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Wong J, Yellamaty R, Gallante C, Lawrence E, Martelly W, Sharma S. Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. RNA 2024; 30:271-280. [PMID: 38164604 PMCID: PMC10870369 DOI: 10.1261/rna.079892.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
The human U1 snRNA is encoded by a multigene family consisting of transcribed variants and defective pseudogenes. Many variant U1 (vU1) snRNAs have been demonstrated to not only be transcribed but also processed by the addition of a trimethylated guanosine cap, packaged into snRNPs, and assembled into spliceosomes; however, their capacity to facilitate pre-mRNA splicing has, so far, not been tested. A recent systematic analysis of the human snRNA genes identified 178 U1 snRNA genes that are present in the genome as either tandem arrays or single genes on multiple chromosomes. Of these, 15 were found to be expressed in human tissues and cell lines, although at significantly low levels from their endogenous loci, <0.001% of the canonical U1 snRNA. In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves the expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell-based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.
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Affiliation(s)
- Jason Wong
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Christina Gallante
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ethan Lawrence
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
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2
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Dong Y, Li W, Meng J, Wang P, Sun M, Zhou F, Li D, Shu J, Cai C. Pathogenicity analysis and splicing rescue of a classical splice site variant (c.1343+1G>T) of CNOT1 gene associated with neurodevelopmental disorders. Am J Med Genet A 2023; 191:2775-2782. [PMID: 37507849 DOI: 10.1002/ajmg.a.63360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Mutations in the CNOT1 gene lead to an incurable rare neurological disorder mainly manifested as a clinical spectrum of intellectual disability, developmental delay, seizures, and behavioral problems. In this study, we investigated a classical splice site variant of CNOT1 (c.1343+1G>T) associated with neurodevelopmental disorders, which was a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. To link CNOT1 dysfunction with the neurodevelopmental phenotype observed in a patient, in vitro minigene assay was used to verify the effect of CNOT1 gene splice site variant c.1343+1G>T on mRNA splicing. We also explored the impact of transient transfection introducing modified U1 snRNA on correcting the splicing variant. Through minigene expression in mammalian cells, we demonstrated that the variant induced complete exon 12 skipping, which explained the patient's clinical condition and provided additional genetic diagnosis evidence for the clinical significance of the variant. Moreover, we confirmed that the aberrant splice pattern could be partially corrected by the modified U1 snRNA at the mRNA level, which provided strong evidence for the therapeutic potential of modified U1 snRNA in neutralizing the hazardous effect of incorrect splicing patterns.
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Affiliation(s)
- Yan Dong
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Weiran Li
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Jing Meng
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Department of Neurology, Tianjin Children's Hospital, Tianjin, China
| | - Ping Wang
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Mei Sun
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Feiyu Zhou
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Department of Neurology, Tianjin Children's Hospital, Tianjin, China
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
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3
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Estell C, Davidson L, Eaton JD, Kimura H, Gold VAM, West S. A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell 2023:S1097-2765(23)00385-4. [PMID: 37329883 DOI: 10.1016/j.molcel.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this is unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction, suggesting their presence in a functional complex. Consistently, ZC3H4, WDR82, and ARS2 co-transcriptionally control an overlapping population of ncRNAs. ZC3H4 is proximal to the negative elongation factor, PNUTS, which we show enables restrictor function and is required to terminate the transcription of all major RNA polymerase II transcript classes. In contrast to short ncRNAs, longer protein-coding transcription is supported by U1 snRNA, which shields transcripts from restrictor and PNUTS at hundreds of genes. These data provide important insights into the mechanism and control of transcription by restrictor and PNUTS.
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Affiliation(s)
- Chris Estell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Lee Davidson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Joshua D Eaton
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Steven West
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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4
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Swirski S, May O, Ahlers M, Wissinger B, Greschner M, Jüschke C, Neidhardt J. In Vivo Efficacy and Safety Evaluations of Therapeutic Splicing Correction Using U1 snRNA in the Mouse Retina. Cells 2023; 12:cells12060955. [PMID: 36980294 PMCID: PMC10047704 DOI: 10.3390/cells12060955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Efficacy and safety considerations constitute essential steps during development of in vivo gene therapies. Herein, we evaluated efficacy and safety of splice factor-based treatments to correct mutation-induced splice defects in an Opa1 mutant mouse line. We applied adeno-associated viruses to the retina. The viruses transduced retinal cells with an engineered U1 snRNA splice factor designed to correct the Opa1 splice defect. We found the treatment to be efficient in increasing wild-type Opa1 transcripts. Correspondingly, Opa1 protein levels increased significantly in treated eyes. Measurements of retinal morphology and function did not reveal therapy-related side-effects supporting the short-term safety of the treatment. Alterations of potential off-target genes were not detected. Our data suggest that treatments of splice defects applying engineered U1 snRNAs represent a promising in vivo therapeutic approach. The therapy increased wild-type Opa1 transcripts and protein levels without detectable morphological, functional or genetic side-effects in the mouse eye. The U1 snRNA-based therapy can be tailored to specific disease gene mutations, hence, raising the possibility of a wider applicability of this promising technology towards treatment of different inherited retinal diseases.
