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Khan AH, Bagley JR, LaPierre N, Gonzalez-Figueroa C, Spencer TC, Choudhury M, Xiao X, Eskin E, Jentsch JD, Smith DJ. Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in a panel of inbred and recombinant inbred mice. Cell Rep 2023; 42:112856. [PMID: 37481717 PMCID: PMC10530068 DOI: 10.1016/j.celrep.2023.112856] [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: 11/16/2022] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 07/25/2023] Open
Abstract
To identify addiction genes, we evaluate intravenous self-administration of cocaine or saline in 84 inbred and recombinant inbred mouse strains over 10 days. We integrate the behavior data with brain RNA-seq data from 41 strains. The self-administration of cocaine and that of saline are genetically distinct. We maximize power to map loci for cocaine intake by using a linear mixed model to account for this longitudinal phenotype while correcting for population structure. A total of 15 unique significant loci are identified in the genome-wide association study. A transcriptome-wide association study highlights the Trpv2 ion channel as a key locus for cocaine self-administration as well as identifying 17 additional genes, including Arhgef26, Slc18b1, and Slco5a1. We find numerous instances where alternate splice site selection or RNA editing altered transcript abundance. Our work emphasizes the importance of Trpv2, an ionotropic cannabinoid receptor, for the response to cocaine.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Jared R Bagley
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Nathan LaPierre
- Department of Computer Science, UCLA, Los Angeles, CA 90095, USA
| | | | - Tadeo C Spencer
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Department of Computational Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James D Jentsch
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | - Desmond J Smith
- Department of Molecular and Medical Pharmacology, Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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2
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Iannone C, Kainov Y, Zhuravskaya A, Hamid F, Nojima T, Makeyev EV. PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells. Mol Cell 2023; 83:203-218.e9. [PMID: 36626906 DOI: 10.1016/j.molcel.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.
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Affiliation(s)
- Camilla Iannone
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Takayuki Nojima
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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3
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Beopoulos A, Géa M, Fasano A, Iris F. RNA epitranscriptomics dysregulation: A major determinant for significantly increased risk of ASD pathogenesis. Front Neurosci 2023; 17:1101422. [PMID: 36875672 PMCID: PMC9978375 DOI: 10.3389/fnins.2023.1101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Autism spectrum disorders (ASDs) are perhaps the most severe, intractable and challenging child psychiatric disorders. They are complex, pervasive and highly heterogeneous and depend on multifactorial neurodevelopmental conditions. Although the pathogenesis of autism remains unclear, it revolves around altered neurodevelopmental patterns and their implications for brain function, although these cannot be specifically linked to symptoms. While these affect neuronal migration and connectivity, little is known about the processes that lead to the disruption of specific laminar excitatory and inhibitory cortical circuits, a key feature of ASD. It is evident that ASD has multiple underlying causes and this multigenic condition has been considered to also dependent on epigenetic effects, although the exact nature of the factors that could be involved remains unclear. However, besides the possibility for differential epigenetic markings directly affecting the relative expression levels of individual genes or groups of genes, there are at least three mRNA epitranscriptomic mechanisms, which function cooperatively and could, in association with both genotypes and environmental conditions, alter spatiotemporal proteins expression patterns during brain development, at both quantitative and qualitative levels, in a tissue-specific, and context-dependent manner. As we have already postulated, sudden changes in environmental conditions, such as those conferred by maternal inflammation/immune activation, influence RNA epitranscriptomic mechanisms, with the combination of these processes altering fetal brain development. Herein, we explore the postulate whereby, in ASD pathogenesis, RNA epitranscriptomics might take precedence over epigenetic modifications. RNA epitranscriptomics affects real-time differential expression of receptor and channel proteins isoforms, playing a prominent role in central nervous system (CNS) development and functions, but also RNAi which, in turn, impact the spatiotemporal expression of receptors, channels and regulatory proteins irrespective of isoforms. Slight dysregulations in few early components of brain development, could, depending upon their extent, snowball into a huge variety of pathological cerebral alterations a few years after birth. This may very well explain the enormous genetic, neuropathological and symptomatic heterogeneities that are systematically associated with ASD and psychiatric disorders at large.
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Affiliation(s)
| | - Manuel Géa
- Bio-Modeling Systems, Tour CIT, Paris, France
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Center for Celiac Research and Treatment, Massachusetts General Hospital for Children, Boston, MA, United States
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4
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Imbriano C, Belluti S. Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer? Int J Mol Sci 2022; 23:ijms23158304. [PMID: 35955433 PMCID: PMC9368390 DOI: 10.3390/ijms23158304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.
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5
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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Southey BR, Rodriguez-Zas SL. Alternative Splicing of Neuropeptide Prohormone and Receptor Genes Associated with Pain Sensitivity Was Detected with Zero-Inflated Models. Biomedicines 2022; 10:biomedicines10040877. [PMID: 35453627 PMCID: PMC9031102 DOI: 10.3390/biomedicines10040877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
Migraine is often accompanied by exacerbated sensitivity to stimuli and pain associated with alternative splicing of genes in signaling pathways. Complementary analyses of alternative splicing of neuropeptide prohormone and receptor genes involved in cell–cell communication in the trigeminal ganglia and nucleus accumbens regions of mice presenting nitroglycerin-elicited hypersensitivity and control mice were conducted. De novo sequence assembly detected 540 isoforms from 168 neuropeptide prohormone and receptor genes. A zero-inflated negative binomial model that accommodates for potential excess of zero isoform counts enabled the detection of 27, 202, and 12 differentially expressed isoforms associated with hypersensitivity, regions, and the interaction between hypersensitivity and regions, respectively. Skipped exons and alternative 3′ splice sites were the most frequent splicing events detected in the genes studied. Significant differential splicing associated with hypersensitivity was identified in CALCA and VGF neuropeptide prohormone genes and ADCYAP1R1, CRHR2, and IGF1R neuropeptide receptor genes. The prevalent region effect on differential isoform levels (202 isoforms) and alternative splicing (82 events) were consistent with the distinct splicing known to differentiate central nervous structures. Our findings highlight the changes in alternative splicing in neuropeptide prohormone and receptor genes associated with hypersensitivity to pain and the necessity to target isoform profiles for enhanced understanding and treatment of associated disorders such as migraine.
