1
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Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
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Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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2
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Steward RA, Pruisscher P, Roberts KT, Wheat CW. Genetic constraints in genes exhibiting splicing plasticity in facultative diapause. Heredity (Edinb) 2024; 132:142-155. [PMID: 38291272 PMCID: PMC10923799 DOI: 10.1038/s41437-024-00669-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.
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Affiliation(s)
- Rachel A Steward
- Zoology Department, Stockholm University, Stockholm, Sweden.
- Biology Department, Lund University, Lund, Sweden.
| | - Peter Pruisscher
- Zoology Department, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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3
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López-Pérez M, Aguirre-Garrido F, Herrera-Zúñiga L, Fernández FJ. Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version. Biosystems 2023; 234:105060. [PMID: 37844827 DOI: 10.1016/j.biosystems.2023.105060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare model, in which two tendencies converge, one focused on rapid adaptation to achieve survival, and the other that prevents an over-adaptation effect. In this context, a revision of the gene concept must be made, which must include these new mechanisms and approaches. In this paper, we propose a new conception of the idea of a gene that moves from a static and defined version of hereditary information to a dynamic idea that preponderates gene interaction (circumscribed to that established between protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid) and the selection it exerts, as the irreducible element that works in a coordinated way in a genomic regulatory network (GRN).
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Affiliation(s)
- Marcos López-Pérez
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico.
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico
| | - Leonardo Herrera-Zúñiga
- Chemistry Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico
| | - Francisco J Fernández
- Biotechnology Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico.
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4
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Novosad VO. Identification of Significant RNA-Binding Proteins in the Process of CD44 Splicing Using the Boosted Beta Regression Algorithm. DOKL BIOCHEM BIOPHYS 2023; 510:99-103. [PMID: 37582871 DOI: 10.1134/s1607672923700199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 08/17/2023]
Abstract
The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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5
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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6
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Koller S, Beltraminelli T, Maggi J, Wlodarczyk A, Feil S, Baehr L, Gerth-Kahlert C, Menghini M, Berger W. Functional Analysis of a Novel, Non-Canonical RPGR Splice Variant Causing X-Linked Retinitis Pigmentosa. Genes (Basel) 2023; 14:genes14040934. [PMID: 37107692 PMCID: PMC10137330 DOI: 10.3390/genes14040934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
X-linked retinitis pigmentosa (XLRP) caused by mutations in the RPGR gene is one of the most severe forms of RP due to its early onset and intractable progression. Most cases have been associated with genetic variants within the purine-rich exon ORF15 region of this gene. RPGR retinal gene therapy is currently being investigated in several clinical trials. Therefore, it is crucial to report and functionally characterize (all novel) potentially pathogenic DNA sequence variants. Whole-exome sequencing (WES) was performed for the index patient. The splicing effects of a non-canonical splice variant were tested on cDNA from whole blood and a minigene assay. WES revealed a rare, non-canonical splice site variant predicted to disrupt the wildtype splice acceptor and create a novel acceptor site 8 nucleotides upstream of RPGR exon 12. Reverse-transcription PCR analyses confirmed the disruption of the correct splicing pattern, leading to the insertion of eight additional nucleotides in the variant transcript. Transcript analyses with minigene assays and cDNA from peripheral blood are useful tools for the characterization of splicing defects due to variants in the RPGR and may increase the diagnostic yield in RP. The functional analysis of non-canonical splice variants is required to classify those variants as pathogenic according to the ACMG's criteria.
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Affiliation(s)
- Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Tim Beltraminelli
- Department of Ophthalmology, Institute of Clinical Neurosciences of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6962 Lugano, Switzerland
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Agnès Wlodarczyk
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Luzy Baehr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital, University of Zurich, 8091 Zurich, Switzerland
| | - Moreno Menghini
- Department of Ophthalmology, Institute of Clinical Neurosciences of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6962 Lugano, Switzerland
- Department of Ophthalmology, University Hospital, University of Zurich, 8091 Zurich, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
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7
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Choi S, Cho N, Kim KK. The implications of alternative pre-mRNA splicing in cell signal transduction. Exp Mol Med 2023; 55:755-766. [PMID: 37009804 PMCID: PMC10167241 DOI: 10.1038/s12276-023-00981-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 04/04/2023] Open
Abstract
Cells produce multiple mRNAs through alternative splicing, which ensures proteome diversity. Because most human genes undergo alternative splicing, key components of signal transduction pathways are no exception. Cells regulate various signal transduction pathways, including those associated with cell proliferation, development, differentiation, migration, and apoptosis. Since proteins produced through alternative splicing can exhibit diverse biological functions, splicing regulatory mechanisms affect all signal transduction pathways. Studies have demonstrated that proteins generated by the selective combination of exons encoding important domains can enhance or attenuate signal transduction and can stably and precisely regulate various signal transduction pathways. However, aberrant splicing regulation via genetic mutation or abnormal expression of splicing factors negatively affects signal transduction pathways and is associated with the onset and progression of various diseases, including cancer. In this review, we describe the effects of alternative splicing regulation on major signal transduction pathways and highlight the significance of alternative splicing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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8
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Hussain SS, Abbas M, Abbas S, Wei M, El-Sappah AH, Sun Y, Li Y, Ragauskas AJ, Li Q. Alternative splicing: transcriptional regulatory network in agroforestry. FRONTIERS IN PLANT SCIENCE 2023; 14:1158965. [PMID: 37123829 PMCID: PMC10132464 DOI: 10.3389/fpls.2023.1158965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Sammar Abbas
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mingke Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Arthur J. Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
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Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022; 23:482. [PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites.
Results
Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in “cryptic” splicing regions beyond canonical donor or acceptor splice sites.
Conclusion
Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
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10
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Zheng Y, Li X, Jiao Y, Wu C. High-Risk Human Papillomavirus Oncogenic E6/E7 mRNAs Splicing Regulation. Front Cell Infect Microbiol 2022; 12:929666. [PMID: 35832386 PMCID: PMC9271614 DOI: 10.3389/fcimb.2022.929666] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/19/2022] [Indexed: 11/22/2022] Open
Abstract
High-risk human papillomavirus infection may develop into a persistent infection that is highly related to the progression of various cancers, including cervical cancer and head and neck squamous cell carcinomas. The most common high-risk subtypes are HPV16 and HPV18. The oncogenic viral proteins expressed by high-risk HPVs E6/E7 are tightly involved in cell proliferation, differentiation, and cancerous transformation since E6/E7 mRNAs are derived from the same pre-mRNA. Hence, the alternative splicing in the E6/E7-coding region affects the balance of the E6/E7 expression level. Interrupting the balance of E6 and E7 levels results in cell apoptosis. Therefore, it is crucial to understand the regulation of E6/E7 splice site selection and the interaction of splicing enhancers and silencers with cellular splicing factors. In this review, we concluded the relationship of different E6/E7 transcripts with cancer progression, the known splicing sites, and the identified cis-regulatory elements within high-risk HPV E6/E7-coding region. Finally, we also reviewed the role of various splicing factors in the regulation of high-risk HPV oncogenic E6/E7 mRNA splicing.
