopathies. Though there is now an appreciation that alternative splicing is a major contributor to proteome diversification, the emergence of improved “targeted” proteomic methodologies for detection of specific protein isoforms will soon allow us to better appreciate the extent to which alternative splicing modifies the activity of proteins (and their ability to interact with other proteins) in the skeletal muscle. In addition, we highlight a continued need to better explore the signaling pathways that contribute to the temporal control of trans-acting splicing factor activity to ensure specific protein isoforms are expressed in the proper cellular context. Conclusions An understanding of the signal-dependent and signal-independent events driving muscle-specific alternative splicing has the potential to provide us with novel therapeutic strategies to treat different myopathies. Electronic supplementary material The online version of this article (10.1186/s13395-018-0152-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kiran Nakka
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - Claudia Ghigna
- Istituto di Genetica Molecolare-Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
| | - Davide Gabellini
- Unit of Gene Expression and Muscular Dystrophy, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, DIBIT2, 5A3-44, via Olgettina 58, 20132, Milan, Italy.
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.
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41
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Zhang F, Bodycombe NE, Haskell KM, Sun YL, Wang ET, Morris CA, Jones LH, Wood LD, Pletcher MT. A flow cytometry-based screen identifies MBNL1 modulators that rescue splicing defects in myotonic dystrophy type I. Hum Mol Genet 2018; 26:3056-3068. [PMID: 28535287 PMCID: PMC5886090 DOI: 10.1093/hmg/ddx190] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 05/08/2017] [Indexed: 11/17/2022] Open
Abstract
Myotonic dystrophy Type 1 (DM1) is a rare genetic disease caused by the expansion of CTG trinucleotide repeats ((CTG)exp) in the 3' untranslated region of the DMPK gene. The repeat transcripts sequester the RNA binding protein Muscleblind-like protein 1 (MBNL1) and hamper its normal function in pre-mRNA splicing. Overexpressing exogenous MBNL1 in the DM1 mouse model has been shown to rescue the splicing defects and reverse myotonia. Although a viable therapeutic strategy, pharmacological modulators of MBNL1 expression have not been identified. Here, we engineered a ZsGreen tag into the endogenous MBNL1 locus in HeLa cells and established a flow cytometry-based screening system to identify compounds that increase MBNL1 level. The initial screen of small molecule compound libraries identified more than thirty hits that increased MBNL1 expression greater than double the baseline levels. Further characterization of two hits revealed that the small molecule HDAC inhibitors, ISOX and vorinostat, increased MBNL1 expression in DM1 patient-derived fibroblasts and partially rescued the splicing defect caused by (CUG)exp repeats in these cells. These findings demonstrate the feasibility of this flow-based cytometry screen to identify both small molecule compounds and druggable targets for MBNL1 upregulation.
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Affiliation(s)
| | - Nicole E Bodycombe
- Medicine Design, Worldwide Research and Development, Pfizer, Cambridge, MA 02139, USA
| | - Keith M Haskell
- Pharmacokinetics, Dynamics and Metabolism - New Chemical Entities, Worldwide Research and Development, Pfizer, CT 06340, USA
| | | | - Eric T Wang
- Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA
| | | | - Lyn H Jones
- Medicine Design, Worldwide Research and Development, Pfizer, Cambridge, MA 02139, USA
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42
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Cywoniuk P, Taylor K, Sznajder ŁJ, Sobczak K. Hybrid splicing minigene and antisense oligonucleotides as efficient tools to determine functional protein/RNA interactions. Sci Rep 2017; 7:17587. [PMID: 29242583 PMCID: PMC5730568 DOI: 10.1038/s41598-017-17816-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing is a complex process that provides a high diversity of proteins from a limited number of protein-coding genes. It is governed by multiple regulatory factors, including RNA-binding proteins (RBPs), that bind to specific RNA sequences embedded in a specific structure. The ability to predict RNA-binding regions recognized by RBPs using whole-transcriptome approaches can deliver a multitude of data, including false-positive hits. Therefore, validation of the global results is indispensable. Here, we report the development of an efficient and rapid approach based on a modular hybrid minigene combined with antisense oligonucleotides to enable verification of functional RBP-binding sites within intronic and exonic sequences of regulated pre-mRNA. This approach also provides valuable information regarding the regulatory properties of pre-mRNA, including the RNA secondary structure context. We also show that the developed approach can be used to effectively identify or better characterize the inhibitory properties of potential therapeutic agents for myotonic dystrophy, which is caused by sequestration of specific RBPs, known as muscleblind-like proteins, by mutated RNA with expanded CUG repeats.
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Affiliation(s)
- Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.,Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida,, Gainesville, Florida, 32610-3610, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614, Poznan, Poland.
