1
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Dørum G, Hänggi NV, Burri D, Marti Y, Banemann R, Kulstein G, Courts C, Gosch A, Hadrys T, Haas C, Neubauer J. Selecting mRNA markers in blood for age estimation of the donor of a biological stain. Forensic Sci Int Genet 2024; 68:102976. [PMID: 38000161 DOI: 10.1016/j.fsigen.2023.102976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/13/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023]
Abstract
RNA has gained a substantial amount of attention within the forensic field over the last decade. There is evidence that RNAs are differentially expressed with biological age. Since RNA can be co-extracted with DNA from the same piece of evidence, RNA-based analysis appears as a promising molecular alternative for predicting the biological age and hence inferring the chronological age of a person. Using RNA-Seq data we searched for markers in blood potentially associated with age. We used our own RNA-Seq data from dried blood stains as well as publicly available RNA-Seq data from whole blood, and compared two different approaches to select candidate markers. The first approach focused on individual gene analysis with DESeq2 to select the genes most correlated with age, while the second approach employed lasso regression to select a set of genes for optimal prediction of age. We present two lists with 270 candidate markers, one for each approach.
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Affiliation(s)
- Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | - Dario Burri
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Yael Marti
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - Cornelius Courts
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Annica Gosch
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office (BLKA), Munich, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Jacqueline Neubauer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
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2
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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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3
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Chen F, Wang S, Zeng C, Tang S, Gu H, Wang Z, Li J, Feng P, Zhang Y, Wang P, Wu Y, Shen H. Silencing circSERPINE2 restrains mesenchymal stem cell senescence via the YBX3/PCNA/p21 axis. Cell Mol Life Sci 2023; 80:325. [PMID: 37831180 PMCID: PMC10575817 DOI: 10.1007/s00018-023-04975-6] [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: 05/24/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Increasing evidence indicates that circular RNAs (circRNAs) accumulate in aging tissues and nonproliferating cells due to their high stability. However, whether upregulation of circRNA expression mediates stem cell senescence and whether circRNAs can be targeted to alleviate aging-related disorders remain unclear. Here, RNA sequencing analysis of differentially expressed circRNAs in long-term-cultured mesenchymal stem cells (MSCs) revealed that circSERPINE2 expression was significantly increased in late passages. CircSERPINE2 small interfering RNA delayed MSC senescence and rejuvenated MSCs, while circSERPINE2 overexpression had the opposite effect. RNA pulldown followed by mass spectrometry revealed an interaction between circSERPINE2 and YBX3. CircSERPINE2 increased the affinity of YBX3 for ZO-1 through the CCAUC motif, resulting in the sequestration of YBX3 in the cytoplasm, inhibiting the association of YBX3 with the PCNA promoter and eventually affecting p21 ubiquitin-mediated degradation. In addition, our results demonstrated that senescence-related downregulation of EIF4A3 gave rise to circSERPINE2. In vivo, intra-articular injection of si-circSerpine2 restrained native joint-resident MSC senescence and cartilage degeneration in mice with aging-related osteoarthritis. Taken together, our findings provide strong evidence for a regulatory role for the circSERPINE2/YBX3/PCNA/p21 axis in MSC senescence and the therapeutic potential of si-circSERPINE2 in alleviating aging-associated syndromes, such as osteoarthritis.
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Affiliation(s)
- Fenglei Chen
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Shan Wang
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Chenying Zeng
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Su'an Tang
- Clinical Research Centre, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, People's Republic of China
| | - Huimin Gu
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Ziming Wang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Jinteng Li
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Pei Feng
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Yunhui Zhang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China
| | - Peng Wang
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
| | - Yanfeng Wu
- Center for Biotherapy, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
| | - Huiyong Shen
- Department of Orthopedics, Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518033, People's Republic of China.
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4
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Wang H, Lu J, Stevens T, Roberts A, Mandel J, Avula R, Ma B, Wu Y, Wang J, Land CV, Finkel T, Vockley JE, Airik M, Airik R, Muzumdar R, Gong Z, Torbenson MS, Prochownik EV. Premature aging and reduced cancer incidence associated with near-complete body-wide Myc inactivation. Cell Rep 2023; 42:112830. [PMID: 37481724 PMCID: PMC10591215 DOI: 10.1016/j.celrep.2023.112830] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
MYC proto-oncogene dysregulation alters metabolism, translation, and other functions in ways that support tumor induction and maintenance. Although Myc+/- mice are healthier and longer-lived than control mice, the long-term ramifications of more complete Myc loss remain unknown. We now describe the chronic consequences of body-wide Myc inactivation initiated postnatally. "MycKO" mice acquire numerous features of premature aging, including altered body composition and habitus, metabolic dysfunction, hepatic steatosis, and dysregulation of gene sets involved in functions that normally deteriorate with aging. Yet, MycKO mice have extended lifespans that correlate with a 3- to 4-fold lower lifetime cancer incidence. Aging tissues from normal mice and humans also downregulate Myc and gradually alter many of the same Myc target gene sets seen in MycKO mice. Normal aging and its associated cancer predisposition are thus highly linked via Myc.
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Affiliation(s)
- Huabo Wang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jie Lu
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Taylor Stevens
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Alexander Roberts
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jordan Mandel
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Raghunandan Avula
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; The University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Bingwei Ma
- Tongji University School of Medicine, Shanghai, China
| | - Yijen Wu
- Department of Developmental Biology, The University of Pittsburgh, Pittsburgh, PA, USA
| | - Jinglin Wang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Central South University, Xiangya School of Medicine, Changsha, Hunan 410013, P.R. China
| | - Clinton Van't Land
- Division of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Toren Finkel
- Division of Cardiology, The Department of Internal Medicine and the UPMC Aging Institute, Pittsburgh, PA 15224, USA
| | - Jerry E Vockley
- Division of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Merlin Airik
- Division of Nephrology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Rannar Airik
- Division of Nephrology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Radhika Muzumdar
- Division of Endocrinology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Zhenwei Gong
- Division of Endocrinology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Michel S Torbenson
- Division of Laboratory Medicine and Pathology, The Mayo Clinic, Rochester, MN 55905, USA
| | - Edward V Prochownik
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA 15261, USA; Hillman Cancer Center of UPMC, Pittsburgh, PA 15232, USA; Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA 15261, USA.
