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Liu L, Nguyen H, Das U, Ogunsola S, Yu J, Lei L, Kung M, Pejhan S, Rastegar M, Xie J. Epigenetic control of adaptive or homeostatic splicing during interval-training activities. Nucleic Acids Res 2024; 52:7211-7224. [PMID: 38661216 PMCID: PMC11229381 DOI: 10.1093/nar/gkae311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/03/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024] Open
Abstract
Interval-training activities induce adaptive cellular changes without altering their fundamental identity, but the precise underlying molecular mechanisms are not fully understood. In this study, we demonstrate that interval-training depolarization (ITD) of pituitary cells triggers distinct adaptive or homeostatic splicing responses of alternative exons. This occurs while preserving the steady-state expression of the Prolactin and other hormone genes. The nature of these splicing responses depends on the exon's DNA methylation status, the methyl-C-binding protein MeCP2 and its associated CA-rich motif-binding hnRNP L. Interestingly, the steady expression of the Prolactin gene is also reliant on MeCP2, whose disruption leads to exacerbated multi-exon aberrant splicing and overexpression of the hormone gene transcripts upon ITD, similar to the observed hyperprolactinemia or activity-dependent aberrant splicing in Rett Syndrome. Therefore, epigenetic control is crucial for both adaptive and homeostatic splicing and particularly the steady expression of the Prolactin hormone gene during ITD. Disruption in this regulation may have significant implications for the development of progressive diseases.
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Affiliation(s)
- Ling Liu
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Hai Nguyen
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Urmi Das
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Samuel Ogunsola
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jiankun Yu
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Lei Lei
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Matthew Kung
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Shervin Pejhan
- Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Mojgan Rastegar
- Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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Hamouzová K, Sen MK, Bharati R, Košnarová P, Chawdhery MRA, Roy A, Soukup J. Calcium signalling in weeds under herbicide stress: An outlook. FRONTIERS IN PLANT SCIENCE 2023; 14:1135845. [PMID: 37035053 PMCID: PMC10080077 DOI: 10.3389/fpls.2023.1135845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
The continuous use of herbicides for controlling weeds has led to the evolution of resistance to all major herbicidal modes of action globally. Every year, new cases of herbicide resistance are reported. Resistance is still in progress in many species, which must be stopped before it becomes a worldwide concern. Several herbicides are known to cause stressful conditions that resemble plant abiotic stresses. Variation in intracellular calcium (Ca2+) concentration is a primary event in a wide range of biological processes in plants, including adaptation to various biotic and abiotic stresses. Ca2+ acts as a secondary messenger, connecting various environmental stimuli to different biological processes, especially during stress rejoindering in plants. Even though many studies involving Ca2+ signalling in plants have been published, there have been no studies on the roles of Ca2+ signalling in herbicide stress response. Hence, this mini-review will highlight the possible sensing and molecular communication via Ca2+ signals in weeds under herbicide stress. It will also discuss some critical points regarding integrating the sensing mechanisms of multiple stress conditions and subsequent molecular communication. These signalling responses must be addressed in the future, enabling researchers to discover new herbicidal targets.
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Affiliation(s)
- Katerina Hamouzová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Excellent Team for Mitigation (E.T.M.), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Pavlína Košnarová
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Md Rafique Ahasan Chawdhery
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Amit Roy
- Excellent Team for Mitigation (E.T.M.), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Josef Soukup
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
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3
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Transcriptome-Wide Detection of Intron/Exon Definition in the Endogenous Pre-mRNA Transcripts of Mammalian Cells and Its Regulation by Depolarization. Int J Mol Sci 2022; 23:ijms231710157. [PMID: 36077555 PMCID: PMC9456152 DOI: 10.3390/ijms231710157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Pairing of splice sites across an intron or exon is the central point of intron or exon definition in pre-mRNA splicing with the latter mode proposed for most mammalian exons. However, transcriptome-wide pairing within endogenous transcripts has not been examined for the prevalence of each mode in mammalian cells. Here we report such pairings in rat GH3 pituitary cells by measuring the relative abundance of nuclear RNA-Seq reads at the intron start or end (RISE). Interestingly, RISE indexes are positively correlated between 5′ and 3′ splice sites specifically across introns or exons but inversely correlated with the usage of adjacent exons. Moreover, the ratios between the paired indexes were globally modulated by depolarization, which was disruptible by 5-aza-Cytidine. The nucleotide matrices of the RISE-positive splice sites deviate significantly from the rat consensus, and short introns or exons are enriched with the cross-intron or -exon RISE pairs, respectively. Functionally, the RISE-positive genes cluster for basic cellular processes including RNA binding/splicing, or more specifically, hormone production if regulated by depolarization. Together, the RISE analysis identified the transcriptome-wide regulation of either intron or exon definition between weak splice sites of short introns/exons in mammalian cells. The analysis also provides a way to further track the splicing intermediates and intron/exon definition during the dynamic regulation of alternative splicing by extracellular factors.