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Affiliation(s)
- Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Correspondence:
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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7
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Does the Expression and Epigenetics of Genes Involved in Monogenic Forms of Parkinson’s Disease Influence Sporadic Forms? Genes (Basel) 2022; 13:genes13030479. [PMID: 35328033 PMCID: PMC8951612 DOI: 10.3390/genes13030479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Parkinson’s disease (PD) is a disorder characterized by a triad of motor symptoms (akinesia, rigidity, resting tremor) related to loss of dopaminergic neurons mainly in the Substantia nigra pars compacta. Diagnosis is often made after a substantial loss of neurons has already occurred, and while dopamine replacement therapies improve symptoms, they do not modify the course of the disease. Although some biological mechanisms involved in the disease have been identified, such as oxidative stress and accumulation of misfolded proteins, they do not explain entirely PD pathophysiology, and a need for a better understanding remains. Neurodegenerative diseases, including PD, appear to be the result of complex interactions between genetic and environmental factors. The latter can alter gene expression by causing epigenetic changes, such as DNA methylation, post-translational modification of histones and non-coding RNAs. Regulation of genes responsible for monogenic forms of PD may be involved in sporadic PD. This review will focus on the epigenetic mechanisms regulating their expression, since these are the genes for which we currently have the most information available. Despite technical challenges, epigenetic epidemiology offers new insights on revealing altered biological pathways and identifying predictive biomarkers for the onset and progression of PD.
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Ferragut Cardoso AP, Banerjee M, Al-Eryani L, Sayed M, Wilkey DW, Merchant ML, Park JW, States JC. Temporal Modulation of Differential Alternative Splicing in HaCaT Human Keratinocyte Cell Line Chronically Exposed to Arsenic for up to 28 Wk. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:17011. [PMID: 35072517 PMCID: PMC8785870 DOI: 10.1289/ehp9676] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Chronic arsenic exposure via drinking water is associated with an increased risk of developing cancer and noncancer chronic diseases. Pre-mRNAs are often subject to alternative splicing, generating mRNA isoforms encoding functionally distinct protein isoforms. The resulting imbalance in isoform species can result in pathogenic changes in critical signaling pathways. Alternative splicing as a mechanism of arsenic-induced toxicity and carcinogenicity is understudied. OBJECTIVE This study aimed to accurately profile differential alternative splicing events in human keratinocytes induced by chronic arsenic exposure that might play a role in carcinogenesis. METHODS Independent quadruplicate cultures of immortalized human keratinocytes (HaCaT) were maintained continuously for 28 wk with 0 or 100 nM sodium arsenite. RNA-sequencing (RNA-Seq) was performed with poly(A) RNA isolated from cells harvested at 7, 19, and 28 wk with subsequent replicate multivariate analysis of transcript splicing (rMATS) analysis to detect and quantify differential alternative splicing events. Reverse transcriptase-polymerase chain reaction (RT-PCR) for selected alternative splicing events was performed to validate RNA-Seq predictions. Functional enrichment was performed by gene ontology (GO) analysis of the differential alternative splicing event data set at each time point. RESULTS At least 600 differential alternative splicing events were detected at each time point tested, comprising all the five main types of alternative splicing and occurring in both open reading frames (ORFs) and untranslated regions (UTRs). Based on functional relevance ELK4, SHC1, and XRRA1 were selected for validation of predicted alternative splicing events at 7 wk by RT-PCR. Densitometric analysis of RT-PCR data corroborated the rMATS predicted alternative splicing for all three events. Protein expression validation of the selected alternative splicing events was challenging given that very few isoform-specific antibodies are available. GO analysis demonstrated that the enriched terms in differential alternatively spliced mRNAs changed dynamically with the time of exposure. Notably, RNA metabolism and splicing regulation pathways were enriched at the 7-wk time point, when the greatest number of differentially alternatively spliced mRNAs are detected. Our preliminary proteomic analysis demonstrated that the expression of the canonical isoforms of the splice regulators DDX42, RMB25, and SRRM2 were induced upon chronic arsenic exposure, corroborating the splicing predictions. DISCUSSION These results using cultures of HaCaT cells suggest that arsenic exposure disrupted an alternative splice factor network and induced time-dependent genome-wide differential alternative splicing that likely contributed to the changing proteomic landscape in arsenic-induced carcinogenesis. However, significant challenges remain in corroborating alternative splicing data at the proteomic level. https://doi.org/10.1289/EHP9676.