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Affiliation(s)
- Yunji Zheng
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xue Li
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yisheng Jiao
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
- *Correspondence: Chengjun Wu,
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11
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Zeng T, Li YI. Predicting RNA splicing from DNA sequence using Pangolin. Genome Biol 2022; 23:103. [PMID: 35449021 PMCID: PMC9022248 DOI: 10.1186/s13059-022-02664-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/04/2022] [Indexed: 11/26/2022] Open
Abstract
Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pangolin outperforms state-of-the-art methods for predicting RNA splicing on a variety of prediction tasks. Pangolin improves prediction of the impact of genetic variants on RNA splicing, including common, rare, and lineage-specific genetic variation. In addition, Pangolin identifies loss-of-function mutations with high accuracy and recall, particularly for mutations that are not missense or nonsense, demonstrating remarkable potential for identifying pathogenic variants.
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Affiliation(s)
- Tony Zeng
- The College, University of Chicago, Chicago, 60637, IL, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, 60637, IL, USA.
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12
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A Novel, Apparently Silent Variant in MFSD8 Causes Neuronal Ceroid Lipofuscinosis with Marked Intrafamilial Variability. Int J Mol Sci 2022; 23:ijms23042271. [PMID: 35216386 PMCID: PMC8877174 DOI: 10.3390/ijms23042271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Variants in MFSD8 can cause neuronal ceroid lipofuscinoses (NCLs) as well as nonsyndromic retinopathy. The mutation spectrum includes mainly missense and stop variants, but splice sites and frameshift variants have also been reported. To date, apparently synonymous substitutions have not been shown to cause MFSD8-associated diseases. We report two closely related subjects from a consanguineous Turkish family who presented classical features of NCLs but demonstrated marked intrafamilial variability in age at the onset and severity of symptoms. In fact, the difference in the onset of first neurologic symptoms was 15 years and that of ophthalmologic symptoms was 12 years. One subject presented an intellectual disability and a considerable cerebellar ataxia syndrome, while the other subject showed no intellectual disability and only a mild atactic syndrome. The diagnostic genetic testing of both subjects based on genome sequencing prioritized a novel, apparently synonymous variant in MFSD8, which was found in homozygosity in both subjects. The variant was not located within an integral part of the splice site consensus sequences. However, the bioinformatic analyses suggested that the mutant allele is more likely to cause exon skipping due to an altered ratio of exonic splice enhancer and silencer motifs. Exon skipping was confirmed in vitro by minigene assays and in vivo by RNA analysis from patient lymphocytes. The mutant transcript is predicted to result in a frameshift and, if translated, in a truncated protein. Synonymous variants are often given a low priority in genetic diagnostics because of their expected lack of functional impact. This study highlights the importance of investigating the impact of synonymous variants on splicing.
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13
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Choi S, Cho N, Kim KK. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms. Int J Biochem Cell Biol 2022; 144:106172. [PMID: 35124219 DOI: 10.1016/j.biocel.2022.106172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of RBFOX2-C., a canonical splice junction-processed RBFOX2 transcript, was different from that of RBFOX2-N.C., which showed nuclear localization. In addition, we confirmed that RBFOX2-C. showed a significantly stronger localization into stress granules than RBFOX2-N.C. upon sodium arsenite treatment. Next, we investigated the importance of non-canonical 3' splice GG sequence selection of specific cis-regulatory elements using minigene constructs of the RBFOX2 gene. We found that the non-canonical 3' splice GG sequence and suboptimal branch point site adjacent region were critical for RBFOX2-N.C. expression through a non-canonical 3' splice selection. Our results suggest a regulatory mechanism for the non-canonical 3' splice selection in the RBFOX2 gene, providing a basis for studies related to the regulation of alternative pre-mRNA splicing through non-canonical splice junction processing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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14
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Çitli Ş, Serdaroglu E. Maternal Germline Mosaicism of a de Novo TUBB2B Mutation Leads to Complex Cortical Dysplasia in Two Siblings. Fetal Pediatr Pathol 2022; 41:155-165. [PMID: 32281916 DOI: 10.1080/15513815.2020.1753270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: Complex cortical dysplasia with other brain malformations-7 (a.k.a. polymicrogyria) caused by mutations in TUBB2B gene is a clinically heterogeneous condition. Case report: We report two siblings with polymicrogyria. Brain MRI showed polymicrogyria, small brainstem, thin corpus callosum and fused basal ganglia. Karyotypes and chromosomal microarray analysis were normal. By whole exome sequencing, there were a de novo variant of c.728C > T (p.P243L) in both siblings and a common single nucleotide polymorphism (SNP) (c.718C > T) in both siblings and the mother. Seminal DNA analysis obtained from father was normal. Conclusion: Maternal germline mosaicism was considered because the sequencing result of the father's sperm was normal, two siblings had the same disease, and both patients and mother had the same SNP.
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Affiliation(s)
- Şenol Çitli
- Medical Genetics, Gaziosmanpasa University Medical Faculty, Tokat, Turkey
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15
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Lai HC, Ho UY, James A, De Souza P, Roberts TL. RNA metabolism and links to inflammatory regulation and disease. Cell Mol Life Sci 2021; 79:21. [PMID: 34971439 PMCID: PMC11072290 DOI: 10.1007/s00018-021-04073-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 09/29/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022]
Abstract
Inflammation is vital to protect the host against foreign organism invasion and cellular damage. It requires tight and concise gene expression for regulation of pro- and anti-inflammatory gene expression in immune cells. Dysregulated immune responses caused by gene mutations and errors in post-transcriptional regulation can lead to chronic inflammatory diseases and cancer. The mechanisms underlying post-transcriptional gene expression regulation include mRNA splicing, mRNA export, mRNA localisation, mRNA stability, RNA/protein interaction, and post-translational events such as protein stability and modification. The majority of studies to date have focused on transcriptional control pathways. However, post-transcriptional regulation of mRNA in eukaryotes is equally important and related information is lacking. In this review, we will focus on the mechanisms involved in the pre-mRNA splicing events, mRNA surveillance, RNA degradation pathways, disorders or symptoms caused by mutations or errors in post-transcriptional regulation during innate immunity especially toll-like receptor mediated pathways.
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Affiliation(s)
- Hui-Chi Lai
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia.
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia.
| | - Uda Y Ho
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Alexander James
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
| | - Paul De Souza
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
| | - Tara L Roberts
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- South West Sydney Clinical School, UNSW Australia, Liverpool, NSW, Australia
- School of Medicine, Western Sydney University, Macarthur, NSW, Australia
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16
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Holm LL, Doktor TK, Hansen MB, Petersen USS, Andresen BS. Vulnerable exons, like ACADM exon 5, are highly dependent on maintaining a correct balance between splicing enhancers and silencers. Hum Mutat 2021; 43:253-265. [PMID: 34923709 DOI: 10.1002/humu.24321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022]
Abstract
It is now widely accepted that aberrant splicing of constitutive exons is often caused by mutations affecting cis-acting splicing regulatory elements, but there is a misconception that all exons have an equal dependency on splicing regulatory elements and thus a similar susceptibility to aberrant splicing. We investigated exonic mutations in ACADM exon 5 to experimentally examine their effect on splicing and found that 7 out of 11 tested mutations affected exon inclusion, demonstrating that this constitutive exon is particularly vulnerable to exonic splicing mutations. Employing ACADM exon 5 and 6 as models, we demonstrate that the balance between splicing enhancers and silencers, flanking intron length, and flanking splice site strength are important factors that determine exon definition and splicing efficiency of the exon in question. Our study shows that two constitutive exons in ACADM have different inherent vulnerabilities to exonic splicing mutations. This suggests that in silico prediction of potential pathogenic effects on splicing from exonic mutations may be improved by also considering the inherent vulnerability of the exon. Moreover, we show that single nucleotide polymorphism that affect either of two different exonic splicing silencers, located far apart in exon 5, all protect against both immediately flanking and more distant exonic splicing mutations.