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Huggett SB, Ikeda AS, McGeary JE, Kaun KR, Palmer RHC. Opioid Use Disorder and Alternative mRNA Splicing in Reward Circuitry. Genes (Basel) 2022; 13:1045. [PMID: 35741807 PMCID: PMC9222793 DOI: 10.3390/genes13061045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
Opiate/opioid use disorder (OUD) is a chronic relapsing brain disorder that has increased in prevalence in the last two decades in the United States. Understanding the molecular correlates of OUD may provide key insights into the pathophysiology of this syndrome. Using publicly available RNA-sequencing data, our study investigated the possible role of alternative mRNA splicing in human brain tissue (dorsal-lateral prefrontal cortex (dlPFC), nucleus accumbens (NAc), and midbrain) of 90 individuals with OUD or matched controls. We found a total of 788 differentially spliced genes across brain regions. Alternative mRNA splicing demonstrated mostly tissue-specific effects, but a functionally characterized splicing change in the clathrin and AP-2-binding (CLAP) domain of the Bridging Integrator 1 (BIN1) gene was significantly linked to OUD across all brain regions. We investigated two hypotheses that may underlie differential splicing in OUD. First, we tested whether spliceosome genes were disrupted in the brains of individuals with OUD. Pathway enrichment analyses indicated spliceosome perturbations in OUD across brain regions. Second, we tested whether alternative mRNA splicing regions were linked to genetic predisposition. Using a genome-wide association study (GWAS) of OUD, we found no evidence that DNA variants within or surrounding differentially spliced genes were implicated in the heritability of OUD. Altogether, our study contributes to the understanding of OUD pathophysiology by providing evidence of a possible role of alternative mRNA splicing in OUD.
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Affiliation(s)
- Spencer B. Huggett
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA 30322, USA; (S.B.H.); (A.S.I.)
| | - Ami S. Ikeda
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA 30322, USA; (S.B.H.); (A.S.I.)
| | - John E. McGeary
- Providence Veterans Affairs Medical Center, Department of Psychiatry and Human Behavior, Brown University, Providence, RI 02908, USA;
| | - Karla R. Kaun
- Department of Neuroscience, Brown University, Providence, RI 02912, USA;
| | - Rohan H. C. Palmer
- Behavioral Genetics of Addiction Laboratory, Department of Psychology at Emory University, Atlanta, GA 30322, USA; (S.B.H.); (A.S.I.)
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Chang S, Huang J, Niu H, Wang J, Si Y, Bai Z, Cheng S, Ding W. Epigenetic regulation of osteopontin splicing isoform c defines its role as a microenvironmental factor to promote the survival of colon cancer cells from 5-FU treatment. Cancer Cell Int 2020; 20:452. [PMID: 32944000 PMCID: PMC7491101 DOI: 10.1186/s12935-020-01541-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/05/2020] [Indexed: 01/04/2023] Open
Abstract
Background Drug resistance to 5-fluorouracil (5-FU) and recurrence after chemotherapy in colorectal cancer remain a challenge to be resolved for the improvement of patient outcomes. It is recognized that a variety of secretory proteins released from the tumor cells exposed to chemo-drugs into the tumor microenvironment (TME) contributed to the cell-to-cell communication, and altered the drug sensitivity. One of these important factors is osteopontin (OPN), which exists in several functional forms from alternative splicing and post-translational processing. In colon cancer cells, increased total OPN expression was observed during the progression of tumors, however, the exact role and regulation of the OPN splicing isoforms was not well understood. Methods We assayed precisely the abundance of major OPN splicing isoforms under 5-FU treatments in colon cancer cell lines with different sensitivities to 5-FU, and also evaluated the effects of the condition medium from OPN splicing isoforms overexpressed cells on cell functions. The methods of nuclear calcium reporter assays and ChIP (chromatin immunoprecipitation) assays were used to investigate the molecular mechanism underlining the production of OPN isoforms. Results We discovered that OPNc was a most increased splicing isoform to a significant abundance following 5-FU treatment of colon cancer cells. OPNc as a secretory protein in the conditioned medium exerted a more potent effect to promote cell survival in 5-FU than other OPN isoforms. The kinetic response of nuclear calcium signals could be used to indicate an immediate effect of the conditioned medium containing OPNc and other isoforms. Methyl-CpG binding protein 2 (MeCP2) was identified to regulate the splicing of opn gene, where the phosphorylation of MeCP2 at S421 site, possibly by calmodulin dependent protein kinase II (CaMKII) was required. Conclusions The results demonstrated that the production of OPNc was highly controlled under epigenetic regulations, where MeCP2 and the activation of nuclear calcium signaling were involved. It was also suggested that OPNc could transmit the stress signal of cells upon chemotherapy in TME and promoted the survival of adjacent colon cancer cells.