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Affiliation(s)
- Sebastian Swirski
- Human Genetics, Department of Human Medicine, Faculty of Medicine and Health Sciences, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Oliver May
- Human Genetics, Department of Human Medicine, Faculty of Medicine and Health Sciences, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Malte Ahlers
- Visual Neuroscience, Department of Neuroscience, Faculty of Medicine and Health Sciences, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Straße 7, 72076 Tübingen, Germany
| | - Martin Greschner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Straße 7, 72076 Tübingen, Germany
- Research Center Neurosensory Science, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Christoph Jüschke
- Human Genetics, Department of Human Medicine, Faculty of Medicine and Health Sciences, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - John Neidhardt
- Human Genetics, Department of Human Medicine, Faculty of Medicine and Health Sciences, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
- Research Center Neurosensory Science, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
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5
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Porpiglia E, Mai T, Kraft P, Holbrook CA, de Morree A, Gonzalez VD, Hilgendorf KI, Frésard L, Trejo A, Bhimaraju S, Jackson PK, Fantl WJ, Blau HM. Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration. Cell Stem Cell 2022; 29:1653-1668.e8. [PMID: 36384141 PMCID: PMC9746883 DOI: 10.1016/j.stem.2022.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/04/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
In aging, skeletal muscle strength and regenerative capacity decline, due in part to functional impairment of muscle stem cells (MuSCs), yet the underlying mechanisms remain elusive. Here, we capitalize on mass cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs (CD47hi) with impaired regenerative capacity that predominate with aging. The prevalent CD47hi MuSC subset suppresses the residual functional CD47lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blockade of CD47 alternative polyadenylation or antibody blockade of thrombospondin-1/CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.
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Affiliation(s)
- Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark.
| | - Thach Mai
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggy Kraft
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Colin A Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica D Gonzalez
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keren I Hilgendorf
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Angelica Trejo
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sriram Bhimaraju
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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6
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Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
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Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
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7
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Covello G, Ibrahim GH, Bacchi N, Casarosa S, Denti MA. Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator ( RPGR) Splice Defect. Nucleic Acid Ther 2022; 32:333-349. [PMID: 35166581 PMCID: PMC9416563 DOI: 10.1089/nat.2021.0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.
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Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Gehan H Ibrahim
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Niccolò Bacchi
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simona Casarosa
- Neural Development and Regeneration Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Centre for Medical Science - CIS Med, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
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8
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Cugusi S, Mitter R, Kelly GP, Walker J, Han Z, Pisano P, Wierer M, Stewart A, Svejstrup JQ. Heat shock induces premature transcript termination and reconfigures the human transcriptome. Mol Cell 2022:S1097-2765(22)00007-7. [PMID: 35114099 DOI: 10.1016/j.molcel.2022.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/30/2021] [Accepted: 01/07/2022] [Indexed: 12/14/2022]
Abstract
The heat shock (HS) response involves rapid induction of HS genes, whereas transcriptional repression is established more slowly at most other genes. Previous data suggested that such repression results from inhibition of RNA polymerase II (RNAPII) pause release, but here, we show that HS strongly affects other phases of the transcription cycle. Intriguingly, while elongation rates increase upon HS, processivity markedly decreases, so that RNAPII frequently fails to reach the end of genes. Indeed, HS results in widespread premature transcript termination at cryptic, intronic polyadenylation (IPA) sites near gene 5'-ends, likely via inhibition of U1 telescripting. This results in dramatic reconfiguration of the human transcriptome with production of new, previously unannotated, short mRNAs that accumulate in the nucleus. Together, these results shed new light on the basic transcription mechanisms induced by growth at elevated temperature and show that a genome-wide shift toward usage of IPA sites can occur under physiological conditions.
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9
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Niño CA, Scotto di Perrotolo R, Polo S. Recurrent Spliceosome Mutations in Cancer: Mechanisms and Consequences of Aberrant Splice Site Selection. Cancers (Basel) 2022; 14:cancers14020281. [PMID: 35053445 PMCID: PMC8773931 DOI: 10.3390/cancers14020281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary The spliceosome ribonucleoprotein complex catalyzes the removal of introns and exons ligation, a fundamental post-transcriptional process that generates mature RNAs. Cancer-associated mutations in spliceosome components give rise to aberrant splice site selection and, therefore, the production of novel isoform variants that support tumorigenesis. In this review, we summarize the current research regarding cancer hotspot mutations identified in spliceosome components acting at the very first step of splicing, namely the U1 snRNA, SF3B1, and U2AF1. Abstract Splicing alterations have been widely documented in tumors where the proliferation and dissemination of cancer cells is supported by the expression of aberrant isoform variants. Splicing is catalyzed by the spliceosome, a ribonucleoprotein complex that orchestrates the complex process of intron removal and exon ligation. In recent years, recurrent hotspot mutations in the spliceosome components U1 snRNA, SF3B1, and U2AF1 have been identified across different tumor types. Such mutations in principle are highly detrimental for cells as all three spliceosome components are crucial for accurate splice site selection: the U1 snRNA is essential for 3′ splice site recognition, and SF3B1 and U2AF1 are important for 5′ splice site selection. Nonetheless, they appear to be selected to promote specific types of cancers. Here, we review the current molecular understanding of these mutations in cancer, focusing on how they influence splice site selection and impact on cancer development.
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Affiliation(s)
- Carlos A. Niño
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), 20139 Milan, Italy;
- Correspondence: (C.A.N.); (S.P.)
| | | | - Simona Polo
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), 20139 Milan, Italy;
- Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, 20122 Milan, Italy
- Correspondence: (C.A.N.); (S.P.)