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5
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Prochownik EV, Wang H. Lessons in aging from Myc knockout mouse models. Front Cell Dev Biol 2023; 11:1244321. [PMID: 37621775 PMCID: PMC10446843 DOI: 10.3389/fcell.2023.1244321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Despite MYC being among the most intensively studied oncogenes, its role in normal development has not been determined as Myc-/- mice do not survival beyond mid-gestation. Myc ± mice live longer than their wild-type counterparts and are slower to accumulate many age-related phenotypes. However, Myc haplo-insufficiency likely conceals other important phenotypes as many high-affinity Myc targets genes continue to be regulated normally. By delaying Myc inactivation until after birth it has recently been possible to study the consequences of its near-complete total body loss and thus to infer its normal function. Against expectation, these "MycKO" mice lived significantly longer than control wild-type mice but manifested a marked premature aging phenotype. This seemingly paradoxical behavior was potentially explained by a >3-fold lower lifetime incidence of cancer, normally the most common cause of death in mice and often Myc-driven. Myc loss accelerated the accumulation of numerous "Aging Hallmarks", including the loss of mitochondrial and ribosomal structural and functional integrity, the generation of reactive oxygen species, the acquisition of genotoxic damage, the detrimental rewiring of metabolism and the onset of senescence. In both mice and humans, normal aging in many tissues was accompaniued by the downregulation of Myc and the loss of Myc target gene regulation. Unlike most mouse models of premature aging, which are based on monogenic disorders of DNA damage recognition and repair, the MycKO mouse model directly impacts most Aging Hallmarks and may therefore more faithfully replicate the normal aging process of both mice and humans. It further establishes that the strong association between aging and cancer can be genetically separated and is maintained by a single gene.
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Affiliation(s)
- Edward V. Prochownik
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
- The Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA, United States
- The Hillman Cancer Center of UPMC, Pittsburgh, PA, United States
- The Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA, United States
| | - Huabo Wang
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
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6
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Kouraki A, Doherty M, Fernandes GS, Zhang W, Walsh DA, Kelly A, Valdes AM. Different genes may be involved in distal and local sensitisation: a genome-wide gene-based association study and meta-analysis. Eur J Pain 2021; 26:740-753. [PMID: 34958702 PMCID: PMC9303629 DOI: 10.1002/ejp.1902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/11/2021] [Accepted: 12/25/2021] [Indexed: 11/22/2022]
Abstract
Background Neuropathic pain symptoms and signs of increased pain sensitization in osteoarthritis (OA) patients may explain persistent pain after total joint replacement (TJR). Therefore, identifying genetic markers associated with pain sensitization and neuropathic‐like pain phenotypes could be clinically important in identifying targets for early intervention. Methods We performed a genome‐wide gene‐based association study (GWGAS) using pressure pain detection thresholds (PPTs) from distal pain‐free sites (anterior tibia), a measure of distal sensitization, and from proximal pain‐affected sites (lateral joint line), a measure of local sensitization, in 320 knee OA participants from the Knee Pain and related health in the Community (KPIC) cohort. We next performed gene‐based fixed‐effects meta‐analysis of PPTs and a neuropathic‐like pain phenotype using genome‐wide association study (GWAS) data from KPIC and from an independent cohort of 613 post‐TJR participants, respectively. Results The most significant genes associated with distal and local sensitization were OR5B3 and BRDT, respectively. We also found previously identified neuropathic pain‐associated genes—KCNA1, MTOR, ADORA1 and SCN3B—associated with PPT at the anterior tibia and an inflammatory pain gene—PTAFR—associated with PPT at the lateral joint line. Meta‐analysis results of anterior tibia and neuropathic‐like pain phenotypes revealed genes associated with bone morphogenesis, neuro‐inflammation, obesity, type 2 diabetes, cardiovascular disease and cognitive function. Conclusions Overall, our results suggest that different biological processes might be involved in distal and local sensitization, and common genetic mechanisms might be implicated in distal sensitization and neuropathic‐like pain. Future studies are needed to replicate these findings. Significance To the best of our knowledge, this is the first GWAS for pain sensitization and the first gene‐based meta‐analysis of pain sensitization and neuropathic‐like pain. Higher pain sensitization and neuropathic pain symptoms are associated with persistent pain after surgery hence, identifying genetic biomarkers and molecular pathways associated with these traits is clinically relevant.