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Affiliation(s)
- Siyuan Chang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Jing Huang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Huan Niu
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Yang Si
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050 People's Republic of China
| | - Shan Cheng
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Wei Ding
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
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6
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Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer 2020; 23:796-810. [PMID: 32333232 DOI: 10.1007/s10120-020-01062-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins. METHODS In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment. RESULTS Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient's own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment. CONCLUSIONS Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | | | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Mitra Biotech, Bangalore, 560100, India
| | | | - Sonali V Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | | | | | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560029, India
| | - Gopal Gopisetty
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | | | | | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Cancer Precision Medicine, QIMR Berghofer, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India. .,Manipal Academy of Higher Education, Manipal, 576104, India. .,Mitra Biotech, Bangalore, 560100, India.
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7
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Cabej NR. A neural mechanism of nuclear receptor expression and regionalization. Dev Dyn 2020; 249:1172-1181. [PMID: 32406963 DOI: 10.1002/dvdy.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/11/2020] [Accepted: 04/28/2020] [Indexed: 11/07/2022] Open
Abstract
Spatially restricted expression of genes by global circulating inducers (hormones, secreted proteins, growth factors, neuromodulators, etc.) was a prerequisite for the evolution of animals. Far from a random occurrence, it is a systematically occurring, certain event, implying that specific information is invested for it to happen. In this minireview, we show for the first time that the expression and regionalization takes place at the level of receptors via a neural mechanism and make an attempt to reconstruct the causal chain from neural signaling to expression of nuclear receptors.
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Affiliation(s)
- Nelson R Cabej
- Department of Biology, University of Tirana, Tirana, Albania
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8
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Nguyen H, Das U, Xie J. Genome-wide evolution of wobble base-pairing nucleotides of branchpoint motifs with increasing organismal complexity. RNA Biol 2019; 17:311-324. [PMID: 31814500 DOI: 10.1080/15476286.2019.1697548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
How have the branchpoint motifs evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G4/A4 ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota, it increases further by about 7 times. The global G4 increase is consistent with A4 to G4 transitions in evolution. Of the G4/A4-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5' splice sites (SS) and U2 snRNA genes, the 5' SS G3/A3 co-vary with the G4 to some extent. However, corresponding increase of the G4-complementary GCAGTA-U2 gene is rare, suggesting wobble-base pairing between the G4-containing branchpoint motif and GTAGTA-U2 in most of these species. Interestingly, the G4/A4 ratio correlates well with the abundance of alternative splicing in the two phyla, and G4 enriched significantly at the alternative 3' SS of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched at the 3' SS of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint motif-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of relaxing the branchpoint signals in the multicellularity and further complexity of fungi.
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Affiliation(s)
- Hai Nguyen
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Department of Applied Computer Sciences, University of Winnipeg, Winnipeg, Canada
| | - Urmi Das
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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Iijima T, Yoshimura T. A Perspective on the Role of Dynamic Alternative RNA Splicing in the Development, Specification, and Function of Axon Initial Segment. Front Mol Neurosci 2019; 12:295. [PMID: 31866821 PMCID: PMC6906172 DOI: 10.3389/fnmol.2019.00295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/15/2019] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is a powerful mechanism for molecular and functional diversification. In neurons, alternative splicing extensively controls various developmental steps as well as the plasticity and remodeling of neuronal activity in the adult brain. The axon initial segment (AIS) is the specialized compartment of proximal axons that initiates action potential (AP). At the AIS, the ion channels and cell adhesion molecules (CAMs) required for AP initiation are densely clustered via the scaffolding and cytoskeletal proteins. Notably, recent studies have elucidated that multiple AIS proteins are controlled by extensive alternative splicing in developing and adult brains. Here, we argue the potential role of dynamic regulation of alternative splicing in the development, specification, and functions of the AIS. In particular, we propose the novel concept that alternative splicing potentially modulates the structural and functional plasticity at the AIS.