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10
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Jüschke C, Klopstock T, Catarino CB, Owczarek-Lipska M, Wissinger B, Neidhardt J. Autosomal dominant optic atrophy: A novel treatment for OPA1 splice defects using U1 snRNA adaption. Mol Ther Nucleic Acids 2021; 26:1186-1197. [PMID: 34853716 PMCID: PMC8604756 DOI: 10.1016/j.omtn.2021.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/03/2021] [Accepted: 10/19/2021] [Indexed: 11/15/2022]
Abstract
Autosomal dominant optic atrophy (ADOA) is frequently caused by mutations in the optic atrophy 1 (OPA1) gene, with haploinsufficiency being the major genetic pathomechanism. Almost 30% of the OPA1-associated cases suffer from splice defects. We identified a novel OPA1 mutation, c.1065+5G>A, in patients with ADOA. In patient-derived fibroblasts, the mutation led to skipping of OPA1 exon 10, reducing the OPA1 protein expression by approximately 50%. We developed a molecular treatment to correct the splice defect in OPA1 using engineered U1 splice factors retargeted to different locations in OPA1 exon 10 or intron 10. The strongest therapeutic effect was detected when U1 binding was engineered to bind to intron 10 at position +18, a position predicted by bioinformatics to be a promising binding site. We were able to significantly silence the effect of the mutation (skipping of exon 10) and simultaneously increase the expression level of normal transcripts. Retargeting U1 to the canonical splice donor site did not lead to a detectable splice correction. This proof-of-concept study indicates for the first time the feasibility of splice mutation correction as a treatment option for ADOA. Increasing the amount of correctly spliced OPA1 transcripts may suffice to overcome the haploinsufficiency.
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Affiliation(s)
- Christoph Jüschke
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany
| | - Thomas Klopstock
- Friedrich-Baur Institute, Department of Neurology, University Hospital, LMU Munich, University of Munich, 80336 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Claudia B. Catarino
- Friedrich-Baur Institute, Department of Neurology, University Hospital, LMU Munich, University of Munich, 80336 Munich, Germany
| | - Marta Owczarek-Lipska
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
- Joint Research Training Group of the Faculty of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
- Correspondence: John Neidhardt, Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany.
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11
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Chen B, Shi H, Zhang J, Zhou C, Han M, Jiang W, Lai Y, Tu X, Li H. CRISPR-based RNA-binding protein mapping in live cells. Biochem Biophys Res Commun 2021; 583:79-85. [PMID: 34735883 DOI: 10.1016/j.bbrc.2021.10.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/24/2021] [Indexed: 12/26/2022]
Abstract
RNA-binding proteins (RBPs) are involved in all aspects of RNA metabolism, and RNA-RBP interactions are important for cell homeostasis and viral replication. The global RNA-binding proteome was recently reported; however, little is known about the proteins that bind to specific RNAs. In this study, we describe a novel CRISPR-based RNA interaction proteomics method in live cells. In brief, dCas13a with an HA tag was expressed in cells and bound to an RNA of interest with the help of gRNA. The RNA-protein complexes physically bound to dCas13a-HA were crosslinked using UV light and captured using anti-HA beads, after which the proteins were purified and identified using mass spectrometry. We optimized this system and subsequently applied it to U1 small nuclear RNA, which revealed 226 proteins.
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Affiliation(s)
- Baiwen Chen
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Haiyan Shi
- Department of ER, CHINA RESOURCES & WISCO GENERAL HOSPITAL, Wuhan University of Science and Technology, No.209 Metallurgical Avenue, Qingshan District, Wuhan, Hubei, 430080, China
| | - Jia Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Chun Zhou
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Miaomiao Han
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Wenxiu Jiang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Yuting Lai
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China
| | - Xia Tu
- Department of ER, CHINA RESOURCES & WISCO GENERAL HOSPITAL, Wuhan University of Science and Technology, No.209 Metallurgical Avenue, Qingshan District, Wuhan, Hubei, 430080, China.
| | - Huabin Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital,Fudan University, Shanghai, 200031, China.
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12
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Mosbach ML, Pfafenrot C, von Strandmann EP, Bindereif A, Preußer C. Molecular Determinants for RNA Release into Extracellular Vesicles. Cells 2021; 10:2674. [PMID: 34685656 PMCID: PMC8534350 DOI: 10.3390/cells10102674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/05/2023] Open
Abstract
Extracellular vesicles (EVs) are important for intercellular communication and act as vehicles for biological material, such as various classes of coding and non-coding RNAs, a few of which were shown to selectively target into vesicles. However, protein factors, mechanisms, and sequence elements contributing to this specificity remain largely elusive. Here, we use a reporter system that results in different types of modified transcripts to decipher the specificity determinants of RNAs released into EVs. First, we found that small RNAs are more efficiently packaged into EVs than large ones, and second, we determined absolute quantities for several endogenous RNA transcripts in EVs (U6 snRNA, U1 snRNA, Y1 RNA, and GAPDH mRNA). We show that RNA polymerase III (pol III) transcripts are more efficiently secreted into EVs compared to pol II-derived transcripts. Surprisingly, our quantitative analysis revealed no RNA accumulation in the vesicles relative to the total cellular levels, based on both overexpressed reporter transcripts and endogenous RNAs. RNA appears to be EV-associated only at low copy numbers, ranging between 0.02 and 1 molecule per EV. This RNA association may reflect internal EV encapsulation or a less tightly bound state at the vesicle surface.