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Affiliation(s)
- Lise L Holm
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Michael B Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M., Denmark.,Department of Molecular Biology and Biochemistry, The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
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17
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Zimowski KL, Petrillo T, Ho MD, Wechsler J, Shields JE, Denning G, Jhita N, Rivera AA, Escobar MA, Kempton CL, Camire RM, Doering CB. F5-Atlanta: A novel mutation in F5 associated with enhanced East Texas splicing and FV-short production. J Thromb Haemost 2021; 19:1653-1665. [PMID: 33773040 DOI: 10.1111/jth.15314] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Elucidating the molecular pathogenesis underlying East Texas bleeding disorder (ET) led to the discovery of alternatively spliced F5 transcripts harboring large deletions within exon 13. These alternatively spliced transcripts produce a shortened form of coagulation factor V (FV) in which a large portion of its B-domain is deleted. These FV isoforms bind tissue factor pathway inhibitor alpha (TFPIα) with high affinity, prolonging its circulatory half-life and enhancing its anticoagulant effects. While two missense pathogenic variants highlighted this alternative splicing event, similar internally deleted FV proteins are found in healthy controls. OBJECTIVE We identified a novel heterozygous 832 base pair deletion within F5 exon 13, termed F5-Atlanta (F5-ATL), in a patient with severe bleeding. Our objective is to investigate the effect of this deletion on F5 and FV expression. METHODS & RESULTS Assessment of patient plasma revealed markedly elevated levels of total and free TFPI and a FV isoform similar in size to the FV-short described in ET. Sequencing analyses of cDNA revealed the presence of a transcript alternatively spliced using the ET splice sites, thereby removing the F5-ATL deletion. This alternative splicing pattern was recapitulated by heterologous expression in mammalian cells. CONCLUSIONS These findings support a mechanistic model consisting of cis-acting regulatory sequences encoded within F5 exon 13 that control alternative splicing at the ET splice sites and thereby regulate circulating FV-short and TFPIα levels.
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Affiliation(s)
- Karen L Zimowski
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Teodolinda Petrillo
- The Children's Hospital of Philadelphia, The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
| | - Michelle D Ho
- The Children's Hospital of Philadelphia, The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
| | - Julie Wechsler
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Jordan E Shields
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | | | | | | | - Miguel A Escobar
- University of Texas Houston Health Science Center, Houston, Texas, USA
| | - Christine L Kempton
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rodney M Camire
- The Children's Hospital of Philadelphia, The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Philadelphia, Pennsylvania, USA
- Division of Hematology, Department of Pediatrics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher B Doering
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
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18
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El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
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Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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19
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Gadgil A, Raczyńska KD. U7 snRNA: A tool for gene therapy. J Gene Med 2021; 23:e3321. [PMID: 33590603 PMCID: PMC8243935 DOI: 10.1002/jgm.3321] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/22/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
Most U-rich small nuclear ribonucleoproteins (snRNPs) are complexes that mediate the splicing of pre-mRNAs. U7 snRNP is an exception in that it is not involved in splicing but is a key factor in the unique 3' end processing of replication-dependent histone mRNAs. However, by introducing controlled changes in the U7 snRNA histone binding sequence and in the Sm motif, it can be used as an effective tool for gene therapy. The modified U7 snRNP (U7 Sm OPT) is thus not involved in the processing of replication-dependent histone pre-mRNA but targets splicing by inducing efficient skipping or inclusion of selected exons. U7 Sm OPT is of therapeutic importance in diseases that are an outcome of splicing defects, such as myotonic dystrophy, Duchenne muscular dystrophy, amyotrophic lateral sclerosis, β-thalassemia, HIV-1 infection and spinal muscular atrophy. The benefits of using U7 Sm OPT for gene therapy are its compact size, ability to accumulate in the nucleus without causing any toxic effects in the cells, and no immunoreactivity. The risk of transgene misregulation by using U7 Sm OPT is also low because it is involved in correcting the expression of an endogenous gene controlled by its own regulatory elements. Altogether, using U7 Sm OPT as a tool in gene therapy can ensure lifelong treatment, whereas an oligonucleotide or other drug/compound would require repeated administration. It would thus be strategic to harness these unique properties of U7 snRNP and deploy it as a tool in gene therapy.
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Affiliation(s)
- Ankur Gadgil
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznanPoland
| | - Katarzyna Dorota Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznanPoland
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20
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Liao SE, Regev O. Splicing at the phase-separated nuclear speckle interface: a model. Nucleic Acids Res 2021; 49:636-645. [PMID: 33337476 PMCID: PMC7826271 DOI: 10.1093/nar/gkaa1209] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of phase separation may play functional roles. Specifically, we propose that interfaces of phase-separated membraneless bodies could have functional roles in spatially organizing biochemical reactions. Here we propose such a model for the nuclear speckle, a membraneless body implicated in RNA splicing. In our model, sequence-dependent RNA positioning along the nuclear speckle interface coordinates RNA splicing. Our model asserts that exons are preferentially sequestered into nuclear speckles through binding by SR proteins, while introns are excluded through binding by nucleoplasmic hnRNP proteins. As a result, splice sites at exon-intron boundaries are preferentially positioned at nuclear speckle interfaces. This positioning exposes splice sites to interface-localized spliceosomes, enabling the subsequent splicing reaction. Our model provides a simple mechanism that seamlessly explains much of the complex logic of splicing. This logic includes experimental results such as the antagonistic duality between splicing factors, the position dependence of splicing sequence motifs, and the collective contribution of many motifs to splicing decisions. Similar functional roles for phase-separated interfaces may exist for other membraneless bodies.
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Affiliation(s)
- Susan E Liao
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Oded Regev
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
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21
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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22
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Jiang W, Chen L. Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. Comput Struct Biotechnol J 2020; 19:183-195. [PMID: 33425250 PMCID: PMC7772363 DOI: 10.1016/j.csbj.2020.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/26/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by allowing one gene to generate multiple distinct protein isoforms. It adds another regulation layer of gene expression. Up to 95% of human multi-exon genes undergo alternative splicing to encode proteins with different functions. Moreover, around 15% of human hereditary diseases and cancers are associated with alternative splicing. Regulation of alternative splicing is attributed to a set of delicate machineries interacting with each other in aid of important biological processes such as cell development and differentiation. Given the importance of alternative splicing events, their accurate mapping and quantification are paramount for downstream analysis, especially for associating disease with alternative splicing. However, deriving accurate isoform expression from high-throughput RNA-seq data remains a challenging task. In this mini-review, we aim to illustrate I) mechanisms and regulation of alternative splicing, II) alternative splicing associated human disease, III) computational tools for the quantification of isoforms and alternative splicing from RNA-seq.
