1
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Sp S, Mitra RN, Zheng M, Chrispell JD, Wang K, Kwon YS, Weiss ER, Han Z. Gene augmentation for autosomal dominant retinitis pigmentosa using rhodopsin genomic loci nanoparticles in the P23H +/- knock-in murine model. Gene Ther 2023; 30:628-640. [PMID: 36935427 DOI: 10.1038/s41434-023-00394-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/21/2023]
Abstract
Gene therapy for autosomal dominant retinitis pigmentosa (adRP) is challenged by the dominant inheritance of the mutant genes, which would seemingly require a combination of mutant suppression and wild-type replacement of the appropriate gene. We explore the possibility that delivery of a nanoparticle (NP)-mediated full-length mouse genomic rhodopsin (gRho) or human genomic rhodopsin (gRHO) locus can overcome the dominant negative effects of the mutant rhodopsin in the clinically relevant P23H+/--knock-in heterozygous mouse model. Our results demonstrate that mice in both gRho and gRHO NP-treated groups exhibit significant structural and functional recovery of the rod photoreceptors, which lasted for 3 months post-injection, indicating a promising reduction in photoreceptor degeneration. We performed miRNA transcriptome analysis using next generation sequencing and detected differentially expressed miRNAs as a first step towards identifying miRNAs that could potentially be used as rhodopsin gene expression enhancers or suppressors for sustained photoreceptor rescue. Our results indicate that delivering an intact genomic locus as a transgene has a greater chance of success compared to the use of the cDNA for treatment of this model of adRP, emphasizing the importance of gene augmentation using a gDNA that includes regulatory elements.
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Affiliation(s)
- Simna Sp
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rajendra N Mitra
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Min Zheng
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jared D Chrispell
- Department of Cell Biology and Physiology, the University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kai Wang
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yong-Su Kwon
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ellen R Weiss
- Department of Cell Biology and Physiology, the University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zongchao Han
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Carolina Institute for NanoMedicine, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Division of Pharmacoengineering & Molecular Pharmaceutics, Eshelman School of Pharmacy, the University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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2
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Bo S, Sun Q, Ning P, Yuan N, Weng Y, Liang Y, Wang H, Lu Z, Li Z, Zhao X. A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA. Front Genet 2023; 14:1151172. [PMID: 36923795 PMCID: PMC10008863 DOI: 10.3389/fgene.2023.1151172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5'and 3'untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5'and 3'UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%-80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5'and 3'UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process.
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Affiliation(s)
- Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Qiuying Sun
- Department of Oncology, Inner Mongolia Cancer Hospital and The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Pengfei Ning
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ningping Yuan
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Yujie Weng
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ying Liang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Huitao Wang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhongxian Li
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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3
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Simna SP, Han Z. Prospects Of Non-Coding Elements In Genomic Dna Based Gene Therapy. Curr Gene Ther 2021; 22:89-103. [PMID: 33874871 DOI: 10.2174/1566523221666210419090357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/22/2022]
Abstract
Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full-length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.
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Affiliation(s)
- S P Simna
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
| | - Zongchao Han
- Department of Ophthalmology, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. United States
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4
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Zerbato JM, Khoury G, Zhao W, Gartner MJ, Pascoe RD, Rhodes A, Dantanarayana A, Gooey M, Anderson J, Bacchetti P, Deeks SG, McMahon J, Roche M, Rasmussen TA, Purcell DF, Lewin SR. Multiply spliced HIV RNA is a predictive measure of virus production ex vivo and in vivo following reversal of HIV latency. EBioMedicine 2021; 65:103241. [PMID: 33647768 PMCID: PMC7920823 DOI: 10.1016/j.ebiom.2021.103241] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND One strategy being pursued to clear latently infected cells that persist in people living with HIV (PLWH) on antiretroviral therapy (ART) is to activate latent HIV infection with a latency reversing agent (LRA). Surrogate markers that accurately measure virus production following an LRA are needed. METHODS We quantified cell-associated unspliced (US), multiply spliced (MS) and supernatant (SN) HIV RNA by qPCR from total and resting CD4+ T cells isolated from seven PLWH on ART before and after treatment ex vivo with different LRAs, including histone deacetylase inhibitors (HDACi). MS and plasma HIV RNA were also quantified from PLWH on ART (n-11) who received the HDACi panobinostat. FINDINGS In total and resting CD4+ T cells from PLWH on ART, detection of US RNA was common while detection of MS RNA was infrequent. Primers used to detect MS RNA, in contrast to US RNA, bound sites of the viral genome that are commonly mutated or deleted in PLWH on ART. Following ex vivo stimulation with LRAs, we identified a strong correlation between the fold change increase in SN and MS RNA, but not the fold change increase in SN and US RNA. In PLWH on ART who received panobinostat, MS RNA was significantly higher in samples with detectable compared to non0detectable plasma HIV RNA. INTERPRETATION Following administration of an LRA, quantification of MS RNA is more likely to reflect an increase in virion production and is therefore a better indicator of meaningful latency reversal. FUNDING NHMRC, NIH DARE collaboratory.