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Affiliation(s)
- Ana P. Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Laila Al-Eryani
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mohammed Sayed
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Juw W. Park
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - J. Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
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Martín E, Vivori C, Rogalska M, Herrero-Vicente J, Valcárcel J. Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation. RNA (NEW YORK, N.Y.) 2021; 27:1557-1576. [PMID: 34544891 PMCID: PMC8594467 DOI: 10.1261/rna.078935.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/11/2021] [Indexed: 06/10/2023]
Abstract
The regulation of pre-mRNA processing has important consequences for cell division and the control of cancer cell proliferation, but the underlying molecular mechanisms remain poorly understood. We report that three splicing factors, SPF45, SR140, and CHERP, form a tight physical and functionally coherent complex that regulates a variety of alternative splicing events, frequently by repressing short exons flanked by suboptimal 3' splice sites. These comprise alternative exons embedded in genes with important functions in cell-cycle progression, including the G2/M key regulator FOXM1 and the spindle regulator SPDL1. Knockdown of either of the three factors leads to G2/M arrest and to enhanced apoptosis in HeLa cells. Promoting the changes in FOXM1 or SPDL1 splicing induced by SPF45/SR140/CHERP knockdown partially recapitulates the effects on cell growth, arguing that the complex orchestrates a program of alternative splicing necessary for efficient cell proliferation.
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Affiliation(s)
- Elena Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Malgorzata Rogalska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Jorge Herrero-Vicente
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Maillot P, Velt A, Rustenholz C, Butterlin G, Merdinoglu D, Duchêne E. Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment. BMC PLANT BIOLOGY 2021; 21:487. [PMID: 34696712 PMCID: PMC8543832 DOI: 10.1186/s12870-021-03266-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. RESULTS A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. CONCLUSIONS The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.
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Affiliation(s)
- Pascale Maillot
- SVQV, INRAE - University of Strasbourg, 68000, Colmar, France.
- University of Haute Alsace, 68000, Mulhouse, France.
| | - Amandine Velt
- SVQV, INRAE - University of Strasbourg, 68000, Colmar, France
| | | | | | | | - Eric Duchêne
- SVQV, INRAE - University of Strasbourg, 68000, Colmar, France
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11
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Rouf Banday A, Onabajo OO, Lin SHY, Obajemu A, Vargas JM, Delviks-Frankenberry KA, Lamy P, Bayanjargal A, Zettelmeyer C, Florez-Vargas O, Pathak VK, Dyrskjøt L, Prokunina-Olsson L. Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity. Commun Biol 2021; 4:386. [PMID: 33753867 PMCID: PMC7985488 DOI: 10.1038/s42003-021-01844-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis. Identification of factors affecting the activity of these enzymes could help modulate mutagenesis and associated clinical outcomes. Here, we show that canonical and alternatively spliced A3A and A3B isoforms produce corresponding mutagenic and non-mutagenic enzymes. Increased expression of the mutagenic A3B isoform predicted shorter progression-free survival in bladder cancer. We demonstrate that the production of mutagenic vs. non-mutagenic A3B protein isoforms was considerably affected by inclusion/skipping of exon 5 in A3B. Furthermore, exon 5 skipping, resulting in lower levels of mutagenic A3B enzyme, could be increased in vitro. Specifically, we showed the effects of treatment with an SF3B1 inhibitor affecting spliceosome interaction with a branch point site in intron 4, or with splice-switching oligonucleotides targeting exon 5 of A3B. Our results underscore the clinical role of A3B and implicate alternative splicing of A3B as a mechanism that could be targeted to restrict APOBEC-mediated mutagenesis.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Seraph Han-Yin Lin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adeola Obajemu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ariunaa Bayanjargal
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Zettelmeyer
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. mSystems 2021; 6:6/2/e01081-20. [PMID: 33688018 PMCID: PMC8561664 DOI: 10.1128/msystems.01081-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterized in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AU content of Plasmodium RNA, but also the limitations of short-read sequencing in deciphering complex splicing events. In this study, we utilized the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or nearly full-length transcripts with comparable quantification to Illumina sequencing. By comparing these data with available gene models, we find widespread alternative splicing, particularly intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This study highlights a strategy in using long-read sequencing to understand splicing events at the whole-transcript level and has implications in the future interpretation of transcriptome sequencing studies. IMPORTANCE We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
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13
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Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Res 2021; 49:1133-1151. [PMID: 33406240 PMCID: PMC7826280 DOI: 10.1093/nar/gkaa1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
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Affiliation(s)
- Armin Fuchs
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Stefan Riegler
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Zahra Ayatollahi
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Nicola Cavallari
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Barbara A Nimeth
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Krishna V Mutanwad
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | | | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Ezequiel Petrillo
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
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14
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Bubenik JL, Hale M, McConnell O, Wang E, Swanson MS, Spitale R, Berglund JA. RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells. RNA (NEW YORK, N.Y.) 2020; 27:rna.077263.120. [PMID: 33310817 PMCID: PMC7901844 DOI: 10.1261/rna.077263.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
In vivo RNA structure analysis has become a powerful tool in molecular biology, largely due to the coupling of an increasingly diverse set of chemical approaches with high-throughput sequencing. This has resulted in a transition from single target to transcriptome-wide approaches. However, these methods require sequencing depths that preclude studying low abundance targets, which are not sufficiently captured in transcriptome-wide approaches. Here we present a ligation-free method to enrich for low abundance RNA sequences, which improves the diversity of molecules analyzed and results in improved analysis. In addition, this method is compatible with any choice of chemical adduct or read-out approach. We utilized this approach to study an autoregulated event in the pre-mRNA of the splicing factor, muscleblind-like splicing regulator 1 (MBNL1).