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Affiliation(s)
- Wei Jiang
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
| | - Liang Chen
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
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23
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Joynt AT, Evans TA, Pellicore MJ, Davis-Marcisak EF, Aksit MA, Eastman AC, Patel SU, Paul KC, Osorio DL, Bowling AD, Cotton CU, Raraigh KS, West NE, Merlo CA, Cutting GR, Sharma N. Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies. PLoS Genet 2020; 16:e1009100. [PMID: 33085659 PMCID: PMC7605713 DOI: 10.1371/journal.pgen.1009100] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/02/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Elucidating the functional consequence of molecular defects underlying genetic diseases enables appropriate design of therapeutic options. Treatment of cystic fibrosis (CF) is an exemplar of this paradigm as the development of CFTR modulator therapies has allowed for targeted and effective treatment of individuals harboring specific genetic variants. However, the mechanism of these drugs limits effectiveness to particular classes of variants that allow production of CFTR protein. Thus, assessment of the molecular mechanism of individual variants is imperative for proper assignment of these precision therapies. This is particularly important when considering variants that affect pre-mRNA splicing, thus limiting success of the existing protein-targeted therapies. Variants affecting splicing can occur throughout exons and introns and the complexity of the process of splicing lends itself to a variety of outcomes, both at the RNA and protein levels, further complicating assessment of disease liability and modulator response. To investigate the scope of this challenge, we evaluated splicing and downstream effects of 52 naturally occurring CFTR variants (exonic = 15, intronic = 37). Expression of constructs containing select CFTR intronic sequences and complete CFTR exonic sequences in cell line models allowed for assessment of RNA and protein-level effects on an allele by allele basis. Characterization of primary nasal epithelial cells obtained from individuals harboring splice variants corroborated in vitro data. Notably, we identified exonic variants that result in complete missplicing and thus a lack of modulator response (e.g. c.2908G>A, c.523A>G), as well as intronic variants that respond to modulators due to the presence of residual normally spliced transcript (e.g. c.4242+2T>C, c.3717+40A>G). Overall, our data reveals diverse molecular outcomes amongst both exonic and intronic variants emphasizing the need to delineate RNA, protein, and functional effects of each variant in order to accurately assign precision therapies. Genetic variants that impact pre-mRNA splicing are a common cause of genetic disease and have varying downstream molecular consequences. As a result, precision therapies that function at the protein level are not always effective for these variants and thus careful assessment is necessary. Here we evaluate RNA-level effects of 52 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and show that study of splicing and its consequences allows for more accurate assignment of precision therapies.
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Affiliation(s)
- Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Taylor A. Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew J. Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily F. Davis-Marcisak
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melis A. Aksit
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alice C. Eastman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Kathleen C. Paul
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Derek L. Osorio
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa D. Bowling
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Calvin U. Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Natalie E. West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
| | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
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24
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
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25
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Eymin B. Targeting the spliceosome machinery: A new therapeutic axis in cancer? Biochem Pharmacol 2020; 189:114039. [PMID: 32417188 DOI: 10.1016/j.bcp.2020.114039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023]
Abstract
Pre-mRNA splicing is the removal of introns and ligation of exons to form mature mRNAs, and it provides a critical mechanism by which eukaryotic cells can regulate their gene expression. Strikingly, more than 90% of protein-encoding transcripts are alternatively spliced, through exon inclusion/skipping, differential use of 5' or 3' alternative splice sites, intron retention or selection of an alternative promoter, thereby drastically increasing protein diversity. Splicing is altered in various pathological conditions, including cancers. In the last decade, high-throughput transcriptomic analyses have identified thousands of splice variants in cancers, which can distinguish between tumoral and normal tissues as well as identify tumor types, subtypes and clinical stages. These abnormal or aberrantly expressed splice variants, found in all cancer hallmarks, can result from mutations in splice sites, deregulated expression or even somatic mutations of components of the spliceosome machinery. Therefore, and based on these recent observations, a new anti-cancer strategy of targeting the spliceosome machinery with small molecules has emerged; however, the potential for these therapies is still a matter of great debate. Notably, more preclinical studies are needed to clarify which splicing patterns are mainly affected by these compounds, which cancer patients could be the most eligible for these treatments and whether using these spliceosome inhibitors alone or in combination with chemotherapies or targeted therapies would provide better therapeutic benefits. In this commentary, I will discuss all of these aspects.
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Affiliation(s)
- Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute For Advanced Biosciences, 38000 Grenoble, France; Université Grenoble Alpes, 38000 Grenoble, France.
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26
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Lang AS, Austin SH, Harris RM, Calisi RM, MacManes MD. Stress-mediated convergence of splicing landscapes in male and female rock doves. BMC Genomics 2020; 21:251. [PMID: 32293250 PMCID: PMC7092514 DOI: 10.1186/s12864-020-6600-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/20/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus contributing to more refined traits on which natural and sexual selection can act. While it has been long known that various forms of environmental stress can negatively affect sexual behavior and reproduction, we know little of how stress can affect the alternative splicing associated with these events, and less still about how splicing may differ between sexes. Using the model of the rock dove (Columba livia), our team previously uncovered sexual dimorphism in the basal and stress-responsive gene transcription of a biological system necessary for facilitating sexual behavior and reproduction, the hypothalamic-pituitary-gonadal (HPG) axis. In this study, we delve further into understanding the mechanistic underpinnings of how changes in the environment can affect reproduction by testing the alternative splicing response of the HPG axis to an external stressor in both sexes. RESULTS This study reveals dramatic baseline differences in HPG alternative splicing between males and females. However, after subjecting subjects to a restraint stress paradigm, we found a significant reduction in these differences between the sexes. In both stress and control treatments, we identified a higher incidence of splicing activity in the pituitary in both sexes as compared to other tissues. Of these splicing events, the core exon event is the most abundant form of splicing and more frequently occurs in the coding regions of the gene. Overall, we observed less splicing activity in the 3'UTR (untranslated region) end of transcripts than the 5'UTR or coding regions. CONCLUSIONS Our results provide vital new insight into sex-specific aspects of the stress response on the HPG axis at an unprecedented proximate level. Males and females uniquely respond to stress, yet exhibit splicing patterns suggesting a convergent, optimal splicing landscape for stress response. This information has the potential to inform evolutionary theory as well as the development of highly-specific drug targets for stress-induced reproductive dysfunction.
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Affiliation(s)
- Andrew S Lang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA.
| | - Suzanne H Austin
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Rayna M Harris
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Rebecca M Calisi
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, USA
| | - Matthew D MacManes
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, USA
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27
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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Ribeiro M, Furtado M, Martins S, Carvalho T, Carmo-Fonseca M. RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21041329. [PMID: 32079122 PMCID: PMC7072897 DOI: 10.3390/ijms21041329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/27/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM), the most common inherited heart disease, is predominantly caused by mutations in genes that encode sarcomere-associated proteins. Effective gene-based diagnosis is critical for the accurate clinical management of patients and their family members. However, the introduction of high-throughput DNA sequencing approaches for clinical diagnostics has vastly expanded the number of variants of uncertain significance, leading to many inconclusive results that limit the clinical utility of genetic testing. More recently, developments in RNA analysis have been improving diagnostic outcomes by identifying new variants that interfere with splicing. This review summarizes recent discoveries of RNA mis-splicing in HCM and provides an overview of research that aims to apply the concept of RNA therapeutics to HCM.