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Affiliation(s)
- Marie-Luise Mosbach
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christina Pfafenrot
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Gießen, 35392 Gießen, Germany; (M.-L.M.); (C.P.)
| | - Christian Preußer
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, 35043 Marburg, Germany;
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13
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Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
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Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
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14
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Martelly W, Fellows B, Kang P, Vashisht A, Wohlschlegel JA, Sharma S. Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing. RNA Biol 2021; 18:2576-2593. [PMID: 34105434 DOI: 10.1080/15476286.2021.1932360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
During spliceosome assembly, interactions that bring the 5' and 3' ends of an intron in proximity are critical for the production of mature mRNA. Here, we report synergistic roles for the stem-loops 3 (SL3) and 4 (SL4) of the human U1 small nuclear RNA (snRNA) in maintaining the optimal U1 snRNP function, and formation of cross-intron contact with the U2 snRNP. We find that SL3 and SL4 bind distinct spliceosomal proteins and combining a U1 snRNA activity assay with siRNA-mediated knockdown, we demonstrate that SL3 and SL4 act through the RNA helicase UAP56 and the U2 protein SF3A1, respectively. In vitro analysis using UV crosslinking and splicing assays indicated that SL3 likely promotes the SL4-SF3A1 interaction leading to enhancement of A complex formation and pre-mRNA splicing. Overall, these results highlight the vital role of the distinct contacts of SL3 and SL4 in bridging the pre-mRNA bound U1 and U2 snRNPs during the early steps of human spliceosome assembly.
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Affiliation(s)
- William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bernice Fellows
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Paul Kang
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
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15
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Cheng Z, Shang Y, Xu X, Dong Z, Zhang Y, Du Z, Lu X, Zhang T. Presenilin 1 mutation likely contributes to U1 small nuclear RNA dysregulation and Alzheimer's disease-like symptoms. Neurobiol Aging 2021; 100:1-10. [PMID: 33450722 DOI: 10.1016/j.neurobiolaging.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 12/15/2022]
Abstract
Previous studies showed that U1 small nuclear RNA (snRNA) was selectively enriched in the brain of individuals with familial Alzheimer's disease (AD), resulting in widespread changes in RNA splicing. Our study further reported that presenilin-1 (PSEN1) induced an increase in U1 snRNA expression, accompanied by changed amyloid precursor protein expression, β-amyloid level, and cell death in SH-SY5Y cells. However, the effect of U1 snRNA overexpression on learning and memory is still unclear. In the present study, we found that neuronal U1 snRNA overexpression could generate U1 snRNA aggregates in the nuclear, accompanied by the widespread alteration of RNA splicing, resulting in the impairments of synaptic plasticity and spatial memory. In addition, more U1 snRNAs is bound to the intron binding sites accompanied by an increased intracellular U1 snRNA level. This suggests that U1 snRNA overexpression regulates RNA splicing and gene expression in neurons by manipulating the recruitment of the U1 snRNA to the nascent transcripts. Using in situ hybridization staining of human central nervous system-type neurons, we identified nuclear aggregates of U1 snRNA in neurons by upregulating the U1 snRNA level. Quantitative polymerase chain reaction analysis showed U1 snRNA accumulation in the insoluble fraction of neurons with PSEN1 mutation neurons rather than other types of U snRNAs. These results show an independent function of U1 snRNA in regulating RNA splicing, suggesting that aberrant RNA processing may mediate neurodegeneration induced by PSEN1 mutation.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yingchun Shang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinxin Xu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Zhiqiang Dong
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Yongwang Zhang
- College of Pharmacy, Nankai University, Tianjin, PR China
| | - Zhanqiang Du
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China
| | - Xinyi Lu
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China; College of Pharmacy, Nankai University, Tianjin, PR China
| | - Tao Zhang
- College of Life Sciences & State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, PR China.
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16
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Martelly W, Fellows B, Senior K, Marlowe T, Sharma S. Identification of a noncanonical RNA binding domain in the U2 snRNP protein SF3A1. RNA 2019; 25:1509-1521. [PMID: 31383795 PMCID: PMC6795144 DOI: 10.1261/rna.072256.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
During splicing of pre-mRNA, 5' and 3' splice sites are brought within proximity by interactions between the pre-mRNA bound U1 and U2 snRNPs, followed by recruitment of the tri-snRNP for assembly of the mature spliceosome. Previously, we identified an interaction between the U2 snRNP-specific protein SF3A1 and the stem-loop 4 (SL4) of the U1 snRNA that occurs during the early steps of spliceosome assembly. Although harboring many annotated domains, SF3A1 lacks a canonical RNA binding domain. To identify the U1-SL4 binding region in SF3A1, we expressed amino- and carboxy-terminal deletion constructs using a HeLa cell-based cell free expression system. UV-crosslinking of the truncated proteins with 32P-U1-SL4 RNA identified the carboxy-terminal ubiquitin-like (UBL) domain of SF3A1 as the RNA binding region. Characterization of the interaction between SF3A1-UBL and U1-SL4 by electrophoretic mobility shift assay and surface plasmon resonance determined high binding affinity (KD = ∼97 nM), and revealed the double-stranded G-C rich stem of U1-SL4 as an important feature for binding to the UBL domain. Further, mutations of two conserved tyrosine residues, Y772 and Y773, were found to cause a two- and fivefold decrease in the binding affinity for U1-SL4, respectively. Finally, we found that SF3A1-UBL can specifically pull down the U1 snRNP from HeLa nuclear extract, demonstrating its capacity to bind U1-SL4 in the context of the intact snRNP. Thus, the data show that the UBL domain of SF3A1 can function as an RNA binding domain and that mutations in this region may interfere with U1-SL4 binding.