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Affiliation(s)
- Takatoshi Iijima
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Takeshi Yoshimura
- Department of Child Development and Molecular Brain Science, United Graduate School of Child Development, Osaka University, Suita, Japan
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10
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Iijima Y, Tanaka M, Suzuki S, Hauser D, Tanaka M, Okada C, Ito M, Ayukawa N, Sato Y, Ohtsuka M, Scheiffele P, Iijima T. SAM68-Specific Splicing Is Required for Proper Selection of Alternative 3' UTR Isoforms in the Nervous System. iScience 2019; 22:318-335. [PMID: 31805436 PMCID: PMC6909182 DOI: 10.1016/j.isci.2019.11.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 11/13/2019] [Indexed: 12/22/2022] Open
Abstract
Neuronal alternative splicing is a core mechanism for functional diversification. We previously found that STAR family proteins (SAM68, SLM1, SLM2) regulate spatiotemporal alternative splicing in the nervous system. However, the whole aspect of alternative splicing programs by STARs remains unclear. Here, we performed a transcriptomic analysis using SAM68 knockout and SAM68/SLM1 double-knockout midbrains. We revealed different alternative splicing activity between SAM68 and SLM1; SAM68 preferentially targets alternative 3′ UTR exons. SAM68 knockout causes a long-to-short isoform switch of a number of neuronal targets through the alteration in alternative last exon (ALE) selection or alternative polyadenylation. The altered ALE usage of a novel target, interleukin 1 receptor accessory protein (Il1rap), results in remarkable conversion from a membrane-bound type to a secreted type in Sam68KO brains. Proper ALE selection is necessary for IL1RAP neuronal function. Thus the SAM68-specific splicing program provides a mechanism for neuronal selection of alternative 3′ UTR isoforms. SAM68 and the related protein SLM1 exhibit distinct alternative splicing activity SAM68 specifically controls 3′ UTR selection of multiple neuronal genes Proper 3′ UTR selection is necessary for IL1RAP neuronal function Neuronal expression of SAM68 requires proper 3′ UTR selection in the nervous system
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Affiliation(s)
- Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - David Hauser
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Masayuki Tanaka
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Chisa Okada
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Masatoshi Ito
- The Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yuji Sato
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Peter Scheiffele
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel 4056, Switzerland
| | - Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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11
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Maury Y, Poydenot P, Brinon B, Lesueur L, Gide J, Roquevière S, Côme J, Polvèche H, Auboeuf D, Alexandre Denis J, Pietu G, Furling D, Lechuga M, Baghdoyan S, Peschanski M, Martinat C. Pluripotent Stem Cell-Based Drug Screening Reveals Cardiac Glycosides as Modulators of Myotonic Dystrophy Type 1. iScience 2019; 11:258-271. [PMID: 30639849 PMCID: PMC6327858 DOI: 10.1016/j.isci.2018.12.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
There is currently no treatment for myotonic dystrophy type 1 (DM1), the most frequent myopathy of genetic origin. This progressive neuromuscular disease is caused by nuclear-retained RNAs containing expanded CUG repeats. These toxic RNAs alter the activities of RNA splicing factors, resulting in alternative splicing misregulation. By combining human mutated pluripotent stem cells and phenotypic drug screening, we revealed that cardiac glycosides act as modulators for both upstream nuclear aggregations of DMPK mRNAs and several downstream alternative mRNA splicing defects. However, these occurred at different drug concentration ranges. Similar biological effects were recorded in a DM1 mouse model. At the mechanistic level, we demonstrated that this effect was calcium dependent and was synergic with inhibition of the ERK pathway. These results further underscore the value of stem-cell-based assays for drug discovery in monogenic diseases. Myotonic dystrophy type 1 hPSCs were adapted for high content screening FDA-approved cardiac glycosides normalize in vitro and in vivo DM1 biological markers Cardiac glycosides synergize with the ERK pathway to normalize DM1 biomarkers This study emphasizes the value of human pluripotent stem cells for drug discovery
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Affiliation(s)
- Yves Maury
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | - Lea Lesueur
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | - Julien Côme
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | | | | | - Geneviève Pietu
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | - Denis Furling
- Sorbonne Universités UPMC Univ Paris 06, INSERM, Centre de Recherche en Myologie - UMRS974, Institut de Myologie, 75013 Paris, France
| | - Marc Lechuga
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France
| | | | - Marc Peschanski
- CECS, I-STEM, AFM, 91100 Corbeil-Essonnes, France; INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France
| | - Cécile Martinat
- INSERM, UMR 861, UEVE, ISTEM, AFM, 91100 Corbeil-Essonnes, France.
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12
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Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. THE PLANT CELL 2018; 30:1424-1444. [PMID: 29764987 DOI: 10.1101/251876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/20/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
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Affiliation(s)
- Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Allan B James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Paige E Panter
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heather Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Hugh G Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
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13
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Kim CK, Torcaso A, Asimes A, Chung WCJ, Pak TR. Structural and functional characteristics of oestrogen receptor β splice variants: Implications for the ageing brain. J Neuroendocrinol 2018; 30:10.1111/jne.12488. [PMID: 28514502 PMCID: PMC5693782 DOI: 10.1111/jne.12488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/07/2017] [Accepted: 05/13/2017] [Indexed: 01/21/2023]
Abstract
Oestrogen receptor (ER)β is a multifunctional nuclear receptor that mediates the actions of oestrogenic compounds. Despite its well defined role in mediating the actions of oestrogens, a substantial body of evidence demonstrates that ERβ has a broad range of physiological functions independent of those normally attributed to oestrogen signalling. These functions can partly be achieved by the activity of several alternatively spliced isoforms that have been identified for ERβ. This short review describes structural differences between the ERβ splice variants that are known to be translated into proteins. Moreover, we discuss how these alternative structures contribute to functional differences in the context of both healthy and pathological conditions. Our review also describes the principal factors that regulate alternative RNA splicing. The alternatively spliced isoforms of ERβ are differentially expressed according to brain region, age and hormonal milieu, emphasising the likelihood that there are precise cell-specific mechanisms regulating ERβ alternative splicing. However, despite these correlative data, the molecular factors regulating alternative ERβ splicing in the brain remain unknown. We also review the basic mechanisms that regulate alternative RNA splicing and use that framework to make logical predictions about ERβ alternative splicing in the brain.