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Affiliation(s)
- Marta Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Department of Bioengineering and iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Sandra Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Teresa Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Correspondence:
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Gu J, Ma S, Zhang Y, Wang D, Cao S, Wang ZY. Genome-Wide Identification of Cassava Serine/Arginine-Rich Proteins: Insights into Alternative Splicing of Pre-mRNAs and Response to Abiotic Stress. PLANT & CELL PHYSIOLOGY 2020; 61:178-191. [PMID: 31596482 DOI: 10.1093/pcp/pcz190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/26/2019] [Indexed: 05/08/2023]
Abstract
Serine/arginine-rich (SR) proteins have an essential role in the splicing of pre-messenger RNA (pre-mRNA) in eukaryote. Pre-mRNA with introns can be alternatively spliced to generate multiple transcripts, thereby increasing adaptation to the external stress conditions in planta. However, pre-mRNA of SR proteins can also be alternatively spliced in different plant tissues and in response to diverse stress treatments, indicating that SR proteins might be involved in regulating plant development and adaptation to environmental changes. We identified and named 18 SR proteins in cassava and systematically studied their splicing and transcriptional changes under tissue-specific and abiotic stress conditions. Fifteen out of 18 SR genes showed alternative splicing in the tissues. 45 transcripts were found from 18 SR genes under normal conditions, whereas 55 transcripts were identified, and 21 transcripts were alternate spliced in some SR genes under salt stress, suggesting that SR proteins might participate in the plant adaptation to salt stress. We then found that overexpression of MeSR34 in Arabidopsis enhanced the tolerance to salt stress through maintaining reactive oxygen species homeostasis and increasing the expression of calcineurin B-like proteins (CBL)-CBL-interacting protein kinases and osmotic stress-related genes. Therefore, our findings highlight the critical role of cassava SR proteins as regulators of RNA splicing and salt tolerance in planta.
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Affiliation(s)
- Jinbao Gu
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, Guangdong 510316, China
| | - Siya Ma
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Yuna Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi 330031, China
| | - Shuqing Cao
- School of Food Science and Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhen-Yu Wang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou, Guangdong 510316, China
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
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Movassat M, Forouzmand E, Reese F, Hertel KJ. Exon size and sequence conservation improves identification of splice-altering nucleotides. RNA (NEW YORK, N.Y.) 2019; 25:1793-1805. [PMID: 31554659 PMCID: PMC6859846 DOI: 10.1261/rna.070987.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Pre-mRNA splicing is regulated through multiple trans-acting splicing factors. These regulators interact with the pre-mRNA at intronic and exonic positions. Given that most exons are protein coding, the evolution of exons must be modulated by a combination of selective coding and splicing pressures. It has previously been demonstrated that selective splicing pressures are more easily deconvoluted when phylogenetic comparisons are made for exons of identical size, suggesting that exon size-filtered sequence alignments may improve identification of nucleotides evolved to mediate efficient exon ligation. To test this hypothesis, an exon size database was created, filtering 76 vertebrate sequence alignments based on exon size conservation. In addition to other genomic parameters, such as splice-site strength, gene position, or flanking intron length, this database permits the identification of exons that are size- and/or sequence-conserved. Highly size-conserved exons are always sequence-conserved. However, sequence conservation does not necessitate exon size conservation. Our analysis identified evolutionarily young exons and demonstrated that length conservation is a strong predictor of alternative splicing. A published data set of approximately 5000 exonic SNPs associated with disease was analyzed to test the hypothesis that exon size-filtered sequence comparisons increase detection of splice-altering nucleotides. Improved splice predictions could be achieved when mutations occur at the third codon position, especially when a mutation decreases exon inclusion efficiency. The results demonstrate that coding pressures dominate nucleotide composition at invariable codon positions and that exon size-filtered sequence alignments permit identification of splice-altering nucleotides at wobble positions.
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Affiliation(s)
- Maliheh Movassat
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Fairlie Reese
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
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Xu B, Shi Y, Wu Y, Meng Y, Jin Y. Role of RNA secondary structures in regulating Dscam alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194381. [DOI: 10.1016/j.bbagrm.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
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Ustaoglu P, Haussmann IU, Liao H, Torres-Mendez A, Arnold R, Irimia M, Soller M. Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. RNA (NEW YORK, N.Y.) 2019; 25:1353-1365. [PMID: 31292260 PMCID: PMC6800468 DOI: 10.1261/rna.071316.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Alternative splicing of pre-mRNA is a major mechanism to diversify protein functionality in metazoans from a limited number of genes. The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene, which is important for neuronal wiring and phagocytosis of bacteria, can generate up to 38,016 isoforms by mutually exclusive alternative splicing in four clusters of variable exons. However, it is not understood how a specific exon is chosen from the many variables and how variable exons are prevented from being spliced together. A main role in the regulation of Dscam alternative splicing has been attributed to RNA binding proteins (RBPs), but how they impact on exon selection is not well understood. Serine-arginine rich (SR) proteins and hnRNP proteins are the two main types of RBPs with major roles in exon definition and splice site selection. Here, we analyzed the role of SR and hnRNP proteins in Dscam exon 9 alternative splicing in mutant Drosophila melanogaster embryos because of their essential function for development. Strikingly, loss or overexpression of canonical SR and hnRNP proteins even when multiple proteins are depleted together, does not affect Dscam alternative exon selection very dramatically. Conversely, noncanonical SR protein Serine-arginine repetitive matrix 2/3/4 (Srrm234) is a main determinant of exon inclusion in the Dscam exon 9 cluster. Since long-range base-pairings are absent in the exon 9 cluster, our data argue for a small complement of regulatory factors as main determinants of exon inclusion in the Dscam exon 9 cluster.
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Affiliation(s)
- Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham B5 3TN, United Kingdom
| | - Hongzhi Liao
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Arnold
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Barcelona 08010, Spain
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Desterro J, Bak-Gordon P, Carmo-Fonseca M. Targeting mRNA processing as an anticancer strategy. Nat Rev Drug Discov 2019; 19:112-129. [PMID: 31554928 DOI: 10.1038/s41573-019-0042-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
Abstract
Discoveries in the past decade have highlighted the potential of mRNA as a therapeutic target for cancer. Specifically, RNA sequencing revealed that, in addition to gene mutations, alterations in mRNA can contribute to the initiation and progression of cancer. Indeed, precursor mRNA processing, which includes the removal of introns by splicing and the formation of 3' ends by cleavage and polyadenylation, is frequently altered in tumours. These alterations result in numerous cancer-specific mRNAs that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumour-suppressor genes. Abnormally spliced and polyadenylated mRNAs are also associated with resistance to cancer treatment and, unexpectedly, certain cancers are highly sensitive to the pharmacological inhibition of splicing. This Review summarizes recent progress in our understanding of how splicing and polyadenylation are altered in cancer and highlights how this knowledge has been translated for drug discovery, resulting in the production of small molecules and oligonucleotides that modulate the spliceosome and are in clinical trials for the treatment of cancer.
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Affiliation(s)
- Joana Desterro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Português de Oncologia de Lisboa, Serviço de Hematologia, Lisboa, Portugal
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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34
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Cheng J, Çelik MH, Nguyen TYD, Avsec Ž, Gagneur J. CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice. Hum Mutat 2019; 40:1243-1251. [PMID: 31070280 DOI: 10.1002/humu.23788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 11/10/2022]
Abstract
Pathogenic genetic variants often primarily affect splicing. However, it remains difficult to quantitatively predict whether and how genetic variants affect splicing. In 2018, the fifth edition of the Critical Assessment of Genome Interpretation proposed two splicing prediction challenges based on experimental perturbation assays: Vex-seq, assessing exon skipping, and MaPSy, assessing splicing efficiency. We developed a modular modeling framework, MMSplice, the performance of which was among the best on both challenges. Here we provide insights into the modeling assumptions of MMSplice and its individual modules. We furthermore illustrate how MMSplice can be applied in practice for individual genome interpretation, using the MMSplice VEP plugin and the Kipoi variant interpretation plugin, which are directly applicable to VCF files.