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Affiliation(s)
- William Martelly
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Bernice Fellows
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Kristen Senior
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Tim Marlowe
- Molecular Analysis Core, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA
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17
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Del Corpo O, Goguen RP, Malard CMG, Daher A, Colby-Germinario S, Scarborough RJ, Gatignol A. A U1i RNA that Enhances HIV-1 RNA Splicing with an Elongated Recognition Domain Is an Optimal Candidate for Combination HIV-1 Gene Therapy. Mol Ther Nucleic Acids 2019; 18:815-830. [PMID: 31734561 PMCID: PMC6861678 DOI: 10.1016/j.omtn.2019.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 11/30/2022]
Abstract
U1 interference (U1i) RNAs can be designed to correct splicing defects and target pathogenic RNA, such as HIV-1 RNA. In this study, we show that U1i RNAs that enhance HIV-1 RNA splicing are more effective at inhibiting HIV-1 production compared to top U1i RNAs that inhibit polyadenylation of HIV-1 RNA. A U1i RNA was also identified targeting a site upstream of the first splice acceptor site in the Gag coding region that was effective at inhibiting HIV-1 production. U1-T6, which enhanced HIV-1 RNA splicing, was superior to an antiviral short hairpin RNA (shRNA) currently in clinical trials. To increase specificity, the recognition domain of U1-T6 was elongated by 3–6 nt. The elongated molecules inhibited HIV-1 production from different HIV-1 strains, including one with a mismatch in the target site. These results suggest that lengthening the recognition domain can enhance the specificity of U1i RNAs for their intended target sites while at the same time allowing them to tolerate single mismatch mutations. Overall, our results demonstrate that U1-T6 with an elongated recognition domain inhibits HIV-1 production and has both the efficacy and specificity to be a promising candidate for HIV-1 gene therapy.
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Affiliation(s)
- Olivier Del Corpo
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada
| | - Ryan P Goguen
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Camille M G Malard
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Aïcha Daher
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada
| | | | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
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18
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Breuel S, Vorm M, Bräuer AU, Owczarek-Lipska M, Neidhardt J. Combining Engineered U1 snRNA and Antisense Oligonucleotides to Improve the Treatment of a BBS1 Splice Site Mutation. Mol Ther Nucleic Acids 2019; 18:123-130. [PMID: 31541798 PMCID: PMC6796732 DOI: 10.1016/j.omtn.2019.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 08/01/2019] [Indexed: 12/23/2022]
Abstract
Manipulation of pre-mRNA processing is a promising approach toward overcoming disease-causing mutations and treating human diseases. We show that a combined treatment applying two splice-manipulating technologies improves therapeutic efficacies to correct mutation-induced splice defects. Previously, we identified a family affected by retinitis pigmentosa caused by the homozygous BBS1 splice donor site mutation c.479G > A. The mutation leads to both exon 5 skipping and intron 5 retention. We developed a therapeutic approach applying lentivirus-mediated gene delivery of engineered U1 small nuclear RNA (U1), which resulted in increased levels of correctly spliced BBS1. Herein, we show that the therapeutic effect of the engineered U1 efficiently reverted exon skipping but failed to reduce the intron retention. To complement the engineered U1 treatment, we identified four different antisense oligonucleotides (AONs) that block intron 5 retention in BBS1 transcripts. A treatment using engineered U1 in combination with AONs showed the highest therapeutic efficacy and increased the amount of correctly spliced BBS1 transcripts. We did not detect elevated levels of apoptotic cell death in AON-treated cell lines. In conclusion, engineered U1 or AONs provide efficient therapies with complementary effects and can be combined to increase efficacy of therapeutic approaches to correct splice defects.
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Affiliation(s)
- Saskia Breuel
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Mariann Vorm
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Anja U Bräuer
- Anatomy, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Germany
| | - Marta Owczarek-Lipska
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - John Neidhardt
- Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University of Oldenburg, Germany; Joint research training group of the Faculty of Medicine and Health Sciences, University of Oldenburg, Germany and the University Medical Center Groningen, Groningen, Netherlands.
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19
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Souček P, Réblová K, Kramárek M, Radová L, Grymová T, Hujová P, Kováčová T, Lexa M, Grodecká L, Freiberger T. High-throughput analysis revealed mutations' diverging effects on SMN1 exon 7 splicing. RNA Biol 2019; 16:1364-1376. [PMID: 31213135 DOI: 10.1080/15476286.2019.1630796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by next-generation sequencing. In our model system, all exonic and six intronic positions of the SMN1 gene's exon 7 were mutated to all possible nucleotide variants, which amounted to 180 unique single-nucleotide mutants and 470 double mutants. The mutations resulted in a wide range of splicing aberrations. Exonic splicing-affecting mutations resulted either in substantial exon skipping, supposedly driven by predicted exonic splicing silencer or cryptic donor splice site (5'ss) and de novo 5'ss strengthening and use. On the other hand, a single disruption of exonic splicing enhancer was not sufficient to cause major exon skipping, suggesting these elements can be substituted during exon recognition. While disrupting the acceptor splice site led only to exon skipping, some 5'ss mutations potentiated the use of three different cryptic 5'ss. Generally, single mutations supporting cryptic 5'ss use displayed better pre-mRNA/U1 snRNA duplex stability and increased splicing regulatory element strength across the original 5'ss. Analyzing double mutants supported the predominating splicing regulatory elements' effect, but U1 snRNA binding could contribute to the global balance of splicing isoforms. Based on these findings, we suggest that creating a new splicing enhancer across the mutated 5'ss can be one of the main factors driving cryptic 5'ss use.