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15
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Esteve-Bruna D, Carrasco-López C, Blanco-Touriñán N, Iserte J, Calleja-Cabrera J, Perea-Resa C, Úrbez C, Carrasco P, Yanovsky MJ, Blázquez MA, Salinas J, Alabadí D. Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8 complex through Hsp90 in Arabidopsis. Nucleic Acids Res 2020; 48:6280-6293. [PMID: 32396196 PMCID: PMC7293050 DOI: 10.1093/nar/gkaa354] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Although originally identified as the components of the complex aiding the cytosolic chaperonin CCT in the folding of actins and tubulins in the cytosol, prefoldins (PFDs) are emerging as novel regulators influencing gene expression in the nucleus. Work conducted mainly in yeast and animals showed that PFDs act as transcriptional regulators and participate in the nuclear proteostasis. To investigate new functions of PFDs, we performed a co-expression analysis in Arabidopsis thaliana. Results revealed co-expression between PFD and the Sm-like (LSM) genes, which encode the LSM2–8 spliceosome core complex, in this model organism. Here, we show that PFDs interact with and are required to maintain adequate levels of the LSM2–8 complex. Our data indicate that levels of the LSM8 protein, which defines and confers the functional specificity of the complex, are reduced in pfd mutants and in response to the Hsp90 inhibitor geldanamycin. We provide biochemical evidence showing that LSM8 is a client of Hsp90 and that PFD4 mediates the interaction between both proteins. Consistent with our results and with the role of the LSM2–8 complex in splicing through the stabilization of the U6 snRNA, pfd mutants showed reduced levels of this snRNA and altered pre-mRNA splicing patterns.
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Affiliation(s)
- David Esteve-Bruna
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Cristian Carrasco-López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), 28040 Madrid, Spain
| | - Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Javier Iserte
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWAE Buenos Aires, Argentina
| | - Julián Calleja-Cabrera
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Carlos Perea-Resa
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), 28040 Madrid, Spain
| | - Cristina Úrbez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Pedro Carrasco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot, Spain
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWAE Buenos Aires, Argentina
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas "Margarita Salas" (CSIC), 28040 Madrid, Spain
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
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16
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Taha TY, Anirudhan V, Limothai U, Loeb DD, Petukhov PA, McLachlan A. Modulation of hepatitis B virus pregenomic RNA stability and splicing by histone deacetylase 5 enhances viral biosynthesis. PLoS Pathog 2020; 16:e1008802. [PMID: 32822428 PMCID: PMC7467325 DOI: 10.1371/journal.ppat.1008802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/02/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus (HBV) is a worldwide health problem without curative treatments. Investigation of the regulation of HBV biosynthesis by class I and II histone deacetylases (HDACs) demonstrated that catalytically active HDAC5 upregulates HBV biosynthesis. HDAC5 expression increased both the stability and splicing of the HBV 3.5 kb RNA without altering the translational efficiency of the viral pregenomic or spliced 2.2 kb RNAs. Together, these observations point to a broader role of HDAC5 in regulating RNA splicing and transcript stability while specifically identifying a potentially novel approach toward antiviral HBV therapeutic development. This study demonstrates that HDAC5 deacetylation of host cellular factor(s) results in increased HBV biosynthesis by enhancing viral transcript stability and splicing via direct or indirect binding of host factors to viral intron sequences. This represents the first demonstration of this type of post-transcriptional regulation in the liver and is similar to observations seen for cellular transcripts in neural and cardiac cell types. These observations suggest a more general phenomenon which could represent an additional post-transcriptional code governing the regulation of RNA:protein interactions and hence RNA metabolism. Therefore, covalent modifications of RNA binding proteins may modulate post-transcriptional gene expression in an analogous manner to the known histone code that controls gene transcription. Although this analysis primarily relates to the mechanism(s) by which HDAC5 governs HBV RNA metabolism, it does have significant therapeutic implications. The inhibition of HDAC5 in combination with current nucleos(t)ide analog drugs targeting the viral reverse transcriptase/DNA polymerase might aid in the treatment and possible resolution of chronic infections by targeting both host and viral factors.
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Affiliation(s)
- Taha Y. Taha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Varada Anirudhan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Umaporn Limothai
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Daniel D. Loeb
- McArdle Laboratory for Cancer Research, University of Wisconsin - Madison, Madison, Wisconsin, United States of America
| | - Pavel A. Petukhov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (PAP); (AM)
| | - Alan McLachlan
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (PAP); (AM)
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17
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Barth E, Sieber P, Stark H, Schuster S. Robustness during Aging-Molecular Biological and Physiological Aspects. Cells 2020; 9:E1862. [PMID: 32784503 PMCID: PMC7465392 DOI: 10.3390/cells9081862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.
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Affiliation(s)
- Emanuel Barth
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Heiko Stark
- Institute of Zoology and Evolutionary Research with Phyletic Museum, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
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18
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Fujita KI, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating Divergent Transcriptomes through mRNA Splicing and Its Modulation Using Various Small Compounds. Int J Mol Sci 2020; 21:ijms21062026. [PMID: 32188117 PMCID: PMC7139312 DOI: 10.3390/ijms21062026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Human transcriptomes are more divergent than genes and contribute to the sophistication of life. This divergence is derived from various isoforms arising from alternative splicing. In addition, alternative splicing regulated by spliceosomal factors and RNA structures, such as the RNA G-quadruplex, is important not only for isoform diversity but also for regulating gene expression. Therefore, abnormal splicing leads to serious diseases such as cancer and neurodegenerative disorders. In the first part of this review, we describe the regulation of divergent transcriptomes using alternative mRNA splicing. In the second part, we present the relationship between the disruption of splicing and diseases. Recently, various compounds with splicing inhibitor activity were established. These splicing inhibitors are recognized as a biological tool to investigate the molecular mechanism of splicing and as a potential therapeutic agent for cancer treatment. Food-derived compounds with similar functions were found and are expected to exhibit anticancer effects. In the final part, we describe the compounds that modulate the messenger RNA (mRNA) splicing process and their availability for basic research and future clinical potential.