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Affiliation(s)
- Jun Cheng
- Department of Informatics, Technical University of Munich, Garching, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | - Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany
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Lages A, Proud CG, Holloway JW, Vorechovsky I. Thioflavin T Monitoring of Guanine Quadruplex Formation in the rs689-Dependent INS Intron 1. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:770-777. [PMID: 31150930 PMCID: PMC6539410 DOI: 10.1016/j.omtn.2019.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/27/2019] [Accepted: 04/27/2019] [Indexed: 12/21/2022]
Abstract
The human proinsulin gene (INS) contains a thymine-to-adenine variant (rs689) located in the 3′ splice site (3′ ss) recognition motif of the first intron. The adenine at rs689 is strongly associated with type 1 diabetes. By weakening the polypyrimidine tract, the adenine allele reduces the efficiency of intron 1 splicing, which can be ameliorated by antisense oligonucleotides blocking a splicing silencer located upstream of the 3′ ss. The silencer is surrounded by guanine-rich tracts that may form guanine quadruplexes (G4s) and modulate the accessibility of the silencer. Here, we employed thioflavin T (ThT) to monitor G4 formation in synthetic DNAs and RNAs derived from INS intron 1. We show that the antisense target is surrounded by ThT-positive segments in each direction, with oligoribonucleotides exhibiting consistently higher fluorescence than their DNA counterparts. The signal was reduced for ThT-positive oligonucleotides that were extended into the silencer, indicating that flanking G4s have a potential to mask target accessibility. Real-time monitoring of ThT fluorescence during INS transcription in vitro revealed a negative correlation with ex vivo splicing activities of corresponding INS constructs. Together, these results provide a better characterization of antisense targets in INS primary transcripts for restorative strategies designed to improve the INS splicing defect associated with type 1 diabetes.
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Affiliation(s)
- Ana Lages
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Christopher G Proud
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK; Lifelong Health and Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - John W Holloway
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK.
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36
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Gu J, Li W, Wang S, Zhang X, Coules A, Ding G, Xu F, Ren J, Lu C, Shi L. Differential Alternative Splicing Genes in Response to Boron Deficiency in Brassica napus. Genes (Basel) 2019; 10:genes10030224. [PMID: 30889858 PMCID: PMC6471828 DOI: 10.3390/genes10030224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/07/2019] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) can increase transcriptome diversity, protein diversity and protein yield, and is an important mechanism to regulate plant responses to stress. Oilseed rape (Brassica napus L.), one of the main oil crops in China, shows higher sensitivity to boron (B) deficiency than other species. Here, we demonstrated AS changes that largely increased the diversity of the mRNA expressed in response to B deficiency in B. napus. Each gene had two or more transcripts on average. A total of 33.3% genes in both Qingyou10 (QY10, B-efficient cultivar) and Westar10 (W10, B-inefficient cultivar) showed AS in both B conditions. The types of AS events were mainly intron retention, 3′ alternative splice site, 5′ alternative splice site and exon skipping. The tolerance ability of QY10 was higher than that of W10, possibly because there were far more differential alternative splicing (DAS) genes identified in QY10 at low B conditions than in W10. The number of genes with both DAS and differentially expressed (DE) was far lower than that of the genes that were either with DAS or DE in QY10 and W10, suggesting that the DAS and DE genes were independent. Four Serine/Arginine-rich (SR) splicing factors, BnaC06g14780D, BnaA01g14750D, BnaA06g15930D and BnaC01g41640D, underwent differentially alternative splicing in both cultivars. There existed gene–gene interactions between BnaC06g14780D and the genes associated with the function of B in oilseed rape at low B supply. This suggests that oilseed rape could regulate the alterative pre-mRNA splicing of SR protein related genes to increase the plant tolerance to B deficiency.
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Affiliation(s)
- Jin Gu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaoyan Zhang
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Anne Coules
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
| | - Chungui Lu
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham NG25 0QF, UK.
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
- Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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Cheng J, Nguyen TYD, Cygan KJ, Çelik MH, Fairbrother WG, Avsec Ž, Gagneur J. MMSplice: modular modeling improves the predictions of genetic variant effects on splicing. Genome Biol 2019; 20:48. [PMID: 30823901 PMCID: PMC6396468 DOI: 10.1186/s13059-019-1653-z] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI5 exon skipping prediction challenge. The MMSplice modules are neural networks scoring exon, intron, and splice sites, trained on distinct large-scale genomics datasets. These modules are combined to predict effects of variants on exon skipping, splice site choice, splicing efficiency, and pathogenicity, with matched or higher performance than state-of-the-art. Our models, available in the repository Kipoi, apply to variants including indels directly from VCF files.
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Affiliation(s)
- Jun Cheng
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748 Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, München, Germany
| | - Thi Yen Duong Nguyen
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748 Germany
| | - Kamil J. Cygan
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island USA
| | - Muhammed Hasan Çelik
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748 Germany
| | - William G. Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island USA
| | - žiga Avsec
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748 Germany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, München, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748 Germany
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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39
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Cheatham AM, Davis SE, Khatua AK, Popik W. Blocking the 5' splice site of exon 4 by a morpholino oligomer triggers APOL1 protein isoform switch. Sci Rep 2018; 8:8739. [PMID: 29880816 PMCID: PMC5992166 DOI: 10.1038/s41598-018-27104-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/21/2018] [Indexed: 12/16/2022] Open
Abstract
APOL1 risk alleles G1 or G2 are associated with a kidney disease phenotype exclusively in people of recent African ancestry. Here we show that exon 4 encoding a part of the APOL1 signal peptide is constitutively spliced in major APOL1 transcripts expressed in kidney glomerular and tubular cells. We demonstrate that constitutive splicing of exon 4 results from a suboptimal hnRNP A1 binding motif found in exon 4. Accordingly, a robust binding of hnRNP A1 protein to a consensus hnRNP A1 cis-acting element in exon 4 results in almost complete exclusion of exon 4 from the APOL1 minigene transcripts. Blocking the 5' splice site at the exon 4/intron boundary with a specific antisense morpholino oligonucleotide excludes exon 4 from the splicing pattern of endogenous APOL1 transcripts. These transcripts are fully functional and produce APOL1 protein isoform that is not normally detectable in podocytes. Together with our previous data showing no cytotoxicity of overexpressed APOL1 isoform lacking exon 4, we propose that morpholino-induced APOL1 isoform switch may provide a new tool to identify in vivo molecular mechanism(s) by which risk alleles promote or mediate the kidney disease phenotype.
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Affiliation(s)
- Amber M Cheatham
- Meharry Medical College, Center for AIDS Health Disparities Research, Department of Microbiology and Immunology, 1005 D. B. Todd Blvd, Nashville, TN, 37028, USA
| | - Shamara E Davis
- Meharry Medical College, Center for AIDS Health Disparities Research, Department of Microbiology and Immunology, 1005 D. B. Todd Blvd, Nashville, TN, 37028, USA
| | - Atanu K Khatua
- Meharry Medical College, Center for AIDS Health Disparities Research, Department of Microbiology and Immunology, 1005 D. B. Todd Blvd, Nashville, TN, 37028, USA
| | - Waldemar Popik
- Meharry Medical College, Center for AIDS Health Disparities Research, Department of Microbiology and Immunology, 1005 D. B. Todd Blvd, Nashville, TN, 37028, USA.
- Department of Internal Medicine, 1005 D. B. Todd Blvd, Nashville, TN, 37028, USA.