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Konieczny P, Stepniak-Konieczna E, Taylor K, Sznajder LJ, Sobczak K. Autoregulation of MBNL1 function by exon 1 exclusion from MBNL1 transcript. Nucleic Acids Res 2017; 45:1760-1775. [PMID: 27903900 PMCID: PMC5389549 DOI: 10.1093/nar/gkw1158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 11/07/2016] [Indexed: 01/14/2023] Open
Abstract
Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed that MBNL1 binds to MBNL1 exon 1 (e1) encoding both the major part of 5΄UTR and an amino-terminal region of MBNL1 protein. We tested several hypotheses regarding the possible autoregulatory function of MBNL1 binding to its own transcript. Our data indicate that MBNLs induce skipping of e1 from precursor MBNL1 mRNA and that e1 exclusion may impact transcript association with polysomes and translation. Furthermore, e1-deficient protein isoform lacking the first two zinc fingers is highly unstable and its EGFP fusion protein has severely compromised splicing activity. We also show that MBNL1 can be transcribed from three different promoters and that the transcription initiation site determines the mode of e1 regulation. Taken together, we demonstrate that MBNL proteins control steady-state levels of MBNL1 through an interaction with e1 in its precursor mRNA. Insights from our study open a new avenue in therapies against DM based on manipulation of the transcription initiation site and e1 splicing of MBNL1 mRNA.
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Affiliation(s)
- Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Ewa Stepniak-Konieczna
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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44
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Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathol Commun 2017; 5:63. [PMID: 28851463 PMCID: PMC5574247 DOI: 10.1186/s40478-017-0468-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.
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Park S, Phukan PD, Zeeb M, Martinez-Yamout MA, Dyson HJ, Wright PE. Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T. Biochemistry 2017; 56:4154-4168. [PMID: 28718627 PMCID: PMC5560242 DOI: 10.1021/acs.biochem.7b00484] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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The human muscleblind-like
proteins (MBNL) regulate tissue-specific
splicing by targeting cardiac troponin T and other pre-mRNAs; aberrant
targeting of CUG and CCUG repeat expansions frequently accompanies
the neuromuscular disease myotonic dystrophy. We show, using biolayer
interferometry (Octet) and NMR spectroscopy, that the zinc finger
domains of MBNL isoform 1 (MBNL1) are necessary and sufficient for
binding CGCU sequences within the pre-mRNA of human cardiac troponin
T. Protein constructs containing zinc fingers 1 and 2 (zf12) and zinc
fingers 3 and 4 (zf34) of MBNL1 each fold into a compact globular
tandem zinc finger structure that participates in RNA binding. NMR
spectra show that the stoichiometry of the interaction between zf12
or zf34 and the CGCU sequence is 1:1, and that the RNA is single-stranded
in the complex. The individual zinc fingers within zf12 or zf34 are
nonequivalent: the primary RNA binding surface is formed in each pair
by the second zinc finger (zf2 or zf4), which interacts with the CGCU
RNA sequence. The NMR structure of the complex between zf12 and a
15-base RNA of sequence 95GUCUCGCUUUUCCCC109, containing a single
CGCU element, shows the single-stranded RNA wrapped around zf2 and
extending to bind to the C-terminal helix. Bases C101, U102, and U103
make well-defined and highly ordered contacts with the protein, whereas
neighboring bases are less well-ordered in the complex. Binding of
the MBNL zinc fingers to cardiac troponin T pre-mRNA is specific and
relatively simple, unlike the complex multiple dimer–trimer
stoichiometries postulated in some previous studies.
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Affiliation(s)
- Sangho Park
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Priti Deka Phukan
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Markus Zeeb
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Relevance of CCM gene polymorphisms for clinical management of sporadic cerebral cavernous malformations. J Neurol Sci 2017; 380:31-37. [PMID: 28870584 DOI: 10.1016/j.jns.2017.06.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 12/13/2022]
Abstract
Cerebral cavernous malformations (CCMs) are clusters of capillaries in the brain that may cause focal deficits or seizures in affected patients. They occur in both sporadic and inherited autosomal dominant form. Germline mutations in CCM1, CCM2 and CCM3 were identified in familial cases. Over the past 13years we performed sequencing and MLPA of the CCM genes in all sporadic and familial CCM cases coming from some hospital clinics of Neurology and Neurosurgery of Messina and other Italian cities. Our results showed that CCM sporadic patients, negative for previously reported CCM gene causative mutations, always carried known CCM polymorphisms. Previously, we reported polymorphisms in CCM2 gene associated with an increase in risk for CCM. Here, we undertook a case-control study to investigate the possible association of others polymorphisms (c.485+65 C/G, c.989+63 C/G, c.1980 A/G in CCM1 gene, c.472+127 C/T in CCM2 and c.150 G/A in CCM3) with CCMs. The five polymorphisms were characterized in 64 sporadic patients and in 90 healthy controls by ASO-PCR. Statistically significant differences in frequencies between patients and controls were found for c.485+65C/G, c.1980 A/G and c.472+127C/T polymorphisms. For c.485+65C/G polymorphism, a higher frequency of mutated allele (G) was found in patients group (9%) than in controls (2%) (p=0.0041); for c.1980 A/G polymorphism, we found a frequency of mutated allele (G) higher in the control group (25%) compared to that of patients (8%) (p=0.0396). Same trend was observed for c.472+127C/T polymorphism (T allele frequency=34% and 6% in control group and patients, respectively; p=0.0001). Polymorphisms c.485+65C/G, c.1980 A/G and c.472+127C/T were associated with an increased risk of CCM as indicated by odds ratio values. Furthermore, c.1980 A/G and c.472+127C/T polymorphisms were associated with less severe CCM symptomatology. Identification of these polymorphisms in CCM sporadic patient may represent a useful tool for clinicians to determine prognosis, scheduled periodic checks and appropriate treatment strategy.