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Affiliation(s)
- Jennifer M Zerbato
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Georges Khoury
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Wei Zhao
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Matthew J Gartner
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Rachel D Pascoe
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ashanti Dantanarayana
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Megan Gooey
- HIV Characterisation Laboratory, Victorian Infectious Diseases Reference Laboratory, the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jenny Anderson
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Steven G Deeks
- Department of Medicine, Division of HIV/AIDS, University of California San Francisco, San Francisco, USA
| | - James McMahon
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Thomas A Rasmussen
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Damian Fj Purcell
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sharon R Lewin
- Department of Infectious Diseases, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia; Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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5
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Khoury G, Mota TM, Li S, Tumpach C, Lee MY, Jacobson J, Harty L, Anderson JL, Lewin SR, Purcell DFJ. HIV latency reversing agents act through Tat post translational modifications. Retrovirology 2018; 15:36. [PMID: 29751762 PMCID: PMC5948896 DOI: 10.1186/s12977-018-0421-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 05/05/2018] [Indexed: 12/18/2022] Open
Abstract
Background Different classes of latency reversing agents (LRAs) are being evaluated to measure their effects in reactivating HIV replication from latently infected cells. A limited number of studies have demonstrated additive effects of LRAs with the viral protein Tat in initiating transcription, but less is known about how LRAs interact with Tat, particularly through basic residues that may be post-translationally modified to alter the behaviour of Tat for processive transcription and co-transcriptional RNA processing. Results Here we show that various lysine and arginine mutations reduce the capacity of Tat to induce both transcription and mRNA splicing. The lysine 28 and lysine 50 residues of Tat, or the acetylation and methylation modifications of these basic amino acids, were essential for Tat transcriptional control, and also for the proviral expression effects elicited by histone deacetylase inhibitors (HDACi) or the bromodomain inhibitor JQ1. We also found that JQ1 was the only LRA tested that could induce HIV mRNA splicing in the absence of Tat, or rescue splicing for Tat lysine mutants in a BRD4-dependent manner. Conclusions Our data provide evidence that Tat activities in both co-transcriptional RNA processing together with transcriptional initiation and processivity are crucial during reactivation of latent HIV infection. The HDACi and JQ1 LRAs act with Tat to increase transcription, but JQ1 also enables post-transcriptional mRNA splicing. Tat residues K28 and K50, or their modifications through acetylation or methylation, are critical for LRAs that function in conjunction with Tat. Electronic supplementary material The online version of this article (10.1186/s12977-018-0421-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georges Khoury
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Talia M Mota
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Shuang Li
- School of Life Sciences, Peking University, Beijing, China
| | - Carolin Tumpach
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Michelle Y Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jonathan Jacobson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leigh Harty
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jenny L Anderson
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia.,Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.
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6
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Gama-Carvalho M, L Garcia-Vaquero M, R Pinto F, Besse F, Weis J, Voigt A, Schulz JB, De Las Rivas J. Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RNA-transcriptome homeostasis: a genomics perspective. J Neurochem 2017; 141:12-30. [PMID: 28054357 DOI: 10.1111/jnc.13945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/02/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
In this review, we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, amyotrophic lateral sclerosis, and spinal muscular atrophy. We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN, and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration. We review reported functional and physical interactions between these four proteins, highlighting their common association with nuclear bodies and small nuclear ribonucleoprotein particle biogenesis and function. We discuss how these interactions are turning out to be particularly relevant for the control of transcription and chromatin homeostasis, including the recent identification of an association between SMN and Senataxin required to ensure the resolution of DNA-RNA hybrid formation and proper termination by RNA polymerase II. These connections strongly support the existence of common pathways underlying the spinal muscular atrophy and amyotrophic lateral sclerosis phenotype. We also discuss the potential of genome-wide expression profiling, in particular RNA sequencing derived data, to contribute to unravelling the underlying mechanisms. We provide a review of publicly available datasets that have addressed both diseases using these approaches, and highlight the value of investing in cross-disease studies to promote our understanding of the pathways leading to neurodegeneration.