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19
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Lee DSM, Ghanem LR, Barash Y. Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations. Nat Commun 2020; 11:527. [PMID: 31988292 PMCID: PMC6985247 DOI: 10.1038/s41467-020-14404-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/03/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5' and 3' UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we find that negative selection acting on central guanines of UTR pG4s is comparable to that of missense variation in protein-coding sequences. At multiple GWAS-implicated SNPs within pG4 UTR sequences, we find robust allelic imbalance in gene expression across diverse tissue contexts in GTEx, suggesting that variants affecting G-quadruplex formation within UTRs may also contribute to phenotypic variation. Our results establish UTR G4s as important cis-regulatory elements and point to a link between disruption of UTR pG4 and disease.
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Affiliation(s)
- David S M Lee
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R Ghanem
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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20
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Nuthalapati NK, Evans JD, Taylor RL, Branton SL, Nanduri B, Pharr GT. Transcriptomic analysis of early B-cell development in the chicken embryo. Poult Sci 2020; 98:5342-5354. [PMID: 31237340 PMCID: PMC6771548 DOI: 10.3382/ps/pez354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/01/2019] [Indexed: 12/19/2022] Open
Abstract
The chicken bursa of Fabricius is a primary lymphoid tissue important for B-cell development. Our long-term goal is to understand the role of bursal microenvironment in an early B-cell differentiation event initiating repertoire development through immunoglobulin gene conversion in the chick embryo. We hypothesize that early bursal B-cell differentiation is guided by signals through cytokine receptors. Our theory is based on previous evidence for expression of the receptor tyrosine kinase superfamily members and interleukin receptors in unseparated populations of bursal B-cells and bursal tissue. Knowledge of the expressed genes that are responsible for B-cell differentiation is a prerequisite for understanding the bursal microenvironment's function. This project uses transcriptomic analysis to evaluate gene expression across early B-cell development. RNA-seq was performed with total RNA isolated from bursal B-cells at embryonic day (ED) 16 and ED 19 (n = 3). Approximately 90 million high-quality clean reads were obtained from the cDNA libraries. The analysis revealed differentially expressed genes involved in the Jak-STAT pathway, Wnt signaling pathway, MAPK signaling pathway, metabolic pathways including tyrosine metabolism, Toll-like receptor signaling pathway, and cell-adhesion molecules. The genes predicted to encode surface receptors, signal transduction proteins, and transcription factors identified in this study represent gene candidates for controlling B-cell development in response to differentiation factors in the bursal microenvironment.
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Affiliation(s)
- Nikhil K Nuthalapati
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State MS 39762, Mississippi State
| | - Jeffrey D Evans
- USDA, Agricultural Research Service, Poultry Research Unit, PO Box 5367, Mississippi State University, Starkville, MS 39762-5367
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506
| | - Scott L Branton
- USDA, Agricultural Research Service, Poultry Research Unit, PO Box 5367, Mississippi State University, Starkville, MS 39762-5367
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State MS 39762, Mississippi State
| | - Gregory T Pharr
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State MS 39762, Mississippi State
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21
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Classes of non-conventional tetraspanins defined by alternative splicing. Sci Rep 2019; 9:14075. [PMID: 31575878 PMCID: PMC6773723 DOI: 10.1038/s41598-019-50267-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/10/2019] [Indexed: 11/08/2022] Open
Abstract
Tetraspanins emerge as a family of membrane proteins mediating an exceptional broad diversity of functions. The naming refers to their four transmembrane segments, which define the tetraspanins' typical membrane topology. In this study, we analyzed alternative splicing of tetraspanins. Besides isoforms with four transmembrane segments, most mRNA sequences are coding for isoforms with one, two or three transmembrane segments, representing structurally mono-, di- and trispanins. Moreover, alternative splicing may alter transmembrane topology, delete parts of the large extracellular loop, or generate alternative N- or C-termini. As a result, we define structure-based classes of non-conventional tetraspanins. The increase in gene products by alternative splicing is associated with an unexpected high structural variability of tetraspanins. We speculate that non-conventional tetraspanins have roles in regulating ER exit and modulating tetraspanin-enriched microdomain function.
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22
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Al-Zeer MA, Dutkiewicz M, von Hacht A, Kreuzmann D, Röhrs V, Kurreck J. Alternatively spliced variants of the 5'-UTR of the ARPC2 mRNA regulate translation by an internal ribosome entry site (IRES) harboring a guanine-quadruplex motif. RNA Biol 2019; 16:1622-1632. [PMID: 31387452 DOI: 10.1080/15476286.2019.1652524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The 5'-UTR of the actin-related protein 2/3 complex subunit 2 (ARPC2) mRNA exists in two variants. Using a bicistronic reporter construct, the present study demonstrates that the longer variant of the 5'-UTR harbours an internal ribosome entry site (IRES) which is lacking in the shorter one. Multiple control assays confirmed that only this variant promotes cap-independent translation. Furthermore, it includes a guanine-rich region that is capable of forming a guanine-quadruplex (G-quadruplex) structure which was found to contribute to the IRES activity. To investigate the cellular function of the IRES element, we determined the expression level of ARPC2 at various cell densities. At high cell density, the relative ARPC2 protein level increases, supporting the presumed function of IRES elements in driving the expression of certain genes under stressful conditions that compromise cap-dependent translation. Based on chemical probing experiments and computer-based predictions, we propose a structural model of the IRES element, which includes the G-quadruplex motif exposed from the central stem-loop element. Taken together, our study describes the functional relevance of two alternative 5'-UTR splice variants of the ARPC2 mRNA, one of which contains an IRES element with a G-quadruplex as a central motif, promoting translation under stressful cellular conditions.