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Affiliation(s)
- A Kouraki
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - M Doherty
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - G S Fernandes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 6EH, United Kingdom
| | - W Zhang
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - D A Walsh
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,Versus Arthritis Centre for Sports, Exercise and Osteoarthritis, University of Nottingham, Nottingham, NG7 2UH, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - A Kelly
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
| | - A M Valdes
- Academic Rheumatology, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, NG5 1PB, United Kingdom.,Pain Centre Versus Arthritis, University of Nottingham, Nottingham, NG5 1PB, United Kingdom.,NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, NG5 1PB, United Kingdom
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7
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Rapid changes of miRNAs-20, -30, -410, -515, -134, and -183 and telomerase with psychological activity: A one year study on the relaxation response and epistemological considerations. J Tradit Complement Med 2021; 11:409-418. [PMID: 34522635 PMCID: PMC8427477 DOI: 10.1016/j.jtcme.2021.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/22/2022] Open
Abstract
Background and aim Mental stress represents a pivotal factor in cardiovascular diseases. The mechanism by which stress produces its deleterious effects is still under study, but one of the most explored pathways is inflammation-aging and cell senescence. In this scenario, circulating microRNAs appear to be regulatory elements of the telomerase activity and alternative splicing within the nuclear factor kappa-light-chain-enhancer (NF-κB) network. Anti-stress techniques appeared to be able to slow down the inflammatory and aging processes. As we recently verified, the practice of the relaxation response (RR) counteracted psychological stress and determined favorable changes of the NF-κB, p53, and toll-like receptor-4 (TLR-4) gene expression and in neurotransmitters, hormones, cytokines, and inflammatory circulating microRNAs. We aimed to verify a possible change in the serum levels of six other micro-RNAs of cardiovascular interest, involved in cell senescence and in the NF-κB network (miRNAs -20, -30, -410, -515, -134, and -183), and tested the activity of telomerase in peripheral blood mononuclear cells (PBMCs). Experimental procedure We measured the aforementioned molecules in the serum of patients with ischemic heart disease (and healthy controls) immediately before and after a relaxation response session, three times (after the baseline), in one year of follow-up. Results According to our data, the miRNA-20 and -30 levels and PBMCs-telomerase activity increased during the RR while the -410 and -515 levels decreased. During the RR sessions, both miRNA-134 and -183 decreased. Conclusion The mediators considered in this exploratory work appeared to vary rapidly with the psychological activity (in particular when focused on relaxation techniques) showing that psychological activity should be part of the future research on epigenetics. Epistemological perspectives are also discussed.
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8
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Lacavalla MA, Cisterna B, Zancanaro C, Malatesta M. Ultrastructural immunocytochemistry shows impairment of RNA pathways in skeletal muscle nuclei of old mice: A link to sarcopenia? Eur J Histochem 2021; 65:3229. [PMID: 33764019 PMCID: PMC8033527 DOI: 10.4081/ejh.2021.3229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
During aging, skeletal muscle is affected by sarcopenia, a progressive decline in muscle mass, strength and endurance that leads to loss of function and disability. Cell nucleus dysfunction is a possible factor contributing to sarcopenia because aging-associated alterations in mRNA and rRNA transcription/maturation machinery have been shown in several cell types including muscle cells. In this study, the distribution and density of key molecular factors involved in RNA pathways namely, nuclear actin (a motor protein and regulator of RNA transcription), 5-methyl cytosine (an epigenetic regulator of gene transcription), and ribonuclease A (an RNA degrading enzyme) were compared in different nuclear compartments of late adult and old mice myonuclei by means of ultrastructural immunocytochemistry. In all nuclear compartments, an age-related decrease of nuclear actin suggested altered chromatin structuring and impaired nucleus-to-cytoplasm transport of both mRNA and ribosomal subunits, while a decrease of 5-methyl cytosine and ribonuclease A in the nucleoli of old mice indicated an age-dependent loss of rRNA genes. These findings provide novel experimental evidence that, in the aging skeletal muscle, nuclear RNA pathways undergo impairment, likely hindering protein synthesis and contributing to the onset and progression of sarcopenia.
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Affiliation(s)
| | - Barbara Cisterna
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona.
| | - Carlo Zancanaro
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona.
| | - Manuela Malatesta
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona.
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9
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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10
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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11
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Qian Y, Cao L, Zhang Q, Amee M, Chen K, Chen L. SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue. BMC PLANT BIOLOGY 2020; 20:366. [PMID: 32746857 PMCID: PMC7397585 DOI: 10.1186/s12870-020-02572-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/23/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND As a cool-season grass species, tall fescue (Festuca arundinacea) is challenged by increasing temperatures. Heat acclimation or activation of leaf senescence, are two main strategies when tall fescue is exposed to heat stress (HS). However, lacking a genome sequence, the complexity of hexaploidy nature, and the short read of second-generation sequencing hinder a comprehensive understanding of the mechanism. This study aims to characterize the molecular mechanism of heat adaptation and heat-induced senescence at transcriptional and post-transcriptional levels. RESULTS Transcriptome of heat-treated (1 h and 72 h) and senescent leaves of tall fescue were generated by combining single-molecular real-time and Illumina sequencing. In total, 4076; 6917, and 11,918 differentially expressed genes (DEGs) were induced by short- and long-term heat stress (HS), and senescence, respectively. Venn and bioinformatics analyses of DEGs showed that short-term HS strongly activated heat shock proteins (Hsps) and heat shock factors (Hsfs), as well as specifically activated FK506-binding proteins (FKBPs), calcium signaling genes, glutathione S-transferase genes, photosynthesis-related genes, and phytohormone signaling genes. By contrast, long-term HS shared most of DEGs with senescence, including the up-regulated chlorophyll catabolic genes, phytohormone synthesis/degradation genes, stress-related genes, and NACs, and the down-regulated photosynthesis-related genes, FKBPs, and catalases. Subsequently, transient overexpression in tobacco showed that FaHsfA2a (up-regulated specifically by short-term HS) reduced cell membrane damages caused by HS, but FaNAC029 and FaNAM-B1 (up-regulated by long-term HS and senescence) increased the damages. Besides, alternative splicing was widely observed in HS and senescence responsive genes, including Hsps, Hsfs, and phytohormone signaling/synthesis genes. CONCLUSIONS The short-term HS can stimulate gene responses and improve thermotolerance, but long-term HS is a damage and may accelerate leaf senescence. These results contribute to our understanding of the molecular mechanism underlying heat adaptation and heat-induced senescence.