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Affiliation(s)
- Margarida Gama-Carvalho
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Marina L Garcia-Vaquero
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Francisco R Pinto
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University, Aachen, Germany
| | - Aaron Voigt
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca, Spain
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7
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Therapeutic activity of modified U1 core spliceosomal particles. Nat Commun 2016; 7:11168. [PMID: 27041075 PMCID: PMC4822034 DOI: 10.1038/ncomms11168] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/25/2016] [Indexed: 12/15/2022] Open
Abstract
Modified U1 snRNAs bound to intronic sequences downstream of the 5′ splice site correct exon skipping caused by different types of mutations. Here we evaluate the therapeutic activity and structural requirements of these exon-specific U1 snRNA (ExSpeU1) particles. In a severe spinal muscular atrophy, mouse model, ExSpeU1, introduced by germline transgenesis, increases SMN2 exon 7 inclusion, SMN protein production and extends life span. In vitro, RNA mutant analysis and silencing experiments show that while U1A protein is dispensable, the 70K and stem loop IV elements mediate most of the splicing rescue activity through improvement of exon and intron definition. Our findings indicate that precise engineering of the U1 core spliceosomal RNA particle has therapeutic potential in pathologies associated with exon-skipping mutations. Modification of the spliceosome is being tested as a potential therapy for exon-skipping diseases, such as spinal muscular atrophy (SMA). Here the authors show that 70K and stem loop IV structural elements of a modified U1 particle are essential for splicing enhancement and effective treatment of SMA mice.
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8
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Zhou K, Salamov A, Kuo A, Aerts AL, Kong X, Grigoriev IV. Alternative splicing acting as a bridge in evolution. Stem Cell Investig 2015; 2:19. [PMID: 27358887 DOI: 10.3978/j.issn.2306-9759.2015.10.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Alternative splicing (AS) regulates diverse cellular and developmental functions through alternative protein structures of different isoforms. Alternative exons dominate AS in vertebrates; however, very little is known about the extent and function of AS in lower eukaryotes. To understand the role of introns in gene evolution, we examined AS from a green algal and five fungal genomes using a novel EST-based gene-modeling algorithm (COMBEST). METHODS AS from each genome was classified with COMBEST that maps EST sequences to genomes to build gene models. Various aspects of AS were analyzed through statistical methods. The interplay of intron 3n length, phase, coding property, and intron retention (RI) were examined with Chi-square testing. RESULTS With 3 to 834 times EST coverage, we identified up to 73% of AS in intron-containing genes and found preponderance of RI among 11 types of AS. The number of exons, expression level, and maximum intron length correlated with number of AS per gene (NAG), and intron-rich genes suppressed AS. Genes with AS were more ancient, and AS was conserved among fungal genomes. Among stopless introns, non-retained introns (NRI) avoided, but major RI preferred 3n length. In contrast, stop-containing introns showed uniform distribution among 3n, 3n+1, and 3n+2 lengths. We found a clue to the intron phase enigma: it was the coding function of introns involved in AS that dictates the intron phase bias. CONCLUSIONS Majority of AS is non-functional, and the extent of AS is suppressed for intron-rich genes. RI through 3n length, stop codon, and phase bias bridges the transition from functionless to functional alternative isoforms.
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Affiliation(s)
- Kemin Zhou
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Asaf Salamov
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Alan Kuo
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Andrea L Aerts
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Xiangyang Kong
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Igor V Grigoriev
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
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9
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Abstract
Efficient transcription of the HIV-1 genome is regulated by Tat, which recruits P-TEFb from the 7SK small nuclear ribonucleoprotein (snRNP) and other nucleoplasmic complexes to phosphorylate RNA polymerase II and other factors associated with the transcription complex. Although Tat activity is dependent on its binding to the viral TAR sequence, little is known about the cellular factors that might also assemble onto this region of the viral transcript. Here, we report that the splicing factor SRSF1 (SF2/ASF) and Tat recognize overlapping sequences within TAR and the 7SK RNA. SRSF1 expression can inhibit Tat transactivation by directly competing for its binding to TAR. Additionally, we provide evidence that SRSF1 can increase the basal level of viral transcription in the absence of Tat. We propose that SRSF1 activates transcription in the early stages of viral infection by recruiting P-TEFb to TAR from the 7SK snRNP. Whereas in the later stages, Tat substitutes for SRSF1 by promoting release of the stalled polymerase and more efficient transcriptional elongation.