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47
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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48
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA. Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility. J Biol Chem 2017; 292:4350-4357. [PMID: 28130447 DOI: 10.1074/jbc.m116.770768] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/25/2017] [Indexed: 12/16/2022] Open
Abstract
Myotonic dystrophy type 2 is a genetic neuromuscular disease caused by the expression of expanded CCUG repeat RNAs from the non-coding region of the CCHC-type zinc finger nucleic acid-binding protein (CNBP) gene. These CCUG repeats bind and sequester a family of RNA-binding proteins known as Muscleblind-like 1, 2, and 3 (MBNL1, MBNL2, and MBNL3), and sequestration plays a significant role in pathogenicity. MBNL proteins are alternative splicing regulators that bind to the consensus RNA sequence YGCY (Y = pyrimidine). This consensus sequence is found in the toxic RNAs (CCUG repeats) and in cellular RNA substrates that MBNL proteins have been shown to bind. Replacing the uridine in CCUG repeats with pseudouridine (Ψ) resulted in a modest reduction of MBNL1 binding. Interestingly, Ψ modification of a minimally structured RNA containing YGCY motifs resulted in more robust inhibition of MBNL1 binding. The different levels of inhibition between CCUG repeat and minimally structured RNA binding appear to be due to the ability to modify both pyrimidines in the YGCY motif, which is not possible in the CCUG repeats. Molecular dynamic studies of unmodified and pseudouridylated minimally structured RNAs suggest that reducing the flexibility of the minimally structured RNA leads to reduced binding by MBNL1.
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Affiliation(s)
- Elaine deLorimier
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Melissa N Hinman
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Jeremy Copperman
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - Kausiki Datta
- the Center for NeuroGenetics, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610-3010
| | - Marina Guenza
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and
| | - J Andrew Berglund
- From the Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403 and .,the Center for NeuroGenetics, Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610-3010
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Sznajder ŁJ, Michalak M, Taylor K, Cywoniuk P, Kabza M, Wojtkowiak-Szlachcic A, Matłoka M, Konieczny P, Sobczak K. Mechanistic determinants of MBNL activity. Nucleic Acids Res 2016; 44:10326-10342. [PMID: 27733504 PMCID: PMC5137450 DOI: 10.1093/nar/gkw915] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Muscleblind-like (MBNL) proteins are critical RNA processing factors in development. MBNL activity is disrupted in the neuromuscular disease myotonic dystrophy type 1 (DM1), due to the instability of a non-coding microsatellite in the DMPK gene and the expression of CUG expansion (CUGexp) RNAs. Pathogenic interactions between MBNL and CUGexp RNA lead to the formation of nuclear complexes termed foci and prevent MBNL function in pre-mRNA processing. The existence of multiple MBNL genes, as well as multiple protein isoforms, raises the question of whether different MBNL proteins possess unique or redundant functions. To address this question, we coexpressed three MBNL paralogs in cells at equivalent levels and characterized both specific and redundant roles of these proteins in alternative splicing and RNA foci dynamics. When coexpressed in the same cells, MBNL1, MBNL2 and MBNL3 bind the same RNA motifs with different affinities. While MBNL1 demonstrated the highest splicing activity, MBNL3 showed the lowest. When forming RNA foci, MBNL1 is the most mobile paralog, while MBNL3 is rather static and the most densely packed on CUGexp RNA. Therefore, our results demonstrate that MBNL paralogs and gene-specific isoforms possess inherent functional differences, an outcome that could be enlisted to improve therapeutic strategies for DM1.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Piotr Cywoniuk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Michał Kabza
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Agnieszka Wojtkowiak-Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Magdalena Matłoka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Patryk Konieczny
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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