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Affiliation(s)
- C K Kim
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - A Torcaso
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - A Asimes
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - W C J Chung
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - T R Pak
- Department of Cell and Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
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14
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Suzuki S, Ayukawa N, Okada C, Tanaka M, Takekoshi S, Iijima Y, Iijima T. Spatio-temporal and dynamic regulation of neurofascin alternative splicing in mouse cerebellar neurons. Sci Rep 2017; 7:11405. [PMID: 28900163 PMCID: PMC5595909 DOI: 10.1038/s41598-017-11319-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing is crucial for molecular diversification, which greatly contributes to the complexity and specificity of neural functions in the central nervous system (CNS). Neurofascin (NF) is a polymorphic cell surface protein that has a number of splicing isoforms. As the alternative splicing of the neurofascin gene (Nfasc) is developmentally regulated, NF isoforms have distinct functions in immature and mature brains. However, the molecular mechanisms underlying the alternative splicing of Nfasc in neurons are not yet understood. Here, we demonstrate that, alongside developmental regulation, Nfasc alternative splicing is spatially controlled in the mouse brain. We then identified distinct Nfasc splicing patterns at the cell-type level in the cerebellum, with Nfasc186 being expressed in Purkinje cells and absent from granule cells (GCs). Furthermore, we show that high K+-induced depolarization triggers a shift in splicing from Nfasc140 to Nfasc186 in cerebellar GCs. Finally, we identified a neural RNA-binding protein, Rbfox, as a key player in neural NF isoform selection, specifically controlling splicing at exons 26−29. Together, our results show that Nfasc alternative splicing is spatio-temporally and dynamically regulated in cerebellar neurons. Our findings provide profound insight into the mechanisms underlying the functional diversity of neuronal cell-adhesive proteins in the mammalian CNS.
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Affiliation(s)
- Satoko Suzuki
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; and 411 Kitakaname, Hiratsuka City, Kanagawa, 259-1292, Japan
| | - Noriko Ayukawa
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; and 411 Kitakaname, Hiratsuka City, Kanagawa, 259-1292, Japan
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa, 259-1193, Japan
| | - Masami Tanaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; and 411 Kitakaname, Hiratsuka City, Kanagawa, 259-1292, Japan
| | - Susumu Takekoshi
- Department of Cell Biology, Division of Host Defense Mechanism, School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa, 259-1193, Japan
| | - Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; and 411 Kitakaname, Hiratsuka City, Kanagawa, 259-1292, Japan
| | - Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; and 411 Kitakaname, Hiratsuka City, Kanagawa, 259-1292, Japan.
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15
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Implications of the thyroid hormone on neuronal development with special emphasis on the calmodulin-kinase IV pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:877-882. [PMID: 27939430 DOI: 10.1016/j.bbamcr.2016.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/29/2016] [Accepted: 12/02/2016] [Indexed: 12/16/2022]
Abstract
Thyroid hormones influence brain development through regulation of gene expression. This is especially true for Ca2+-dependent regulation since a major pathway is controlled by the Ca2+/calmodulin-dependent protein kinase IV (CaMKIV) which in turn is induced by the thyroid hormone T3. In addition, CaMKIV is involved in regulation of alternative splicing of a number of protein isoforms, among them PMCA1a, the neuronal specific isoform of the plasma membrane calcium pump. On the other hand, hypothyroidism or CaMKIV deficiency can have a severe influence on brain development. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
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16
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Sharma A, Nguyen H, Cai L, Lou H. Histone hyperacetylation and exon skipping: a calcium-mediated dynamic regulation in cardiomyocytes. Nucleus 2016; 6:273-8. [PMID: 26325491 DOI: 10.1080/19491034.2015.1081324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In contrast to cell type-specific pre-mRNA alternative splicing, mechanisms controlling activity-dependent alternative splicing is under-studied and not well understood. In a recent study, we conducted a comprehensive analysis of calcium-mediated mechanism that regulates alternative exon skipping in mouse cardiomyocytes. Our results reveal a strong link between histone hyperacetylation and skipping of cassette exons, and provide support to the kinetic coupling model of the epigenetic regulation of alternative splicing at the chromatin level.