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Affiliation(s)
- Sean Paz
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
| | | | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
- To whom correspondence should be addressed. Tel: +1 5612970627;
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10
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Dal Mas A, Rogalska M, Bussani E, Pagani F. Improvement of SMN2 pre-mRNA processing mediated by exon-specific U1 small nuclear RNA. Am J Hum Genet 2015; 96:93-103. [PMID: 25557785 PMCID: PMC4289686 DOI: 10.1016/j.ajhg.2014.12.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022] Open
Abstract
Exon-specific U1 snRNAs (ExSpe U1s) are modified U1 snRNAs that interact with intronic sequences downstream of the 5′ splice site (ss) by complementarity. This process restores exon skipping caused by different types of mutation. We have investigated the molecular mechanism and activity of these molecules in spinal muscular atrophy (SMA), a genetic neuromuscular disease where a silent exonic transition on the survival motor neuron 2 (SMN2) leads to exon 7 (E7) skipping. By using different cellular models, we show that a single chromosome-integrated copy of ExSpe U1 induced a significant correction of endogenous SMN2 E7 splicing and resulted in the restoration of the corresponding SMN protein levels. Interestingly, the analysis of pre-mRNA transcript abundance and decay showed that ExSpe U1s promote E7 inclusion and stabilizes the SMN pre-mRNA intermediate. This selective effect on pre-mRNA stability resulted in higher levels of SMN mRNAs in comparison with those after treatment with an antisense oligonucleotide (AON) that targets corresponding intronic sequences. In mice harboring the SMN2 transgene, AAV-mediated delivery of ExSpe U1 increased E7 inclusion in brain, heart, liver, kidney, and skeletal muscle. The positive effect of ExSpe U1s on SMN pre-mRNA processing highlights their therapeutic potential in SMA and in other pathologies caused by exon-skipping mutations.
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11
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Mueller N, van Bel N, Berkhout B, Das AT. HIV-1 splicing at the major splice donor site is restricted by RNA structure. Virology 2014; 468-470:609-620. [PMID: 25305540 DOI: 10.1016/j.virol.2014.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/11/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Abstract
The 5' leader region of the HIV-1 RNA contains the major 5' splice site (ss) that is used in the production of all spliced viral RNAs. This splice-donor (SD) region can fold a stem-loop structure. We demonstrate that whereas stabilization of this SD hairpin reduces splicing efficiency, destabilization increases splicing. Both stabilization and destabilization reduce viral fitness. These results demonstrate that the stability of the SD hairpin can modulate the level of splicing, most likely by controlling the accessibility of the 5'ss for the splicing machinery. The natural stability of the SD hairpin restricts splicing and this stability seems to be fine-tuned to reach the optimal balance between unspliced and spliced RNAs for efficient virus replication. The 5'ss region of different HIV-1 isolates and the related SIVmac239 can fold a similar structure. This evolutionary conservation supports the importance of this structure in viral replication.
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Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Nikki van Bel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
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12
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Liu B, Xiang D, Long Y, Tong C. Real time monitoring of junction ribonuclease activity of RNase H using chimeric molecular beacons. Analyst 2013; 138:3238-45. [DOI: 10.1039/c3an36414c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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13
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Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O. Functional insights into the core-TFIIH from a comparative survey. Genomics 2012; 101:178-86. [PMID: 23147676 DOI: 10.1016/j.ygeno.2012.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
Abstract
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk activating kinase) and the core-TFIIH. The core-TFIIH, composed of seven subunits (XPB, XPD, P62, P52, P44, P34, and P8), plays a crucial role in transcription and repair. Here, we performed an extended sequence analysis to establish the accurate phylogenetic distribution of the core-TFIIH in 63 eukaryotic organisms. In spite of the high conservation of the seven subunits at the sequence and genomic levels, the non-enzymatic P8, P34, P52 and P62 are absent from one or a few unicellular species. To gain insight into their respective roles, we undertook a comparative genomic analysis of the whole proteome to identify the gene sets sharing similar presence/absence patterns. While little information was inferred for P8 and P62, our studies confirm the known role of P52 in repair and suggest for the first time the implication of the core TFIIH in mRNA splicing via P34.