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Affiliation(s)
- Přemysl Souček
- Medical Genomics RG, Central European Institute of Technology, Masaryk University , Brno , Czech Republic.,Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic
| | - Kamila Réblová
- Medical Genomics RG, Central European Institute of Technology, Masaryk University , Brno , Czech Republic
| | - Michal Kramárek
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic
| | - Lenka Radová
- Medical Genomics RG, Central European Institute of Technology, Masaryk University , Brno , Czech Republic
| | - Tereza Grymová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic
| | - Pavla Hujová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic
| | - Tatiana Kováčová
- Medical Genomics RG, Central European Institute of Technology, Masaryk University , Brno , Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University , Brno , Czech Republic
| | - Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic
| | - Tomáš Freiberger
- Medical Genomics RG, Central European Institute of Technology, Masaryk University , Brno , Czech Republic.,Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation , Brno , Czech Republic.,Faculty of Medicine, Masaryk University , Brno , Czech Republic
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20
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Lee B, Kim YR, Kim SJ, Goh SH, Kim JH, Oh SK, Baek JI, Kim UK, Lee KY. Modified U1 snRNA and antisense oligonucleotides rescue splice mutations in SLC26A4 that cause hereditary hearing loss. Hum Mutat 2019; 40:1172-1180. [PMID: 31033086 DOI: 10.1002/humu.23774] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022]
Abstract
One of most important factors for messenger RNA (mRNA) transcription is the spliceosomal component U1 small nuclear RNA (snRNA), which recognizes 5' splicing donor sites at specific regions in pre-mRNA. Mutations in these sites disrupt U1 snRNA binding and cause abnormal splicing. In this study, we investigated mutations at splice sites in SLC26A4 (HGNC 8818), one of the major causative genes of hearing loss, which may result in the synthesis of abnormal pendrin, the channel protein encoded by the gene. Seventeen SLC26A4 variants with mutations in the U1 snRNA binding sites were assessed by minigene splicing assays, and 11 were found to result in abnormal splicing. Interestingly, eight of the 11 pathogenic mutations were intronic, suggesting the importance of conserved sequences at the intronic splice site. The application of modified U1 snRNA effectively rescued the abnormal splicing for most of these mutations. Although three were cryptic mutations, they were rescued by cotransfection of modified U1 snRNA and modified antisense oligonucleotides. Our results demonstrate the important role of snRNA in SLC26A4 mutations, suggesting the therapeutic potential of modified U1 snRNA and antisense oligonucleotides for neutralizing the pathogenic effect of the splice-site mutations that may result in hearing loss.
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Affiliation(s)
- Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Ye-Ri Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Joo Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Ho Goh
- Therapeutic Target Discovery Branch, National Cancer Center, Goyang-si, Gyeonggi-do, Republic of Korea
| | - Jong-Heun Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Se-Kyung Oh
- Laboratory Animal Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Jeong-In Baek
- Department of Aroma-Applied Industry, Daegu Haany University, Gyeongsan, Republic of Korea
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea.,BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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21
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Kumari E, Shang Y, Cheng Z, Zhang T. U1 snRNA over-expression affects neural oscillations and short-term memory deficits in mice. Cogn Neurodyn 2019; 13:313-323. [PMID: 31354878 DOI: 10.1007/s11571-019-09528-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/15/2019] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
Small nuclear RNAs (snRNAs) and other RNA spliceosomal components are involved in neurological and psychiatric disorders. U1 snRNA has recently been demonstrated to be altered in pathology in some neurodegenerative diseases, but whether it has a causative role is not clear. Here we have studied this by overexpressing U1 snRNA in mice and measured their hippocampal oscillatory patterns and brain functions. Novel object recognition test showed that the recognition index was significantly decreased in the U1 snRNA over-expression mice compared to that in the C57BL mice. U1 snRNA over-expression regulated not only the pattern of neural oscillations but also the expression of neuron excitatory and inhibitory proteins. Here we show that U1 snRNA over-expression contains the shrinkage distribution of theta-power, theta-phase lock synchronization, and theta and low-gamma cross-frequency coupling in the hippocampus. The alternations of neuron receptors by the U1 snRNA overexpression also modulated the decreasing of recognition index, the energy distribution of theta power spectrum with the reductions of theta phase synchronization and phase-amplitude coupling between theta and low-gamma. Linking these all together, our results suggest that U1 snRNA overexpression particularly causes a deficit in short-term memory. These findings make a bedrock of our research that U1 snRNA bridges the gap about the mechanism behind short-term memory based on the molecular and mesoscopic level.