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Affiliation(s)
- Alok Sharma
- a Department of Genetics and Genome Sciences ; Case Western Reserve University ; Cleveland , OH USA
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17
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Iijima T, Hidaka C, Iijima Y. Spatio-temporal regulations and functions of neuronal alternative RNA splicing in developing and adult brains. Neurosci Res 2016; 109:1-8. [PMID: 26853282 DOI: 10.1016/j.neures.2016.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 10/25/2022]
Abstract
Alternative pre-mRNA splicing is a fundamental mechanism that generates molecular diversity from a single gene. In the central nervous system (CNS), key neural developmental steps are thought to be controlled by alternative splicing decisions, including the molecular diversity underlying synaptic wiring, plasticity, and remodeling. Significant progress has been made in understanding the molecular mechanisms and functions of alternative pre-mRNA splicing in neurons through studies in invertebrate systems; however, recent studies have begun to uncover the potential role of neuronal alternative splicing in the mammalian CNS. This article provides an overview of recent findings regarding the regulation and function of neuronal alternative splicing. In particular, we focus on the spatio-temporal regulation of neurexin, a synaptic adhesion molecule, by neuronal cell type-specific factors and neuronal activity, which are thought to be especially important for characterizing neural development and function within the mammalian CNS. Notably, there is increasing evidence that implicates the dysregulation of neuronal splicing events in several neurological disorders. Therefore, understanding the detailed mechanisms of neuronal alternative splicing in the mammalian CNS may provide plausible treatment strategies for these diseases.
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Affiliation(s)
- Takatoshi Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan.
| | - Chiharu Hidaka
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
| | - Yoko Iijima
- Tokai University Institute of Innovative Science and Technology, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan; Tokai University Institute of Innovative Science and Technology, 4-1-1 Kitakaname, Hiratsuka City, Kanagawa 259-1292, Japan; School of Medicine, Tokai University, 143 Shimokasuya, Isehara City, Kanagawa 259-1193, Japan
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18
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Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
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Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
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19
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Warns JA, Davie JR, Dhasarathy A. Connecting the dots: chromatin and alternative splicing in EMT. Biochem Cell Biol 2015; 94:12-25. [PMID: 26291837 DOI: 10.1139/bcb-2015-0053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nature has devised sophisticated cellular machinery to process mRNA transcripts produced by RNA Polymerase II, removing intronic regions and connecting exons together, to produce mature RNAs. This process, known as splicing, is very closely linked to transcription. Alternative splicing, or the ability to produce different combinations of exons that are spliced together from the same genomic template, is a fundamental means of regulating protein complexity. Similar to transcription, both constitutive and alternative splicing can be regulated by chromatin and its associated factors in response to various signal transduction pathways activated by external stimuli. This regulation can vary between different cell types, and interference with these pathways can lead to changes in splicing, often resulting in aberrant cellular states and disease. The epithelial to mesenchymal transition (EMT), which leads to cancer metastasis, is influenced by alternative splicing events of chromatin remodelers and epigenetic factors such as DNA methylation and non-coding RNAs. In this review, we will discuss the role of epigenetic factors including chromatin, chromatin remodelers, DNA methyltransferases, and microRNAs in the context of alternative splicing, and discuss their potential involvement in alternative splicing during the EMT process.
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Affiliation(s)
- Jessica A Warns
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
| | - James R Davie
- b Children's Hospital Research Institute of Manitoba, John Buhler Research Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Archana Dhasarathy
- a Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, 501 N. Columbia Road Stop 9061, Grand Forks, ND 58202-9061, USA
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20
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Koumbadinga GA, Mahmood N, Lei L, Kan Y, Cao W, Lobo VG, Yao X, Zhang S, Xie J. Increased stability of heterogeneous ribonucleoproteins by a deacetylase inhibitor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1095-103. [PMID: 25959059 DOI: 10.1016/j.bbagrm.2015.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 04/27/2015] [Accepted: 05/01/2015] [Indexed: 11/15/2022]
Abstract
Splicing factors are often influenced by various signaling pathways, contributing to the dynamic changes of protein isoforms in cells. Heterogeneous ribonucleoproteins (hnRNPs) regulate many steps of RNA metabolism including pre-mRNA splicing but their control by cell signaling particularly through acetylation and ubiquitination pathways remains largely unknown. Here we show that TSA, a deacetylase inhibitor, reduced the ratio of Bcl-x splice variants Bcl-xL/xS in MDA-MB-231 breast cancer cells. This TSA effect was independent of TGFβ1; however, only in the presence of TGFβ1 was TSA able to change the splicing regulators hnRNP F/H by slightly reducing their mRNA transcripts but strongly preventing protein degradation. The latter was also efficiently prevented by lactacystin, a proteasome inhibitor, suggesting their protein stability control by both acetylation and ubiquitination pathways. Three lysines K87, K98 and K224 of hnRNP F are potential targets of the mutually exclusive acetylation or ubiquitination (K(Ac/Ub)) in the protein modification database PhosphoSitePlus. Mutating each of them but not a control non-K(Ac/Ub) (K68) specifically abolished the TSA enhancement of protein stability. Moreover, mutating K98 (K98R) and K224 (K224R) also abolished the TSA regulation of alternative splicing of a Bcl-x mini-gene. Furthermore, about 86% (30 of 35) of the multi-functional hnRNP proteins in the database contain lysines that are potential sites for acetylation/ubiquitination. We demonstrate that the degradation of three of them (A1, I and L) are also prevented by TSA. Thus, the deacetylase inhibitor TSA enhances hnRNP F stability through the K(Ac/Ub) lysines, with some of them essential for its regulation of alternative splicing. Such a regulation of protein stability is perhaps common for a group of hnRNPs and RNA metabolism.