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Affiliation(s)
- Florence Bedez
- Laboratoire de Bioinformatique et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire (CNRS, INSERM, UDS), BP163, 67404 Illkirch Cedex, France
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14
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Girard C, Will CL, Peng J, Makarov EM, Kastner B, Lemm I, Urlaub H, Hartmuth K, Lührmann R. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat Commun 2012; 3:994. [PMID: 22871813 DOI: 10.1038/ncomms1998] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 07/10/2012] [Indexed: 12/26/2022] Open
Abstract
There is little quantitative information regarding how much splicing occurs co-transcriptionally in higher eukaryotes, and it remains unclear where precisely splicing occurs in the nucleus. Here we determine the global extent of co- and post-transcriptional splicing in mammalian cells, and their respective subnuclear locations, using antibodies that specifically recognize phosphorylated SF3b155 (P-SF3b155) found only in catalytically activated/active spliceosomes. Quantification of chromatin- and nucleoplasm-associated P-SF3b155 after fractionation of HeLa cell nuclei, reveals that ~80% of pre-mRNA splicing occurs co-transcriptionally. Active spliceosomes localize in situ to regions of decompacted chromatin, at the periphery of or within nuclear speckles. Immunofluorescence microscopy with anti-P-SF3b155 antibodies, coupled with transcription inhibition and a block in splicing after SF3b155 phosphorylation, indicates that post-transcriptional splicing occurs in nuclear speckles and that release of post-transcriptionally spliced mRNA from speckles is coupled to the nuclear mRNA export pathway. Our data provide new insights into when and where splicing occurs in cells.
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Affiliation(s)
- Cyrille Girard
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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15
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Kramski M, Center RJ, Wheatley AK, Jacobson JC, Alexander MR, Rawlin G, Purcell DFJ. Hyperimmune bovine colostrum as a low-cost, large-scale source of antibodies with broad neutralizing activity for HIV-1 envelope with potential use in microbicides. Antimicrob Agents Chemother 2012; 56:4310-9. [PMID: 22664963 PMCID: PMC3421555 DOI: 10.1128/aac.00453-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/23/2012] [Indexed: 11/20/2022] Open
Abstract
Bovine colostrum (first milk) contains very high concentrations of IgG, and on average 1 kg (500 g/liter) of IgG can be harvested from each immunized cow immediately after calving. We used a modified vaccination strategy together with established production systems from the dairy food industry for the large-scale manufacture of broadly neutralizing HIV-1 IgG. This approach provides a low-cost mucosal HIV preventive agent potentially suitable for a topical microbicide. Four cows were vaccinated pre- and/or postconception with recombinant HIV-1 gp140 envelope (Env) oligomers of clade B or A, B, and C. Colostrum and purified colostrum IgG were assessed for cross-clade binding and neutralization against a panel of 27 Env-pseudotyped reporter viruses. Vaccination elicited high anti-gp140 IgG titers in serum and colostrum with reciprocal endpoint titers of up to 1 × 10(5). While nonimmune colostrum showed some intrinsic neutralizing activity, colostrum from 2 cows receiving a longer-duration vaccination regimen demonstrated broad HIV-1-neutralizing activity. Colostrum-purified polyclonal IgG retained gp140 reactivity and neutralization activity and blocked the binding of the b12 monoclonal antibody to gp140, showing specificity for the CD4 binding site. Colostrum-derived anti-HIV antibodies offer a cost-effective option for preparing the substantial quantities of broadly neutralizing antibodies that would be needed in a low-cost topical combination HIV-1 microbicide.
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Affiliation(s)
- Marit Kramski
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Rob J. Center
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Jonathan C. Jacobson
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Marina R. Alexander
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Grant Rawlin
- Immuron Ltd., North Melbourne, Victoria, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
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16
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Hnilicová J, Staněk D. Where splicing joins chromatin. Nucleus 2012; 2:182-8. [PMID: 21818411 DOI: 10.4161/nucl.2.3.15876] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 12/14/2022] Open
Abstract
There are numerous data suggesting that two key steps in gene expression-transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and methylation and potential mechanisms of their role in splicing. It seems that whereas histone acetylation acts mainly by alterating the transcription rate, histone methylation can also influence splicing directly by recruiting various splicing components.