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Affiliation(s)
- Yiguang Qian
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, People’s Republic of China
| | - Liwen Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Qiang Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Maurice Amee
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ke Chen
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, People’s Republic of China
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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12
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Shen T, Li H, Song Y, Li L, Lin J, Wei G, Ni T. Alternative polyadenylation dependent function of splicing factor SRSF3 contributes to cellular senescence. Aging (Albany NY) 2020; 11:1356-1388. [PMID: 30835716 PMCID: PMC6428108 DOI: 10.18632/aging.101836] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 02/17/2019] [Indexed: 12/18/2022]
Abstract
Down-regulated splicing factor SRSF3 is known to promote cellular senescence, an important biological process in preventing cancer and contributing to individual aging, via its alternative splicing dependent function in human cells. Here we discovered alternative polyadenylation (APA) dependent function of SRSF3 as a novel mechanism explaining SRSF3 downregulation induced cellular senescence. Knockdown of SRSF3 resulted in preference usage of proximal poly(A) sites and thus global shortening of 3′ untranslated regions (3′ UTRs) of mRNAs. SRSF3-depletion also induced senescence-related phenotypes in both human and mouse cells. These 3′ UTR shortened genes were enriched in senescence-associated pathways. Shortened 3′ UTRs tended to produce more proteins than the longer ones. Simulating the effects of 3′ UTR shortening by overexpression of three candidate genes (PTEN, PIAS1 and DNMT3A) all led to senescence-associated phenotypes. Mechanistically, SRSF3 has higher binding density near proximal poly(A) site than distal one in 3′ UTR shortened genes. Further, upregulation of PTEN by either ectopic overexpression or SRSF3-knockdown induction both led to reduced phosphorylation of AKT and ultimately senescence-associated phenotypes. We revealed for the first time that reduced SRSF3 expression could promote cellular senescence through its APA-dependent function, largely extending our mechanistic understanding in splicing factor regulated cellular senescence.
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Affiliation(s)
- Ting Shen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
| | - Huan Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
| | - Yifang Song
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
| | - Li Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, China
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13
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Valdés-Sánchez L, Calado SM, de la Cerda B, Aramburu A, García-Delgado AB, Massalini S, Montero-Sánchez A, Bhatia V, Rodríguez-Bocanegra E, Diez-Lloret A, Rodríguez-Martínez D, Chakarova C, Bhattacharya SS, Díaz-Corrales FJ. Retinal pigment epithelium degeneration caused by aggregation of PRPF31 and the role of HSP70 family of proteins. Mol Med 2019; 26:1. [PMID: 31892304 PMCID: PMC6938640 DOI: 10.1186/s10020-019-0124-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mutations in pre-mRNA splicing factor PRPF31 can lead to retinitis pigmentosa (RP). Although the exact disease mechanism remains unknown, it has been hypothesized that haploinsufficiency might be involved in the pathophysiology of the disease. METHODS In this study, we have analyzed a mouse model containing the p.A216P mutation in Prpf31 gene. RESULTS We found that mutant Prpf31 protein produces cytoplasmic aggregates in the retinal pigment epithelium and decreasing the protein levels of this splicing factor in the nucleus. Additionally, normal protein was recruited in insoluble aggregates when the mutant protein was overexpressed in vitro. In response to protein aggregation, Hspa4l is overexpressed. This member of the HSP70 family of chaperones might contribute to the correct folding and solubilization of the mutant protein, allowing its translocation to the nucleus. CONCLUSIONS Our data suggests that a mechanism haploinsufficiency and dominant-negative is involved in retinal degeneration due to mutations in PRPF31. HSP70 over-expression might be a new therapeutic target for the treatment of retinal degeneration due to PRPF31 mutations.
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Affiliation(s)
- Lourdes Valdés-Sánchez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Sofia M Calado
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Center for Biomedical Research (CBMR), University of Algarve, 8800-139, Faro, Portugal
| | - Berta de la Cerda
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Ana Aramburu
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Clinique de l'Oeil, Avenue Bois de la Chapelle 15, 1213, Onex, Switzerland
| | - Ana Belén García-Delgado
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Simone Massalini
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Center for Molecular and Cellular Bioengineering (CMCB) DFG-Research Center for Regenerative Therapies Dresden (CRTD) Cluster of Excellence, Technische Universität Dresden, Fetscherstraße, 105 01307, Dresden, Germany
| | - Adoración Montero-Sánchez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Vaibhav Bhatia
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Eduardo Rodríguez-Bocanegra
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
- Present Address: Universitätsklinikum Tübingen, Forschungsinstitut für Augenheilkunde, Elfriede-Aulhorn-Str. 7, 72076, Tübingen, Germany
| | - Andrea Diez-Lloret
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Daniel Rodríguez-Martínez
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain
| | - Christina Chakarova
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Shom S Bhattacharya
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Francisco J Díaz-Corrales
- Regeneration and Cell Therapy Department, Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER (Junta de Andalucía), CSIC, Universidad de Sevilla, Universidad Pablo de Olavide, Avda. Americo Vespucio 24, 41092, Seville, Spain.
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Altered function of neuronal L-type calcium channels in ageing and neuroinflammation: Implications in age-related synaptic dysfunction and cognitive decline. Ageing Res Rev 2018; 42:86-99. [PMID: 29339150 DOI: 10.1016/j.arr.2018.01.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/29/2022]
Abstract
The rapid developments in science have led to an increase in human life expectancy and thus, ageing and age-related disorders/diseases have become one of the greatest concerns in the 21st century. Cognitive abilities tend to decline as we get older. This age-related cognitive decline is mainly attributed to aberrant changes in synaptic plasticity and neuronal connections. Recent studies show that alterations in Ca2+ homeostasis underlie the increased vulnerability of neurons to age-related processes like cognitive decline and synaptic dysfunctions. Dysregulation of Ca2+ can lead to dramatic changes in neuronal functions. We discuss in this review, the recent advances on the potential role of dysregulated Ca2+ homeostasis through altered function of L-type voltage gated Ca2+ channels (LTCC) in ageing, with an emphasis on cognitive decline. This review therefore focuses on age-related changes mainly in the hippocampus, and with mention of other brain areas, that are important for learning and memory. This review also highlights age-related memory deficits via synaptic alterations and neuroinflammation. An understanding of these mechanisms will help us formulate strategies to reverse or ameliorate age-related disorders like cognitive decline.