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Affiliation(s)
- Geremy A Koumbadinga
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Niaz Mahmood
- Biochemistry & Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Lei Lei
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Yunchao Kan
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Nanyang Normal University, Nanyang, Henan, PR China
| | - Wenguang Cao
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Vincent G Lobo
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Xiaojian Yao
- Department of Medical Microbiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Shetuan Zhang
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, ON, Canada
| | - Jiuyong Xie
- Department of Physiology & Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Biochemistry & Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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21
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Feng D, Su RC, Zou L, Triggs-Raine B, Huang S, Xie J. Increase of a group of PTC(+) transcripts by curcumin through inhibition of the NMD pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1104-15. [PMID: 25934542 DOI: 10.1016/j.bbagrm.2015.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/07/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD), an mRNA surveillance mechanism, eliminates premature termination codon-containing (PTC⁺) transcripts. For instance, it maintains the homeostasis of splicing factors and degrades aberrant transcripts of human genetic disease genes. Here we examine the inhibitory effect on the NMD pathway and consequent increase of PTC+ transcripts by the dietary compound curcumin. We have found that several PTC⁺ transcripts including that of serine/arginine-rich splicing factor 1 (SRSF1) were specifically increased in cells by curcumin. We also observed a similar curcumin effect on the PTC⁺ mutant transcript from a Tay-Sachs-causing HEXA allele or from a beta-globin reporter gene. The curcumin effect was accompanied by significantly reduced expression of the NMD factors UPF1, 2, 3A and 3B. Consistently, in chromatin immunoprecipitation assays, curcumin specifically reduced the occupancy of acetyl-histone H3 and RNA polymerase II at the promoter region (-376 to -247nt) of human UPF1, in a time- and dosage-dependent way. Importantly, knocking down UPF1 abolished or substantially reduced the difference of PTC(+) transcript levels between control and curcumin-treated cells. The disrupted curcumin effect was efficiently rescued by expression of exogenous Myc-UPF1 in the knockdown cells. Together, our data demonstrate that a group of PTC⁺ transcripts are stabilized by a dietary compound curcumin through the inhibition of UPF factor expression and the NMD pathway.
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Affiliation(s)
- Dairong Feng
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China; Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Ruey-Chyi Su
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Liping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Barbara Triggs-Raine
- Department of Biochemistry & Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Shangzhi Huang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China.
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada.
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22
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Sohail M, Cao W, Mahmood N, Myschyshyn M, Hong SP, Xie J. Evolutionarily emerged G tracts between the polypyrimidine tract and 3' AG are splicing silencers enriched in genes involved in cancer. BMC Genomics 2014; 15:1143. [PMID: 25523808 PMCID: PMC4320613 DOI: 10.1186/1471-2164-15-1143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/10/2014] [Indexed: 12/23/2022] Open
Abstract
Background The 3′ splice site (SS) at the end of pre-mRNA introns has a consensus sequence (Y)nNYAG for constitutive splicing of mammalian genes. Deviation from this consensus could change or interrupt the usage of the splice site leading to alternative or aberrant splicing, which could affect normal cell function or even the development of diseases. We have shown that the position “N” can be replaced by a CA-rich RNA element called CaRRE1 to regulate the alternative splicing of a group of genes. Results Taking it a step further, we searched the human genome for purine-rich elements between the -3 and -10 positions of the 3′ splice sites of annotated introns. This identified several thousand such 3′SS; more than a thousand of them contain at least one copy of G tract. These sites deviate significantly from the consensus of constitutive splice sites and are highly associated with alterative splicing events, particularly alternative 3′ splice and intron retention. We show by mutagenesis analysis and RNA interference that the G tracts are splicing silencers and a group of the associated exons are controlled by the G tract binding proteins hnRNP H/F. Species comparison of a group of the 3′SS among vertebrates suggests that most (~87%) of the G tracts emerged in ancestors of mammals during evolution. Moreover, the host genes are most significantly associated with cancer. Conclusion We call these elements together with CaRRE1 regulatory RNA elements between the Py and 3′AG (REPA). The emergence of REPA in this highly constrained region indicates that this location has been remarkably permissive for the emergence of de novo regulatory RNA elements, even purine-rich motifs, in a large group of mammalian genes during evolution. This evolutionary change controls alternative splicing, likely to diversify proteomes for particular cellular functions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1143) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Jiuyong Xie
- Department of Physiology, University of Manitoba, 440 BMSB, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada.