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SRSF1 suppresses selection of intron-distal 5' splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein. Sci Rep 2017; 7:10446. [PMID: 28874828 PMCID: PMC5585400 DOI: 10.1038/s41598-017-11036-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/18/2017] [Indexed: 01/23/2023] Open
Abstract
Dok-7 is a non-catalytic adaptor protein that facilitates agrin-induced clustering of acetylcholine receptors (AChR) at the neuromuscular junction. Alternative selection of 5′ splice sites (SSs) of DOK7 intron 4 generates canonical and frame-shifted transcripts. We found that the canonical full-length Dok-7 enhanced AChR clustering, whereas the truncated Dok-7 did not. We identified a splicing cis-element close to the 3′ end of exon 4 by block-scanning mutagenesis. RNA affinity purification and mass spectrometry revealed that SRSF1 binds to the cis-element. Knocking down of SRSF1 enhanced selection of the intron-distal 5′ SS of DOK7 intron 4, whereas MS2-mediated artificial tethering of SRSF1 to the identified cis-element suppressed it. Isolation of an early spliceosomal complex revealed that SRSF1 inhibited association of U1 snRNP to the intron-distal 5′ SS, and rather enhanced association of U1 snRNP to the intron-proximal 5′ SS, which led to upregulation of the canonical DOK7 transcript. Integrated global analysis of CLIP-seq and RNA-seq also indicated that binding of SRSF1 immediately upstream to two competing 5′ SSs suppresses selection of the intron-distal 5′ SS in hundreds of human genes. We demonstrate that SRSF1 critically regulates alternative selection of adjacently placed 5′ SSs by modulating binding of U1 snRNP.
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Wei HH, Liu Y, Wang Y, Lu Q, Yang X, Li J, Wang Z. Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells. J Vis Exp 2017. [PMID: 28518098 DOI: 10.3791/54967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The processing of most eukaryotic RNAs is mediated by RNA Binding Proteins (RBPs) with modular configurations, including an RNA recognition module, which specifically binds the pre-mRNA target and an effector domain. Previously, we have taken advantage of the unique RNA binding mode of the PUF domain in human Pumilio 1 to generate a programmable RNA binding scaffold, which was used to engineer various artificial RBPs to manipulate RNA metabolism. Here, a detailed protocol is described to construct Engineered Splicing Factors (ESFs) that are specifically designed to modulate the alternative splicing of target genes. The protocol includes how to design and construct a customized PUF scaffold for a specific RNA target, how to construct an ESF expression plasmid by fusing a designer PUF domain and an effector domain, and how to use ESFs to manipulate the splicing of target genes. In the representative results of this method, we have also described the common assays of ESF activities using splicing reporters, the application of ESF in cultured human cells, and the subsequent effect of splicing changes. By following the detailed protocols in this report, it is possible to design and generate ESFs for the regulation of different types of Alternative Splicing (AS), providing a new strategy to study splicing regulation and the function of different splicing isoforms. Moreover, by fusing different functional domains with a designed PUF domain, researchers can engineer artificial factors that target specific RNAs to manipulate various steps of RNA processing.
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Affiliation(s)
- Huan-Huan Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yuanlong Liu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Yang Wang
- Institute of Cancer Stem Cell, Second Affiliated Hospital, Cancer Center, Dalian Medical University
| | - Qianyun Lu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Xuerong Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Jiefu Li
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS)
| | - Zefeng Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences (SIBS);
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Serine/Arginine-Rich Splicing Factor 3 and Heterogeneous Nuclear Ribonucleoprotein A1 Regulate Alternative RNA Splicing and Gene Expression of Human Papillomavirus 18 through Two Functionally Distinguishable cis Elements. J Virol 2016; 90:9138-52. [PMID: 27489271 DOI: 10.1128/jvi.00965-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/25/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED Human papillomavirus 18 (HPV18) is the second most common oncogenic HPV type associated with cervical, anogenital, and oropharyngeal cancers. Like other oncogenic HPVs, HPV18 encodes two major (one early and one late) polycistronic pre-mRNAs that are regulated by alternative RNA splicing to produce a repertoire of viral transcripts for the expression of individual viral genes. However, RNA cis-regulatory elements and trans-acting factors contributing to HPV18 alternative RNA splicing remain unknown. In this study, an exonic splicing enhancer (ESE) in the nucleotide (nt) 3520 to 3550 region in the HPV18 genome was identified and characterized for promotion of HPV18 929^3434 splicing and E1^E4 production through interaction with SRSF3, a host oncogenic splicing factor differentially expressed in epithelial cells and keratinocytes. Introduction of point mutations in the SRSF3-binding site or knockdown of SRSF3 expression in cells reduces 929^3434 splicing and E1^E4 production but activates other, minor 929^3465 and 929^3506 splicing. Knockdown of SRSF3 expression also enhances the expression of E2 and L1 mRNAs. An exonic splicing silencer (ESS) in the HPV18 nt 612 to 639 region was identified as being inhibitory to the 233^416 splicing of HPV18 E6E7 pre-mRNAs via binding to hnRNP A1, a well-characterized, abundantly and ubiquitously expressed RNA-binding protein. Introduction of point mutations into the hnRNP A1-binding site or knockdown of hnRNP A1 expression promoted 233^416 splicing and reduced E6 expression. These data provide the first evidence that the alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host trans-acting splicing factors. IMPORTANCE Expression of HPV18 genes is regulated by alternative RNA splicing of viral polycistronic pre-mRNAs to produce a repertoire of viral early and late transcripts. RNA cis elements and trans-acting factors contributing to HPV18 alternative RNA splicing have been discovered in this study for the first time. The identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnRNP A1, and regulates E6 and E7 expression of the early E6E7 polycistronic pre-mRNA. The identified ESE at the E1^E4 ORF promotes HPV18 929^3434 splicing of both viral early and late pre-mRNAs and E1^E4 production through interaction with SRSF3. This study provides important observations on how alternative RNA splicing of HPV18 pre-mRNAs is subject to regulation by viral RNA cis elements and host splicing factors and offers potential therapeutic targets to overcome HPV-related cancer.
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Zhang Z, Zhou N, Huang J, Ho TT, Zhu Z, Qiu Z, Zhou X, Bai C, Wu F, Xu M, Mo YY. Regulation of androgen receptor splice variant AR3 by PCGEM1. Oncotarget 2016; 7:15481-91. [PMID: 26848868 PMCID: PMC4941255 DOI: 10.18632/oncotarget.7139] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
The androgen receptor (AR) is required for prostate development and is also a major driver of prostate cancer pathogenesis. Thus androgen deprivation therapy (ADT) is the mainstay of treatment for advanced prostate cancer. However, castration resistance due to expression of constitutively active AR splice variants is a significant challenge to prostate cancer therapy; little is known why effectiveness of ADT can only last for a relatively short time. In the present study, we show that PCGEM1 interacts with splicing factors heterogeneous nuclear ribonucleoprotein (hnRNP) A1 and U2AF65, as determined by RNA precipitation and Western blot, suggesting a role for PCGEM1 in alternative splicing. In support of this possibility, PCGEM1 is correlated with AR3, a predominant and clinically important form of AR splice variants in prostate cancer. Moreover, androgen deprivation (AD) induces PCGEM1 and causes its accumulation in nuclear speckles. Finally, we show that the AD-induced PCGEM1 regulates the competition between hnRNP A1 and U2AF65 for AR pre-mRNA. AD promotes PCGEM1 to interact with both hnRNP A1 and U2AF65 with different consequences. While the interaction of PCGEM1 with hnRNP A1 suppresses AR3 by exon skipping, its interaction with U2AF65 promotes AR3 by exonization. Together, we demonstrate an AD-mediated AR3 expression involving PCGEM1 and splicing factors.