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Affiliation(s)
- Munir A Al-Zeer
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Mariola Dutkiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | | | - Denise Kreuzmann
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Viola Röhrs
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Jens Kurreck
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
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23
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Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes. Int J Mol Sci 2019; 20:ijms20153834. [PMID: 31390737 PMCID: PMC6695735 DOI: 10.3390/ijms20153834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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24
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Nakagaki-Silva EE, Gooding C, Llorian M, Jacob AG, Richards F, Buckroyd A, Sinha S, Smith CW. Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers. eLife 2019; 8:46327. [PMID: 31283468 PMCID: PMC6613909 DOI: 10.7554/elife.46327] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing (AS) programs are primarily controlled by regulatory RNA-binding proteins (RBPs). It has been proposed that a small number of master splicing regulators might control cell-specific splicing networks and that these RBPs could be identified by proximity of their genes to transcriptional super-enhancers. Using this approach we identified RBPMS as a critical splicing regulator in differentiated vascular smooth muscle cells (SMCs). RBPMS is highly down-regulated during phenotypic switching of SMCs from a contractile to a motile and proliferative phenotype and is responsible for 20% of the AS changes during this transition. RBPMS directly regulates AS of numerous components of the actin cytoskeleton and focal adhesion machineries whose activity is critical for SMC function in both phenotypes. RBPMS also regulates splicing of other splicing, post-transcriptional and transcription regulators including the key SMC transcription factor Myocardin, thereby matching many of the criteria of a master regulator of AS in SMCs.
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Affiliation(s)
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Francis Crick Institute, London, United Kingdom
| | - Aishwarya G Jacob
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Anne McLaren Laboratory, Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Frederick Richards
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Buckroyd
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sanjay Sinha
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Anne McLaren Laboratory, Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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25
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Hamid FM, Makeyev EV. A mechanism underlying position-specific regulation of alternative splicing. Nucleic Acids Res 2019; 45:12455-12468. [PMID: 30053257 PMCID: PMC5716086 DOI: 10.1093/nar/gkx901] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/26/2017] [Indexed: 01/01/2023] Open
Abstract
Many RNA-binding proteins including a master regulator of splicing in developing brain and muscle, polypyrimidine tract-binding protein 1 (PTBP1), can either activate or repress alternative exons depending on the pre-mRNA recruitment position. When bound upstream or within regulated exons PTBP1 tends to promote their skipping, whereas binding to downstream sites often stimulates inclusion. How this switch is orchestrated at the molecular level is poorly understood. Using bioinformatics and biochemical approaches we show that interaction of PTBP1 with downstream intronic sequences can activate natural cassette exons by promoting productive docking of the spliceosomal U1 snRNP to a suboptimal 5' splice site. Strikingly, introducing upstream PTBP1 sites to this circuitry leads to a potent splicing repression accompanied by the assembly of an exonic ribonucleoprotein complex with a tightly bound U1 but not U2 snRNP. Our data suggest a molecular mechanism underlying the transition between a better-known repressive function of PTBP1 and its role as a bona fide splicing activator. More generally, we argue that the functional outcome of individual RNA contacts made by an RNA-binding protein is subject to extensive context-specific modulation.
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Affiliation(s)
- Fursham M Hamid
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
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26
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Gómez-Gallego T, Benabdellah K, Merlos MA, Jiménez-Jiménez AM, Alcon C, Berthomieu P, Ferrol N. The Rhizophagus irregularis Genome Encodes Two CTR Copper Transporters That Mediate Cu Import Into the Cytosol and a CTR-Like Protein Likely Involved in Copper Tolerance. FRONTIERS IN PLANT SCIENCE 2019; 10:604. [PMID: 31156674 PMCID: PMC6531763 DOI: 10.3389/fpls.2019.00604] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/24/2019] [Indexed: 05/31/2023]
Abstract
Arbuscular mycorrhizal fungi increase fitness of their host plants under Cu deficient and toxic conditions. In this study, we have characterized two Cu transporters of the CTR family (RiCTR1 and RiCTR2) and a CTR-like protein (RiCTR3A) of Rhizophagus irregularis. Functional analyses in yeast revealed that RiCTR1 encodes a plasma membrane Cu transporter, RiCTR2 a vacuolar Cu transporter and RiCTR3A a plasma membrane protein involved in Cu tolerance. RiCTR1 was more highly expressed in the extraradical mycelia (ERM) and RiCTR2 in the intraradical mycelia (IRM). In the ERM, RiCTR1 expression was up-regulated by Cu deficiency and down-regulated by Cu toxicity. RiCTR2 expression increased only in the ERM grown under severe Cu-deficient conditions. These data suggest that RiCTR1 is involved in Cu uptake by the ERM and RiCTR2 in mobilization of vacuolar Cu stores. Cu deficiency decreased mycorrhizal colonization and arbuscule frequency, but increased RiCTR1 and RiCTR2 expression in the IRM, which suggest that the IRM has a high Cu demand. The two alternatively spliced products of RiCTR3, RiCTR3A and RiCTR3B, were more highly expressed in the ERM. Up-regulation of RiCTR3A by Cu toxicity and the yeast complementation assays suggest that RiCTR3A might function as a Cu receptor involved in Cu tolerance.