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15
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Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity. Nat Commun 2017; 8:306. [PMID: 28824175 PMCID: PMC5563511 DOI: 10.1038/s41467-017-00370-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 06/23/2017] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing (AS) coupled to nonsense-mediated decay (AS-NMD) is a conserved mechanism for post-transcriptional gene regulation. Here we show that, during dietary restriction (DR), AS is enhanced in Caenorhabditis elegans and mice. A splicing mediator hrpu-1 regulates a significant part of these AS events in C. elegans; knocking it down suppresses DR-mediated longevity. Concurrently, due to increased AS, NMD pathway genes are upregulated and knocking down UPF1 homologue smg-2 suppresses DR lifespan. Knockdown of NMD during DR significantly increases the inclusion of PTC-containing introns and the lengths of the 3′UTRs. Finally, we demonstrate that PHA-4/FOXA transcriptionally regulates the AS-NMD genes. Our study suggests that DR uses AS to amplify the proteome, supporting physiological remodelling required for enhanced longevity. This increases the dependence on NMD, but also helps fine-tune the expression of metabolic and splicing mediators. AS-NMD may thus provide an energetically favourable level of dynamic gene expression control during dietary restriction. Alternative splicing coupled to nonsense-mediated decay (AS-NMD) is a conserved mechanism for post-transcriptional gene regulation. Here, the authors provide evidence that AS-NMD is enhanced during dietary restriction (DR) and is required for DR-mediated longevity assurance in C. elegans.
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16
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Bhaumik P, Ghosh P, Ghosh S, Feingold E, Ozbek U, Sarkar B, Dey SK. Combined association of Presenilin-1 and Apolipoprotein E polymorphisms with maternal meiosis II error in Down syndrome births. Genet Mol Biol 2017; 40:577-585. [PMID: 28767121 PMCID: PMC5596362 DOI: 10.1590/1678-4685-gmb-2016-0138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease and Down syndrome often exhibit close association and predictively share common genetic risk-factors. Presenilin-1 (PSEN-1) and Apolipoprotein E (APOE) genes are associated with early and late onset of Alzheimer's disease, respectively. Presenilin -1 is involved in faithful chromosomal segregation. A higher frequency of the APOE ε4 allele has been reported among young mothers giving birth to Down syndrome children. In this study, 170 Down syndrome patients, grouped according to maternal meiotic stage of nondisjunction and maternal age at conception, and their parents were genotyped for PSEN-1 intron-8 and APOE polymorphisms. The control group consisted of 186 mothers of karyotypically normal children. The frequencies of the PSEN-1 T allele and TT genotype, in the presence of the APOE ε4 allele, were significantly higher among young mothers (< 35 years) with meiosis II nondisjunction than in young control mothers (96.43% vs. 65.91% P = 0.0002 and 92.86% vs. 45.45% P < 0.0001 respectively) but not among mothers with meiosis I nondisjunction. We infer that the co-occurrence of the PSEN-1 T allele and the APOE ε4 allele associatively increases the risk of meiotic segregation error II among young women.
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Affiliation(s)
- Pranami Bhaumik
- Department of Biotechnology, School of Biotechnology and Biological
Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Priyanka Ghosh
- Department of Biotechnology, School of Biotechnology and Biological
Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Sujay Ghosh
- Department of Zoology, University of Calcutta, Ballygunge Science
college campus, Kolkata, West Bengal, India
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health,
University of Pittsburgh, PA, USA
- Department of Biostatistics, Graduate School of Public Health,
University of Pittsburgh, Pittsburgh, PA, USA
| | - Umut Ozbek
- Department of Biostatistics, Graduate School of Public Health,
University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Subrata Kumar Dey
- Department of Biotechnology, School of Biotechnology and Biological
Sciences. Maulana Abul Kalam Azad University of Technology, West Bengal, India
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Lee BP, Pilling LC, Emond F, Flurkey K, Harrison DE, Yuan R, Peters LL, Kuchel GA, Ferrucci L, Melzer D, Harries LW. Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans. Aging Cell 2016; 15:903-13. [PMID: 27363602 PMCID: PMC5013025 DOI: 10.1111/acel.12499] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2016] [Indexed: 12/31/2022] Open
Abstract
Dysregulation of splicing factor expression and altered alternative splicing are associated with aging in humans and other species, and also with replicative senescence in cultured cells. Here, we assess whether expression changes of key splicing regulator genes and consequent effects on alternative splicing are also associated with strain longevity in old and young mice, across 6 different mouse strains with varying lifespan (A/J, NOD.B10Sn-H2(b) /J, PWD.Phj, 129S1/SvlmJ, C57BL/6J and WSB/EiJ). Splicing factor expression and changes to alternative splicing were associated with strain lifespan in spleen and to a lesser extent in muscle. These changes mainly involved hnRNP splicing inhibitor transcripts with most changes more marked in spleens of young animals from long-lived strains. Changes in spleen isoform expression were suggestive of reduced cellular senescence and retained cellular proliferative capacity in long-lived strains. Changes in muscle isoform expression were consistent with reduced pro-inflammatory signalling in longer-lived strains. Two splicing regulators, HNRNPA1 and HNRNPA2B1, were also associated with parental longevity in humans, in the InCHIANTI aging study. Splicing factors may represent a driver, mediator or early marker of lifespan in mouse, as expression differences were present in the young animals of long-lived strains. Changes to alternative splicing patterns of key senescence genes in spleen and key remodelling genes in muscle suggest that correct regulation of alternative splicing may enhance lifespan in mice. Expression of some splicing factors in humans was also associated with parental longevity, suggesting that splicing regulation may also influence lifespan in humans.