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Sharma A, Nguyen H, Geng C, Hinman MN, Luo G, Lou H. Calcium-mediated histone modifications regulate alternative splicing in cardiomyocytes. Proc Natl Acad Sci U S A 2014; 111:E4920-8. [PMID: 25368158 PMCID: PMC4246288 DOI: 10.1073/pnas.1408964111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In cardiomyocytes, calcium is known to control gene expression at the level of transcription, whereas its role in regulating alternative splicing has not been explored. Here we report that, in mouse primary or embryonic stem cell-derived cardiomyocytes, increased calcium levels induce robust and reversible skipping of several alternative exons from endogenously expressed genes. Interestingly, we demonstrate a calcium-mediated splicing regulatory mechanism that depends on changes of histone modifications. Specifically, the regulation occurs through changes in calcium-responsive kinase activities that lead to alterations in histone modifications and subsequent changes in the transcriptional elongation rate and exon skipping. We demonstrate that increased intracellular calcium levels lead to histone hyperacetylation along the body of the genes containing calcium-responsive alternative exons by disrupting the histone deacetylase-to-histone acetyltransferase balance in the nucleus. Consequently, the RNA polymerase II elongation rate increases significantly on those genes, resulting in skipping of the alternative exons. These studies reveal a mechanism by which calcium-level changes in cardiomyocytes impact on the output of gene expression through altering alternative pre-mRNA splicing patterns.
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Affiliation(s)
| | | | - Cuiyu Geng
- Department of Genetics and Genome Sciences
| | | | - Guangbin Luo
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, and
| | - Hua Lou
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, and Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
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24
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Xie J. Differential evolution of signal-responsive RNA elements and upstream factors that control alternative splicing. Cell Mol Life Sci 2014; 71:4347-60. [PMID: 25064062 PMCID: PMC11113106 DOI: 10.1007/s00018-014-1688-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/13/2014] [Accepted: 07/17/2014] [Indexed: 12/17/2022]
Abstract
Cell signal-regulated alternative splicing occurs for many genes but the evolutionary origin of the regulatory components and their relationship remain unclear. This review focuses on the alternative splicing components of several systems based on the available bioinformatics data. Eight mammalian RNA elements for signal-regulated splicing were aligned among corresponding sequences from dozens of representative vertebrate species to allow for assessment of the trends in evolutionary changes. Four distinct trends were observed. Four of the elements are highly conserved in bird, reptile and fish species examined (i); two elements can be found in fish but the sequences have been changing till in marsupials or higher mammals (ii); one element is almost exclusively found in mammals with mostly the same sequence (iii); and one element can be found in birds or lower vertebrates but expanded abruptly to have variable numbers of copies in mammals (iv). All examined prototype trans-acting factors and protein kinases emerged earlier than the RNA elements but additional (paralog) factors emerged in the same or later species. Thus, after their emergence mainly in fish or mammals with pre-existing prototype trans-acting factors/kinases, half of the elements have been highly conserved from fish to humans but the other half have evolved differentially with additional trans-acting factors. Their differential evolution likely contributes to the exon- and species/class-specific control of alternative splicing and its regulation by cell signals. The evolvement of a group of mammal-specific components would help relay signals from extracellular stimuli to the splicing machinery and thus contribute to higher proteomic diversity.
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Affiliation(s)
- Jiuyong Xie
- Departments of Physiology, Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada,
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Refinement of the spectra of exon usage by combined effects of extracellular stimulus and intracellular factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:537-45. [PMID: 24844182 DOI: 10.1016/j.bbagrm.2014.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 11/23/2022]
Abstract
Finely tuned differential expression of alternative splice variants contributes to important physiological processes such as the fine-tuning of electrical firing or hearing frequencies; yet the underlying molecular basis for the expression control is not clear. The inclusion levels of four depolarization-regulated alternative exons were measured by RT-PCR in GH3 pituitary cells under different conditions of stimulation and/or RNA interference of splicing factors. The usage of the exons was reduced by membrane depolarization to various extents and was differentially modulated by the knock-down of splicing factors hnRNP L, L-like, I (PTBP1) or K or their combinations. A spectrum of each exon's level was produced under six knock-down conditions and was significantly shifted by depolarization. When all these conditions were considered together, a more refined or expanded spectrum of exon usage was obtained for each of the four exons. As a proof of principle for the molecular basis of the fine-tuning of exon usage, we show in the cases of hnRNP L and LL that their differential effects through the same element or different combinations of RNA sequences by the same factor hnRNP L are critical. The results thus demonstrate that the combined effect of varying extracellular stimuli and intracellular factors/RNA sequences refines or expands the spectra of endogenous exon usage, likely contributing to the fine-tuning of cellular properties.
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