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Affiliation(s)
- Tamara Gómez-Gallego
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Miguel A. Merlos
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Ana M. Jiménez-Jiménez
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Carine Alcon
- Biochimie et Physiologie Moléculaire des Plantes, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, Montpellier, France
| | - Pierre Berthomieu
- Biochimie et Physiologie Moléculaire des Plantes, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, Montpellier, France
| | - Nuria Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Katsumata Y, Nelson PT, Estus S, Fardo DW. Translating Alzheimer's disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. Neurobiol Aging 2019; 74:135-146. [PMID: 30448613 PMCID: PMC6331247 DOI: 10.1016/j.neurobiolaging.2018.10.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/24/2018] [Accepted: 10/14/2018] [Indexed: 12/12/2022]
Abstract
The International Genomics of Alzheimer's Project (IGAP) is a consortium for characterizing the genetic landscape of Alzheimer's disease (AD). The identified and/or confirmed 19 single-nucleotide polymorphisms (SNPs) associated with AD are located on non-coding DNA regions, and their functional impacts on AD are as yet poorly understood. We evaluated the roles of the IGAP SNPs by integrating data from many resources, based on whether the IGAP SNP was (1) a proxy for a coding SNP or (2) associated with altered mRNA transcript levels. For (1), we confirmed that 12 AD-associated coding common SNPs and five nonsynonymous rare variants are in linkage disequilibrium with the IGAP SNPs. For (2), the IGAP SNPs in CELF1 and MS4A6A were associated with expression of their neighboring genes, MYBPC3 and MS4A6A, respectively, in blood. The IGAP SNP in DSG2 was an expression quantitative trait loci (eQTL) for DLGAP1 and NETO1 in the human frontal cortex. The IGAP SNPs in ABCA7, CD2AP, and CD33 each acted as eQTL for AD-associated genes in brain. Our approach for identifying proxies and examining eQTL highlighted potentially impactful, novel gene regulatory phenomena pertinent to the AD phenotype.
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Affiliation(s)
- Yuriko Katsumata
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Peter T. Nelson
- Department of Pathology, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology, University of Kentucky, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | | | - David W. Fardo
- Department of Biostatistics, University of Kentucky, Lexington, KY, USA
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
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Furlanis E, Scheiffele P. Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing. Annu Rev Cell Dev Biol 2018; 34:451-469. [PMID: 30028642 DOI: 10.1146/annurev-cellbio-100617-062826] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Posttranscriptional mechanisms provide powerful means to expand the coding power of genomes. In nervous systems, alternative splicing has emerged as a fundamental mechanism not only for the diversification of protein isoforms but also for the spatiotemporal control of transcripts. Thus, alternative splicing programs play instructive roles in the development of neuronal cell type-specific properties, neuronal growth, self-recognition, synapse specification, and neuronal network function. Here we discuss the most recent genome-wide efforts on mapping RNA codes and RNA-binding proteins for neuronal alternative splicing regulation. We illustrate how alternative splicing shapes key steps of neuronal development, neuronal maturation, and synaptic properties. Finally, we highlight efforts to dissect the spatiotemporal dynamics of alternative splicing and their potential contribution to neuronal plasticity and the mature nervous system.
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Mazin PV, Jiang X, Fu N, Han D, Guo M, Gelfand MS, Khaitovich P. Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques. RNA (NEW YORK, N.Y.) 2018; 24:585-596. [PMID: 29363555 PMCID: PMC5855957 DOI: 10.1261/rna.064931.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 01/10/2018] [Indexed: 05/03/2023]
Abstract
Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different ages. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences. A reconstructed trans-regulatory network containing 21 RNA-binding proteins explains a further 4% of splicing variations within species. While most age-dependent splicing patterns are conserved among the three species, developmental changes in intron retention are substantially more pronounced in humans.
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Affiliation(s)
- Pavel V Mazin
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127051, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow 125319, Russia
| | - Xi Jiang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Ning Fu
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Meng Guo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mikhail S Gelfand
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127051, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow 125319, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Philipp Khaitovich
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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30
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Cardoso TF, Quintanilla R, Castelló A, González-Prendes R, Amills M, Cánovas Á. Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. BMC Genomics 2018; 19:145. [PMID: 29444639 PMCID: PMC5813380 DOI: 10.1186/s12864-018-4515-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/31/2018] [Indexed: 01/03/2023] Open
Abstract
Background The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). Results Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs. Conclusions The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest. Electronic supplementary material The online version of this article (10.1186/s12864-018-4515-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F, 70.040-020, Brazil
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
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Abstract
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes. In cancer, promoter DNA hypermethylation events sustained the mechanistic hypothesis of epigenetic transcriptional silencing of an increasing number of tumor suppressor genes. CGI hypomethylation-mediated reactivation of oncogenes was also documented in several cancer types. In this chapter, we aim to summarize the functional consequences of the differential DNA methylation at CpG dinucleotides in cancer, focused in CGIs. Interestingly, cancer methylome is being recently explored, looking for biomarkers for diagnosis, prognosis, and predictors of drug response.
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Affiliation(s)
- Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
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Joris M, Schloesser M, Baurain D, Hanikenne M, Muller M, Motte P. Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors. Nucleic Acids Res 2017; 45:9547-9557. [PMID: 28934490 PMCID: PMC5766196 DOI: 10.1093/nar/gkx638] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022] Open
Abstract
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets. While microinjection of MOs directed against srsf5a (sMOsrsf5a) led to developmental defects, the corresponding homozygous mutants did not display any phenotypic traits. Furthermore, microinjection of sMOsrsf5a into srsf5a−/− led to the previously observed morphant phenotype. Similar findings were observed for other SR genes. sMOsrsf5a alternative target genes were identified using deep mRNA sequencing. We uncovered that only 11 consecutive bases complementary to sMOsrsf5a are sufficient for binding and subsequent blocking of splice sites. In addition, we observed that sMOsrsf5a secondary targets can be reduced by increasing embryos growth temperature after microinjection. Our data contribute to the debate about MO specificity, efficacy and the number of unknown targeted sequences.