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Affiliation(s)
| | - Luke C. Pilling
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
| | | | - Kevin Flurkey
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - David E. Harrison
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Rong Yuan
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Luanne L. Peters
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - George A. Kuchel
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
| | | | - David Melzer
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
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18
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Rodríguez SA, Grochová D, McKenna T, Borate B, Trivedi NS, Erdos MR, Eriksson M. Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging. Aging Cell 2016; 15:267-78. [PMID: 26685868 PMCID: PMC4783335 DOI: 10.1111/acel.12433] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2015] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome‐wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus, and white adipose tissue from wild‐type C57BL6/J male mice (4 and 18 months old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone, and white adipose tissue between the different age groups (ranging from 27 to 246 AS genes corresponding to 0.3–3.2% of the total number of genes analyzed). For skin, skeletal muscle, and bone, we included a later age group (28 months old) that showed that the number of alternatively spliced genes increased with age in all three tissues (P < 0.01). Analysis of alternatively spliced genes across all tissues by gene ontology and pathway analysis identified 158 genes involved in RNA processing. Additional analysis of AS in a mouse model for the premature aging disease Hutchinson–Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with an impaired developmental splicing. As progerin accumulates, the number of genes with AS increases compared to in wild‐type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.
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Affiliation(s)
- Sofía A. Rodríguez
- Department of Biosciences and Nutrition; Center for Innovative Medicine; Karolinska Institutet; Novum SE-141 83 Huddinge Sweden
| | - Diana Grochová
- Department of Biosciences and Nutrition; Center for Innovative Medicine; Karolinska Institutet; Novum SE-141 83 Huddinge Sweden
| | - Tomás McKenna
- Department of Biosciences and Nutrition; Center for Innovative Medicine; Karolinska Institutet; Novum SE-141 83 Huddinge Sweden
| | - Bhavesh Borate
- National Human Genome Research Institute; National Institutes of Health; Bethesda MD USA
| | - Niraj S. Trivedi
- National Human Genome Research Institute; National Institutes of Health; Bethesda MD USA
| | - Michael R. Erdos
- National Human Genome Research Institute; National Institutes of Health; Bethesda MD USA
| | - Maria Eriksson
- Department of Biosciences and Nutrition; Center for Innovative Medicine; Karolinska Institutet; Novum SE-141 83 Huddinge Sweden
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19
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Wille M, Schümann A, Wree A, Kreutzer M, Glocker MO, Mutzbauer G, Schmitt O. The Proteome Profiles of the Cerebellum of Juvenile, Adult and Aged Rats--An Ontogenetic Study. Int J Mol Sci 2015; 16:21454-85. [PMID: 26370973 PMCID: PMC4613263 DOI: 10.3390/ijms160921454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/04/2015] [Accepted: 08/25/2015] [Indexed: 11/16/2022] Open
Abstract
In this study, we searched for proteins that change their expression in the cerebellum (Ce) of rats during ontogenesis. This study focuses on the question of whether specific proteins exist which are differentially expressed with regard to postnatal stages of development. A better characterization of the microenvironment and its development may result from these study findings. A differential two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of the samples revealed that the number of proteins of the functional classes differed depending on the developmental stages. Especially members of the functional classes of biosynthesis, regulatory proteins, chaperones and structural proteins show the highest differential expression within the analyzed stages of development. Therefore, members of these functional protein groups seem to be involved in the development and differentiation of the Ce within the analyzed development stages. In this study, changes in the expression of proteins in the Ce at different postnatal developmental stages (postnatal days (P) 7, 90, and 637) could be observed. At the same time, an identification of proteins which are involved in cell migration and differentiation was possible. Especially proteins involved in processes of the biosynthesis and regulation, the dynamic organization of the cytoskeleton as well as chaperones showed a high amount of differentially expressed proteins between the analyzed dates.
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Affiliation(s)
- Michael Wille
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Antje Schümann
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Andreas Wree
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Michael Kreutzer
- Proteome Center Rostock, Schillingallee 69, 18055 Rostock, Germany.
| | | | - Grit Mutzbauer
- Department of Pathology, Josef-Schneider-Str. 2, 97080 Würzburg, Germany.
| | - Oliver Schmitt
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
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Farrokh S, Brillen AL, Haendeler J, Altschmied J, Schaal H. Critical regulators of endothelial cell functions: for a change being alternative. Antioxid Redox Signal 2015; 22:1212-29. [PMID: 25203279 DOI: 10.1089/ars.2014.6023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
SIGNIFICANCE The endothelium regulates vessel dilation and constriction, balances hemostasis, and inhibits thrombosis. In addition, pro- and anti-angiogenic molecules orchestrate proliferation, survival, and migration of endothelial cells. Regulation of all these processes requires fine-tuning of signaling pathways, which can easily be tricked into running the opposite direction when exogenous or endogenous signals get out of hand. Surprisingly, some critical regulators of physiological endothelial functions can turn malicious by mere alternative splicing, leading to the expression of protein isoforms with opposite functions. RECENT ADVANCES While reviewing the evidence of alternative splicing on cellular physiology, it became evident that expression of splice factors and their activities are regulated by externally triggered signaling cascades. Furthermore, genome-wide identification of RNA-binding sites of splicing regulatory proteins now offer a glimpse into the splicing code responsible for alternative splicing of molecules regulating endothelial functions. CRITICAL ISSUES Due to the constantly growing number of transcript and protein isoforms, it will become more and more important to identify and characterize all transcripts and proteins regulating endothelial cell functions. One critical issue will be a non-ambiguous nomenclature to keep consistency throughout different laboratories. FUTURE DIRECTIONS RNA-deep sequencing focusing on exon-exon junction needs to more reliably identify alternative splicing events combined with functional analyses that will uncover more splice variants contributing to or inhibiting proper endothelial functions. In addition, understanding the signals mediating alternative splicing and its regulation might allow us to derive new strategies to preserve endothelial function by suppressing or upregulating specific protein isoforms. Antioxid. Redox Signal. 22, 1212-1229.