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Affiliation(s)
- Ekta Kumari
- 1College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, No. 94 Weijin Road, Tianjin, 300071 People's Republic of China
| | - Yingchun Shang
- 1College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, No. 94 Weijin Road, Tianjin, 300071 People's Republic of China
| | - Zhi Cheng
- 1College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, No. 94 Weijin Road, Tianjin, 300071 People's Republic of China.,2State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People's Republic of China
| | - Tao Zhang
- 1College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, No. 94 Weijin Road, Tianjin, 300071 People's Republic of China
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Cheng Z, Du Z, Zhai B, Yang Z, Zhang T. U1 small nuclear RNA overexpression implicates autophagic-lysosomal system associated with AD. Neurosci Res 2018; 136:48-55. [PMID: 29395359 DOI: 10.1016/j.neures.2018.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 11/20/2022]
Abstract
Recently, we reported that presenilin 1 considerably increased the expression level of U1 small nuclear RNA (snRNA) accompanied with the adverse change of amyloid precursor protein (APP) expression, β-amyloid (Aβ) production and cell apoptosis. In the present study, it was found that U1 snRNA overexpression significantly elevated the expression level of autophagy. Moreover, rapamycin further enhanced the Aβ production and cell apoptosis, whereas these processes were effectively inhibited by 3-MA. Acridine orange staining images showed that U1 snRNA overexpression not only activated autophagy pathway, but also led to the autophagic-lysosomal system dysfunction in cells. Immunofluorescence assay showed autophagic vacuoles localization with APP, which was the precursor protein of main component of toxic protein in AD. Meanwhile, the superoxide dismutase activity was remarkably decreased and MDA level was significantly increased by U1 snRNA overexpression in cells, suggesting that there was a possible pathway to elucidate how the U1 snRNA overexpression induced cell damage. We further found that U1 snRNA overexpression altered lysosomal biogenesis and autophagic-lysosomal fusion. In combination with our previous results, it suggests that the malfunction of autophagy pathway provides important insight into molecular mechanisms of augment the aggregation of Aβ and induction of cell apoptosis contributed to AD.
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Abstract
Spinal muscular atrophy (SMA) is one of the major genetic disorders associated with infant mortality. More than 90% cases of SMA result from deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, does not compensate for the loss of SMN1 due to predominant skipping of exon 7. However, correction of SMN2 exon 7 splicing has proven to confer therapeutic benefits in SMA patients. The only approved drug for SMA is an antisense oligonucleotide (Spinraza™/Nusinersen), which corrects SMN2 exon 7 splicing by blocking intronic splicing silencer N1 (ISS-N1) located immediately downstream of exon 7. ISS-N1 is a complex regulatory element encompassing overlapping negative motifs and sequestering a cryptic splice site. More than 40 protein factors have been implicated in the regulation of SMN exon 7 splicing. There is evidence to support that multiple exons of SMN are alternatively spliced during oxidative stress, which is associated with a growing number of pathological conditions. Here, we provide the most up to date account of the mechanism of splicing regulation of the SMN genes.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
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24
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Cheng Z, Sun Y, Niu X, Shang Y, Ruan J, Chen Z, Gao S, Zhang T. Gene expression profiling reveals U1 snRNA regulates cancer gene expression. Oncotarget 2017; 8:112867-112874. [PMID: 29348872 PMCID: PMC5762557 DOI: 10.18632/oncotarget.22842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/10/2017] [Indexed: 11/25/2022] Open
Abstract
U1 small nuclear RNA (U1 snRNA), as one of the most abundant ncRNAs in human cells, plays an important role in splicing of pre-mRNAs. Compared to previous studies which have focused on the primary function of U1 snRNA and the neurodegenerative diseases caused by abnormalities of U1 snRNA, this study is to investigate how U1 snRNA over-expression affects the expression of mammal genes on a genome-wide scale. By comparing the gene expression profiles of U1 snRNA over-expressed cells with those of their controls using microarray experiments, 916 genes or loci were identified significantly Differentially Expressed (DE). These 595 up-regulated DE genes and 321 down-regulated DE genes were analyzed using annotations from GO categories and pathways from the KEGG database. As a result, three of 12 enriched pathways were well-known cancer pathways, while the other nine pathways were associated to cancers in previous studies. The further analysis of 73 genes involved in 12 pathways suggested that U1 snRNA could regulate cancer gene expression. The microarray data under the GEO Series accession number GSE84304 is available in the NCBI GEO database.
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Affiliation(s)
- Zhi Cheng
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Yu Sun
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Xiaoran Niu
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Yingchun Shang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin 300071, P.R. China
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, Gansu 730046, P.R. China
| | - Shan Gao
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
- Institute of Statistics, Nankai University, Tianjin 300071, P.R. China
| | - Tao Zhang
- College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin 300071, P.R. China
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25
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Abstract
We recently reported that presenilin-1 (PS1) induced an increase of U1 snRNA expression accompanied with the change of amyloid precursor protein expression, β-amyloid level and cell death. In the present study, our data showed that both overexpression and knockdown of U1 snRNA could cause the loss in the function of U1 snRNA and resulted in PCPA as well as the same downstream phenomena including the expression changes of genes specific to AD, tau hyperphosphorylation on the site of Thr212, the decrease of acetylated α-tubulin, the reduction of cell viability and upregulation of RIPK1, RIPK3 and caspase8. These findings not only helped researchers better understand the functions of U1 snRNA, but also paved the way to reveal the mechanisms of AD from a different point of view and may find a new therapeutic target for the disease.