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Affiliation(s)
- Jarmila Hnilicová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague
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17
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Wheatley AK, Kramski M, Alexander MR, Toe JG, Center RJ, Purcell DFJ. Co-expression of miRNA targeting the expression of PERK, but not PKR, enhances cellular immunity from an HIV-1 Env DNA vaccine. PLoS One 2011; 6:e18225. [PMID: 21464971 PMCID: PMC3064671 DOI: 10.1371/journal.pone.0018225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/28/2011] [Indexed: 01/03/2023] Open
Abstract
Small non-coding micro-RNAs (miRNA) are important post-transcriptional regulators of mammalian gene expression that can be used to direct the knockdown of expression from targeted genes. We examined whether DNA vaccine vectors co-expressing miRNA with HIV-1 envelope (Env) antigens could influence the magnitude or quality of the immune responses to Env in mice. Human miR-155 and flanking regions from the non-protein encoding gene mirhg155 were introduced into an artificial intron within an expression vector for HIV-1 Env gp140. Using the miR-155-expressing intron as a scaffold, we developed novel vectors for miRNA-mediated targeting of the cellular antiviral proteins PKR and PERK, which significantly down-modulated target gene expression and led to increased Env expression in vitro. Finally, vaccinating BALB/c mice with a DNA vaccine vector delivering miRNA targeting PERK, but not PKR, was able to augment the generation of Env-specific T-cell immunity. This study provides proof-of-concept evidence that miRNA effectors incorporated into vaccine constructs can positively influence vaccine immunogenicity. Further testing of vaccine-encoded miRNA will determine if such strategies can enhance protective efficacy from vaccines against HIV-1 for eventual human use.
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Affiliation(s)
- Adam K. Wheatley
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marit Kramski
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marina R. Alexander
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jesse G. Toe
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Infection and Immunity, The Walter & Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Rob J. Center
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
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18
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Excessive RNA splicing and inhibition of HIV-1 replication induced by modified U1 small nuclear RNAs. J Virol 2010; 84:12790-800. [PMID: 20926575 DOI: 10.1128/jvi.01257-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 RNA undergoes a complex splicing process whereby over 40 different mRNA species are produced by alternative splicing. In addition, approximately half of the RNA transcripts remain unspliced and either are used to encode Gag and Gag-Pol proteins or are packaged into virions as genomic RNA. It has previously been shown that HIV-1 splicing is regulated by cis elements that bind to cellular factors. These factors either enhance or repress definition of exons that are flanked by the HIV-1 3' splice sites. Here we report that expression of modified U1 snRNPs with increased affinity to HIV-1 downstream 5' splice sites and to sequences within the first tat coding exon act to selectively increase splicing at the upstream 3' splice sites in cotransfected 293T cells. This results in a decrease of unspliced viral RNA levels and an approximately 10-fold decrease in virus production. In addition, excessive splicing of viral RNA is concomitant with a striking reduction in the relative amounts of Gag processing intermediates and products. We also show that T cell lines expressing modified U1 snRNAs exhibit reduced HIV-1 replication. Our results suggest that induction of excessive HIV-1 RNA splicing may be a novel strategy to inhibit virus replication in human patients.
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19
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Spiluttini B, Gu B, Belagal P, Smirnova AS, Nguyen VT, Hébert C, Schmidt U, Bertrand E, Darzacq X, Bensaude O. Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells. J Cell Sci 2010; 123:2085-93. [PMID: 20519584 DOI: 10.1242/jcs.061358] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Numerous non-coding RNAs are known to be involved in the regulation of gene expression. In this work, we analyzed RNAs that co-immunoprecipitated with human RNA polymerase II from mitotic cell extracts and identified U1 small nuclear RNA (snRNA) as a major species. To investigate a possible splicing-independent recruitment of U1 snRNA to transcription units, we established cell lines having integrated a reporter gene containing a functional intron or a splicing-deficient construction. Recruitment of U snRNAs and some splicing factors to transcription sites was evaluated using fluorescence in situ hybridization (FISH) and immunofluorescence. To analyze imaging data, we developed a quantitative procedure, 'radial analysis', based on averaging data from multiple fluorescence images. The major splicing snRNAs (U2, U4 and U6 snRNAs) as well as the U2AF65 and SC35 splicing factors were found to be recruited only to transcription units containing a functional intron. By contrast, U1 snRNA, the U1-70K (also known as snRNP70) U1-associated protein as well as the ASF/SF2 (also known as SFRS1) serine/arginine-rich (SR) protein were efficiently recruited both to normally spliced and splicing-deficient transcription units. The constitutive association of U1 small nuclear ribonucleoprotein (snRNP) with the transcription machinery might play a role in coupling transcription with pre-mRNA maturation.
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Affiliation(s)
- Béatrice Spiluttini
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France
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