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Affiliation(s)
- Sabrina Farrokh
- 1 Heisenberg-Group-Environmentally-Induced Cardiovascular Degeneration, IUF-Leibniz Research Institute for Environmental Medicine , Düsseldorf, Germany
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21
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Age-related nuclear translocation of P2X6 subunit modifies splicing activity interacting with splicing factor 3A1. PLoS One 2015; 10:e0123121. [PMID: 25874565 PMCID: PMC4395284 DOI: 10.1371/journal.pone.0123121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/18/2015] [Indexed: 01/13/2023] Open
Abstract
P2X receptors are ligand-gated ion channels sensitive to extracellular nucleotides formed by the assembling of three equal or different P2X subunits. In this work we report, for the first time, the accumulation of the P2X6 subunit inside the nucleus of hippocampal neurons in an age-dependent way. This location is favored by its anchorage to endoplasmic reticulum through its N-terminal domain. The extracellular domain of P2X6 subunit is the key to reach the nucleus, where it presents a speckled distribution pattern and is retained by interaction with the nuclear envelope protein spectrin α2. The in vivo results showed that, once inside the nucleus, P2X6 subunit interacts with the splicing factor 3A1, which ultimately results in a reduction of the mRNA splicing activity. Our data provide new insights into post-transcriptional regulation of mRNA splicing, describing a novel mechanism that could explain why this process is sensitive to changes that occur with age.
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22
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Tseng CY, Kao SH, Wan CL, Cho Y, Tung SY, Hsu HJ. Notch signaling mediates the age-associated decrease in adhesion of germline stem cells to the niche. PLoS Genet 2014; 10:e1004888. [PMID: 25521289 PMCID: PMC4270478 DOI: 10.1371/journal.pgen.1004888] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/12/2014] [Indexed: 11/18/2022] Open
Abstract
Stem cells have an innate ability to occupy their stem cell niche, which in turn, is optimized to house stem cells. Organ aging is associated with reduced stem cell occupancy in the niche, but the mechanisms involved are poorly understood. Here, we report that Notch signaling is increased with age in Drosophila female germline stem cells (GSCs), and this results in their removal from the niche. Clonal analysis revealed that GSCs with low levels of Notch signaling exhibit increased adhesiveness to the niche, thereby out-competing their neighbors with higher levels of Notch; adhesiveness is altered through regulation of E-cadherin expression. Experimental enhancement of Notch signaling in GSCs hastens their age-dependent loss from the niche, and such loss is at least partially mediated by Sex lethal. However, disruption of Notch signaling in GSCs does not delay GSC loss during aging, and nor does it affect BMP signaling, which promotes self-renewal of GSCs. Finally, we show that in contrast to GSCs, Notch activation in the niche (which maintains niche integrity, and thus mediates GSC retention) is reduced with age, indicating that Notch signaling regulates GSC niche occupancy both intrinsically and extrinsically. Our findings expose a novel role of Notch signaling in controlling GSC-niche adhesion in response to aging, and are also of relevance to metastatic cancer cells, in which Notch signaling suppresses cell adhesion. Aging is frequently associated with a decline in the size of stem cell pools, but little is known regarding the molecular mechanisms underlying this process. Here, we report that Notch signaling is increased in GSCs as they age, and this promotes their removal from the niche in an E-cadherin dependent manner. In contrast to GSCs, niche cells exhibit decreased Notch signaling with age; Notch signaling in these cells controls niche integrity, and consequently GSC retention. While Notch signaling in the niche is regulated by insulin signaling, Notch signaling in GSCs is controlled by Sex lethal, an RNA-binding protein. These results imply that Notch signaling is regulated in a cell-type-dependent manner, and coordination between GSCs and their niche facilitates the removal of cells from the niche during the aging process.
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Affiliation(s)
- Chen-Yuan Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Han Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Ling Wan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yueh Cho
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Yun Tung
- Genomic Core Facility, Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hwei-Jan Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Karambataki M, Malousi A, Kouidou S. Risk-associated coding synonymous SNPs in type 2 diabetes and neurodegenerative diseases: genetic silence and the underrated association with splicing regulation and epigenetics. Mutat Res 2014; 770:85-93. [PMID: 25771874 DOI: 10.1016/j.mrfmmm.2014.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 06/04/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are tentatively critical with regard to disease predisposition, but coding synonymous SNPs (sSNPs) are generally considered "neutral". Nevertheless, sSNPs in serine/arginine-rich (SR) and splice-site (SS) exonic splicing enhancers (ESEs) or in exonic CpG methylation targets, could be decisive for splicing, particularly in aging-related conditions, where mis-splicing is frequently observed. We presently identified 33 genes T2D-related and 28 related to neurodegenerative diseases, by investigating the impact of the corresponding coding sSNPs on splicing and using gene ontology data and computational tools. Potentially critical (prominent) sSNPs comply with the following criteria: changing the splicing potential of prominent SR-ESEs or of significant SS-ESEs by >1.5 units (Δscore), or formation/deletion of ESEs with maximum splicing score. We also noted the formation/disruption of CpGs (tentative methylation sites of epigenetic sSNPs). All disease association studies involving sSNPs are also reported. Only 21/670 coding SNPs, mostly epigenetic, reported in 33 T2D-related genes, were found to be prominent coding synonymous. No prominent sSNPs have been recorded in three key T2D-related genes (GCGR, PPARGC1A, IGF1). Similarly, 20/366 coding synonymous were identified in ND related genes, mostly epigenetic. Meta-analysis showed that 17 of the above prominent sSNPs were previously investigated in association with various pathological conditions. Three out of four sSNPs (all epigenetic) were associated with T2D and one with NDs (branch site sSNP). Five were associated with other or related pathological conditions. None of the four sSNPs introducing new ESEs was found to be disease-associated. sSNPs introducing smaller Δscore changes (<1.5) in key proteins (INSR, IRS1, DISC1) were also correlated to pathological conditions. This data reveals that genetic variation in splicing-regulatory and particularly CpG sites might be related to disease predisposition and that in-silico analysis is useful for identifying sSNPs, which might be falsely identified as silent or synonymous.