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Affiliation(s)
- Ziqiang Zhang
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pulmonary Medicine, Tongji Hospital, Tongji University, Shanghai, China
| | - Nanjiang Zhou
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jianguo Huang
- Department of Biochemistry and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Tsui-Ting Ho
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Zhuxian Zhu
- Department of Nephrology, Tongji Hospital, Tongji University, Shanghai, China
| | - Zhongmin Qiu
- Department of Pulmonary Medicine, Tongji Hospital, Tongji University, Shanghai, China
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chunxue Bai
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, PR China
| | | | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yin-Yuan Mo
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
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Wang Y, Wang Z. Design of RNA-Binding Proteins: Manipulate Alternative Splicing in Human Cells with Artificial Splicing Factors. Methods Mol Biol 2016; 1421:227-41. [PMID: 26965269 DOI: 10.1007/978-1-4939-3591-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The majority of human genes undergo alternative splicing to produce multiple isoforms with distinct functions. The dysregulations of alternative splicing have been found to be closely associated with various human diseases; thus new approaches to modulate disease-associated splicing events will provide great therapeutic potentials. Here we report protocols for constructing novel artificial splicing factors that can be designed to specifically modulate alternative splicing of target genes. By following the method outlined in this protocol, it is possible to design and generate artificial splicing factors with diverse activities in regulating different types of alternative splicing. The artificial splicing factors can be used to change splicing of either minigenes or endogenous genes in cultured human cells, providing a new strategy to study the regulation of alternative splicing and function of alternatively spliced products.
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Affiliation(s)
- Yang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, China
| | - Zefeng Wang
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, CB # 7365, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
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45
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The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration. Nat Commun 2015; 5:3078. [PMID: 24452013 PMCID: PMC4146490 DOI: 10.1038/ncomms4078] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/06/2013] [Indexed: 01/15/2023] Open
Abstract
Alternative splicing of pre-messenger RNA (mRNA) is a critical stage of gene regulation in response to environmental stimuli. Here we show that DAZAP1, an RNA-binding protein involved in mammalian development and spermatogenesis, promotes inclusion of weak exons through specific recognition of diverse cis-elements. The carboxy-terminal proline-rich domain of DAZAP1 interacts with and neutralizes general splicing inhibitors, and is sufficient to activate splicing when recruited to pre-mRNA. This domain is phosphorylated by the MEK/Erk (extracellular signal-regulated protein kinase) pathway and this modification is essential for the splicing regulatory activity and the nuclear/cytoplasmic translocation of DAZAP1. Using mRNA-seq, we identify endogenous splicing events regulated by DAZAP1, many of which are involved in maintaining cell growth. Knockdown or over-expression of DAZAP1 causes a cell proliferation defect. Taken together, these studies reveal a molecular mechanism that integrates splicing control into MEK/Erk-regulated cell proliferation.
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46
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Price N, Graur D. Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol 2015; 82:51-64. [PMID: 26563252 DOI: 10.1007/s00239-015-9719-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 11/04/2015] [Indexed: 11/28/2022]
Abstract
It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.
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Affiliation(s)
- Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Dan Graur
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
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Rosenberg AB, Patwardhan RP, Shendure J, Seelig G. Learning the sequence determinants of alternative splicing from millions of random sequences. Cell 2015; 163:698-711. [PMID: 26496609 DOI: 10.1016/j.cell.2015.09.054] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/28/2015] [Accepted: 09/21/2015] [Indexed: 01/24/2023]
Abstract
Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Toward better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of over two million (M) synthetic mini-genes, which include degenerate subsequences totaling over 100 M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing, as well as to gain new mechanistic insights. Our results show that the vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5' splicing also enhance (suppress) exon inclusion in alternative 3' or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.
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Affiliation(s)
- Alexander B Rosenberg
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rupali P Patwardhan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA.
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Zhang Z, Wang X, Li R, Ju Z, Qi C, Zhang Y, Guo F, Luo G, Li Q, Wang C, Zhong J, Xu Y, Huang J. Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli. Microbiol Res 2015; 174:24-32. [PMID: 25946326 DOI: 10.1016/j.micres.2015.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 11/18/2022]
Abstract
Neutrophil cytosolic factor 1 (NCF1) plays a crucial role in host defense against microbial pathogens. In this study, we investigated the potential alternative splicing patterns, expression and splice-relevant single nucleotide polymorphisms (SNPs) of the bovine NCF1 gene to increase insights into its potential role against bovine mastitis caused by Escherichia coli infection. Using RT-PCR and clone sequencing methods, we found two novel splice variants designed as NCF1-TV1 (retained intron 6) and NCF1-TV2 (retained part of intron 8), respectively, encoding two putative truncated proteins (239AA and 283AA). Two splice variants were drastically up-regulated in the mastitis-infected cows' mammary tissues, blood and neutrophils compared with these of healthy cows using real-time RT-PCR. Genomic sequencing analysis identified four novel SNPs g.10112 G>A, g.10766 T>C, SNPs g.12085 G>A and g.12430 T>C at the ends of intron 6 and intron 8 of NCF1. ESE motif predicted that the SNP (g.10766 T>C) might affect the binding with splicing-related factors and subsequently caused the production of aberrant splice variant NCF1-TV1, which is one of the potential reasons that the functional SNP was associated with increased milk somatic cell score in cow. Our results would help in better understanding the NCF1 gene function in the process against pathogen infection, and the effect of splicing-related SNP on the production of aberrant splice variant and careful functional characterization in dairy cattle.
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Affiliation(s)
- Zijing Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Rongling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Chao Qi
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Fang Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Guojing Luo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qiuling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yinxue Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1).
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Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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The association of ADORA2A and ADORA2B polymorphisms with the risk and severity of chronic heart failure: a case-control study of a northern Chinese population. Int J Mol Sci 2015; 16:2732-46. [PMID: 25629231 PMCID: PMC4346862 DOI: 10.3390/ijms16022732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/22/2015] [Indexed: 01/28/2023] Open
Abstract
The causes of chronic heart failure (CHF) and its progression are likely to be due to complex genetic factors. Adenosine receptors A2A and A2B (ADORA2A and ADORA2B, respectively) play an important role in cardio-protection. Therefore, polymorphisms in the genes encoding those receptors may affect the risk and severity of CHF. This study was a case-control comparative investigation of 300 northern Chinese Han CHF patients and 400 ethnicity-matched healthy controls. Four common single-nucleotide polymorphisms (SNPs) of ADORA2A (rs2236625, rs2236624, rs4822489, and rs5751876) and one SNP of ADORA2B (rs7208480) were genotyped and an association between SNPs and clinical outcomes was evaluated. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association. The rs4822489 was significantly associated with the severity of CHF after adjustment for traditional cardiovascular risk factors (p = 0.040, OR = 1.912, 95% CI = 1.029–3.550). However, the five SNPs as well as the haplotypes were not found to be associated with CHF susceptibility. The findings of this study suggest that rs4822489 may contribute to the severity of CHF in the northern Chinese. However, further studies performed in larger populations and aimed at better defining the role of this gene are required.
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