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Affiliation(s)
- Zhi Cheng
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Yingchun Shang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Shan Gao
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
| | - Tao Zhang
- a College of Life Sciences and Key Laboratory of Bioactive Materials Ministry of Education , Nankai University , Tianjin , PR China
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26
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Gong Q, Stump MR, Zhou Z. Upregulation of functional Kv11.1a isoform expression by modified U1 small nuclear RNA. Gene 2017; 641:220-225. [PMID: 29066300 DOI: 10.1016/j.gene.2017.10.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/04/2017] [Accepted: 10/20/2017] [Indexed: 01/14/2023]
Abstract
The KCNH2 or human ether-a go-go-related gene (hERG) encodes the Kv11.1 potassium channel that conducts the rapidly activating delayed rectifier potassium current in the heart. The expression of Kv11.1 C-terminal isoforms is directed by the alternative splicing and polyadenylation of intron 9. Splicing of intron 9 leads to the formation of a functional, full-length Kv11.1a isoform and polyadenylation of intron 9 results in the production of a non-functional, C-terminally truncated Kv11.1a-USO isoform. The relative expression of Kv11.1a and Kv11.1a-USO plays an important role in regulating Kv11.1 channel function. In the heart, only one-third of KCNH2 pre-mRNA is processed to Kv11.1a due to the weak 5' splice site of intron 9. We previously showed that the weak 5' splice site is caused by sequence deviation from the consensus, and that mutations toward the consensus sequence increased the efficiency of intron 9 splicing. It is well established that 5' splice sites are recognized by complementary base-paring with U1 small nuclear RNA (U1 snRNA). In this study, we modified the sequence of U1 snRNA to increase its complementarity to the 5' splice site of KCNH2 intron 9 and observed a significant increase in the efficiency of intron 9 splicing. RNase protection assay and western blot analysis showed that modified U1 snRNA increased the expression of the functional Kv11.1a isoform and concomitantly decreased the expression of the non-functional Kv11.1a-USO isoform. In patch-clamp experiments, modified U1 snRNA significantly increased Kv11.1 current. Our findings suggest that relative expression of Kv11.1 C-terminal isoforms can be regulated by modified U1 snRNA.
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Affiliation(s)
- Qiuming Gong
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, United States
| | - Matthew R Stump
- Department of Biology, George Fox University, Newberg, OR, United States
| | - Zhengfeng Zhou
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, United States.
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Abstract
In many eukaryotes, including mammals, plants, yeast, and insects, introns can increase gene expression without functioning as a binding site for transcription factors. This phenomenon was termed 'intron-mediated enhancement'. Introns can increase transcript levels by affecting the rate of transcription, nuclear export, and transcript stability. Moreover, introns can also increase the efficiency of mRNA translation. This review discusses the current knowledge about these processes. The role of splicing in IME and the significance of intron position relative to the sites of transcription and translation initiation are elaborated. Particular emphasis is placed on the question why different introns, present at the same location of the same genes and spliced at a similar high efficiency, can have very different impacts on expression - from almost no effect to considerable stimulation. This situation can be at least partly accounted for by the identification of splicing-unrelated intronic elements with a special ability to enhance mRNA accumulation or translational efficiency. The many factors that could lead to the large variation observed between the impact of introns in different genes and experimental systems are highlighted. It is suggested that there is no sole, definite answer to the question "how do introns enhance gene expression". Rather, each intron-gene combination might undergo its own unique mixture of processes that lead to the perceptible outcome.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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28
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Abstract
More than 15% of all disease-causing mutations result in mRNA splicing defects. U1 snRNA binds to the 5' splice site (5'ss) through base pairing. Mutation-adapted U1 snRNA (with compensatory U1 snRNA changes) and exon-specific U1 snRNA (complementary to intronic sequences) have been shown to suppress 5'ss mutations in cellular and animal models. Areas covered: The history, mechanism of action, and efficacy of U1 snRNA-mediated gene therapy are covered. The clinical utility of this technology and its limitations will be discussed. Expert commentary: Recently, gene therapies with mutation-adapted U1 snRNAs have been conducted on animal models, including aromatic l-amino acid decarboxylase deficiency and spinal muscular atrophy. However, although U1-mediated therapy has the advantage of maintaining the regulated expression of defective genes, its accuracy and efficacy needs to be improved before clinical application of this technique is possible.
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Affiliation(s)
- Wuh-Liang Hwu
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Yu-May Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
| | - Ni-Chung Lee
- a Department of Pediatrics and Medical Genetics , National Taiwan University Hospital and National Taiwan University College of Medicine , Taipei , Taiwan
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Dal Mas A, Fortugno P, Donadon I, Levati L, Castiglia D, Pagani F. Exon-Specific U1s Correct SPINK5 Exon 11 Skipping Caused by a Synonymous Substitution that Affects a Bifunctional Splicing Regulatory Element. Hum Mutat 2015; 36:504-12. [PMID: 25665175 DOI: 10.1002/humu.22762] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/27/2015] [Indexed: 12/20/2022]
Abstract
The c.891C>T synonymous transition in SPINK5 induces exon 11 (E11) skipping and causes Netherton syndrome (NS). Using a specific RNA-protein interaction assay followed by mass spectrometry analysis along with silencing and overexpression of splicing factors, we showed that this mutation affects an exonic bifunctional splicing regulatory element composed by two partially overlapping silencer and enhancer sequences, recognized by hnRNPA1 and Tra2β splicing factors, respectively. The C-to-T substitution concomitantly increases hnRNPA1 and weakens Tra2β-binding sites, leading to pathological E11 skipping. In hybrid minigenes, exon-specific U1 small nuclear RNAs (ExSpe U1s) that target by complementarity intronic sequences downstream of the donor splice site rescued the E11 skipping defect caused by the c.891C>T mutation. ExSpe U1 lentiviral-mediated transduction of primary NS keratinocytes from a patient bearing the mutation recovered the correct full-length SPINK5 mRNA and the corresponding functional lympho-epithelial Kazal-type related inhibitor protein in a dose-dependent manner. This study documents the reliability of a mutation-specific, ExSpe U1-based, splicing therapy for a relatively large subset of European NS patients. Usage of ExSpe U1 may represent a general approach for correction of splicing defects affecting skin disease genes.
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Affiliation(s)
- Andrea Dal Mas
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Human Molecular Genetics, Trieste, Italy
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