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Affiliation(s)
- Marine Joris
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Marie Schloesser
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, 4000 Liège, Belgium
| | - Marc Hanikenne
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration, GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Patrick Motte
- Laboratory of Functional Genomics and Plant Molecular Imaging, InBioS, PhytoSystems and Centre for Assistance in Technology of Microscopy (CAREm), University of Liège, 4000 Liège, Belgium
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33
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Park JE, Ryoo G, Lee W. Alternative Splicing: Expanding Diversity in Major ABC and SLC Drug Transporters. AAPS JOURNAL 2017; 19:1643-1655. [DOI: 10.1208/s12248-017-0150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/10/2017] [Indexed: 01/18/2023]
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Iñiguez LP, Ramírez M, Barbazuk WB, Hernández G. Identification and analysis of alternative splicing events in Phaseolus vulgaris and Glycine max. BMC Genomics 2017; 18:650. [PMID: 28830361 PMCID: PMC5568362 DOI: 10.1186/s12864-017-4054-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/11/2017] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The vast diversification of proteins in eukaryotic cells has been related with multiple transcript isoforms from a single gene that result in alternative splicing (AS) of primary transcripts. Analysis of RNA sequencing data from expressed sequence tags and next generation RNA sequencing has been crucial for AS identification and genome-wide AS studies. For the identification of AS events from the related legume species Phaseolus vulgaris and Glycine max, 157 and 88 publicly available RNA-seq libraries, respectively, were analyzed. RESULTS We identified 85,570 AS events from P. vulgaris in 72% of expressed genes and 134,316 AS events in 70% of expressed genes from G. max. These were categorized in seven AS event types with intron retention being the most abundant followed by alternative acceptor and alternative donor, representing ~75% of all AS events in both plants. Conservation of AS events in homologous genes between the two species was analyzed where an overrepresentation of AS affecting 5'UTR regions was observed for certain types of AS events. The conservation of AS events was experimentally validated for 8 selected genes, through RT-PCR analysis. The different types of AS events also varied by relative position in the genes. The results were consistent in both species. CONCLUSIONS The identification and analysis of AS events are first steps to understand their biological relevance. The results presented here from two related legume species reveal high conservation, over ~15-20 MY of divergence, and may point to the biological relevance of AS.
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Affiliation(s)
- Luis P. Iñiguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | | | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
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Beyond proteome diversity: alternative splicing as a regulator of neuronal transcript dynamics. Curr Opin Neurobiol 2017; 45:162-168. [PMID: 28609697 DOI: 10.1016/j.conb.2017.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/07/2017] [Accepted: 05/14/2017] [Indexed: 12/21/2022]
Abstract
Brain development and function are governed by tightly controlled gene expression programs. Transcriptional repertoires in neurons are highly specific to developmental stage, neuronal cell type and can undergo rapid changes upon neuronal stimulation. Dedicated molecular mechanisms are required to achieve such fine-tuned regulation. In addition to transcriptional programs, post-transcriptional processes and notably alternative splicing substantially contribute to the elaboration of neuronal gene expression. While alternative splicing has been viewed primarily as a means for expanding proteome diversity, it emerges to also be a major regulator of transcript levels and dynamics. In this review we will describe some of the principal alternative splicing-linked mechanisms that control neuronal transcriptomes and discuss their implications for the central nervous system.
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Verbeeren J, Verma B, Niemelä EH, Yap K, Makeyev EV, Frilander MJ. Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA. PLoS Genet 2017; 13:e1006824. [PMID: 28549066 PMCID: PMC5473595 DOI: 10.1371/journal.pgen.1006824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/16/2017] [Accepted: 05/16/2017] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm. The cellular homeostasis of many components of the eukaryotic RNA processing machinery is regulated via negative feed-back pathways that result in the formation of both productive and non-productive mRNA species. Typically, the formation of non-productive mRNAs species results from changes in alternative splicing that disrupt the reading frame of the protein coding region and leads to destabilization of the mRNA. Here, we have investigated the homeostasis regulation of the U11/U12-65K mRNA that encodes an essential protein component of the minor (U12-dependent) spliceosome intron recognition complex. We show that homeostasis is regulated at the level of nuclear mRNA export and mRNA 3′-end formation, and that it can be further regulated during neuronal differentiation. We describe a multilayered regulatory system utilizing alternative exon definition interactions that use the input from both spliceosomes and the polyadenylation machinery to decide between productive and non-productive mRNA formation. Because the 65K protein is an essential component of the minor spliceosome, this regulatory pathway can potentially affect the expression of ~700 genes containing U12-type introns.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elina H. Niemelä
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
| | - Karen Yap
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Eugene V. Makeyev
- Centre for Developmental Neurobiology, King’s College London, London, United Kingdom
| | - Mikko J. Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Helsinki, Finland
- * E-mail:
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37
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Liu J, Sun Y, Yang C, Zhang Y, Jiang Q, Huang J, Ju Z, Wang X, Zhong J, Wang C. Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls. PLoS One 2016; 11:e0162730. [PMID: 27669152 PMCID: PMC5036895 DOI: 10.1371/journal.pone.0162730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022] Open
Abstract
Inner centromere protein (INCENP) plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC). To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs) g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE) motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P < 0.05). Bulls with H11H11 and H2H10 exhibited higher initial sperm motility than those with H2H2 (P < 0.05). The expression levels of INCENP in bulls with H1H12 and H11H11 were significantly higher than those in bulls with H9H12 (P < 0.05), as determined by qRT-PCR. Findings suggest that g.19970 A>G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.
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Affiliation(s)
- Juan Liu
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- College of Agronomic Sciences in Shandong Agricultural University, Taian, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P. R. China
- * E-mail:
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