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Affiliation(s)
- M Karambataki
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Malousi
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - S Kouidou
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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Li B, Ngo S, Wu W, Xu H, Xie Z, Li Q, Pan Z. Identification and characterization of yak (Bos grunniens) b-Boule gene and its alternative splice variants. Gene 2014; 550:193-9. [PMID: 25149018 DOI: 10.1016/j.gene.2014.08.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 01/31/2023]
Abstract
Boule is responsible for meiotic arrest of sperms and male sterility during mammalian spermatogenesis. In the present study, we first identified yak b-Boule gene and its two alternative splice variants. The full length coding region of yak b-Boule is 888bp and encodes a 295-amino acid protein with a typical RNA-recognition motif (RRM) and a Deleted in Azoospermia (DAZ) repetitive sequence motif. Two alternative splice variants of yak b-Boule were generated following the consensus "GT-AG" rule and named b-Boule1 (36bp deletion in exon 3) and b-Boule2 (deletion of integral exon 7), respectively. In male yak, b-Boule, b-Boule1 and b-Boule2 were found to be exclusively expressed in the testes at a ratio of 81:0.1:1. Intriguingly, the mRNA expression levels of b-Boule and b-Boule1 in yak testis were significantly higher than those in cattle-yak, although no significant difference was observed for b-Boule2 expression between the yak and cattle-yak. These results suggest that b-Boule gene, which is partially regulated by alternative splicing, may be involved in the process of yak spermatogenesis.
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Affiliation(s)
- Bojiang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Sherry Ngo
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Wangjun Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongtao Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhuang Xie
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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25
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Anvar SY, Raz Y, Verway N, van der Sluijs B, Venema A, Goeman JJ, Vissing J, van der Maarel SM, 't Hoen PAC, van Engelen BGM, Raz V. A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging. Aging (Albany NY) 2013; 5:412-26. [PMID: 23793615 PMCID: PMC3824410 DOI: 10.18632/aging.100567] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is caused by trinucleotide repeat expansion mutations in Poly(A) binding protein 1 (PABPN1). PABPN1 is a regulator of mRNA stability and is ubiquitously expressed. Here we investigated how symptoms in OPMD initiate only at midlife and why a subset of skeletal muscles is predominantly affected. Genome-wide RNA expression profiles from Vastus lateralis muscles human carriers of expanded-PABPN1 at pre-symptomatic and symptomatic stages were compared with healthy controls. Major expression changes were found to be associated with age rather than with expression of expanded-PABPN1, instead transcriptomes of OPMD and elderly muscles were significantly similar (P<0.05). Using k-means clustering we identified age-dependent trends in both OPMD and controls, but trends were often accelerated in OPMD. We report an age-regulated decline in PABPN1 levels in Vastus lateralis muscles from the fifth decade. In concurrence with severe muscle degeneration in OPMD, the decline in PABPN1 accelerated in OPMD and was specific to skeletal muscles. Reduced PABPN1 levels (30% to 60%) in muscle cells induced myogenic defects and morphological signatures of cellular aging in proportion to PABPN1 expression levels. We suggest that PABPN1 levels regulate muscle cell aging and OPMD represents an accelerated muscle aging disorder.
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Affiliation(s)
- Seyed Yahya Anvar
- Center for Human and Clinical Genetics, Leiden University Medical Center, the Netherlands
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26
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Newman M, Wilson L, Verdile G, Lim A, Khan I, Moussavi Nik SH, Pursglove S, Chapman G, Martins RN, Lardelli M. Differential, dominant activation and inhibition of Notch signalling and APP cleavage by truncations of PSEN1 in human disease. Hum Mol Genet 2013; 23:602-17. [DOI: 10.1093/hmg/ddt448] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Holly AC, Melzer D, Pilling LC, Fellows AC, Tanaka T, Ferrucci L, Harries LW. Changes in splicing factor expression are associated with advancing age in man. Mech Ageing Dev 2013; 134:356-66. [PMID: 23747814 PMCID: PMC5863542 DOI: 10.1016/j.mad.2013.05.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/16/2013] [Accepted: 05/25/2013] [Indexed: 11/22/2022]
Abstract
Human ageing is associated with decreased cellular plasticity and adaptability. Changes in alternative splicing with advancing age have been reported in man, which may arise from age-related alterations in splicing factor expression. We determined whether the mRNA expression of key splicing factors differed with age, by microarray analysis in blood from two human populations and by qRT-PCR in senescent primary fibroblasts and endothelial cells. Potential regulators of splicing factor expression were investigated by siRNA analysis. Approximately one third of splicing factors demonstrated age-related transcript expression changes in two human populations. Ataxia Telangiectasia Mutated (ATM) transcript expression correlated with splicing factor expression in human microarray data. Senescent primary fibroblasts and endothelial cells also demonstrated alterations in splicing factor expression, and changes in alternative splicing. Targeted knockdown of the ATM gene in primary fibroblasts resulted in up-regulation of some age-responsive splicing factor transcripts. We conclude that isoform ratios and splicing factor expression alters with age in vivo and in vitro, and that ATM may have an inhibitory role on the expression of some splicing factors. These findings suggest for the first time that ATM, a core element in the DNA damage response, is a key regulator of the splicing machinery in man.
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Affiliation(s)
- Alice C. Holly
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
| | - David Melzer
- Epidemiology and Public Health, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
| | - Luke C. Pilling
- Epidemiology and Public Health, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
| | - Alexander C. Fellows
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
| | | | | | - Lorna W. Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX1 2LU, UK
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28
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The ING1a tumor suppressor regulates endocytosis to induce cellular senescence via the Rb-E2F pathway. PLoS Biol 2013; 11:e1001502. [PMID: 23472054 PMCID: PMC3589274 DOI: 10.1371/journal.pbio.1001502] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/24/2013] [Indexed: 02/07/2023] Open
Abstract
An age-associated isoform of ING1, ING1a, induces cell senescence by altering endocytosis, subsequently activating the retinoblastoma tumor suppressor. The INhibitor of Growth (ING) proteins act as type II tumor suppressors and epigenetic regulators, being stoichiometric members of histone acetyltransferase and histone deacetylase complexes. Expression of the alternatively spliced ING1a tumor suppressor increases >10-fold during replicative senescence. ING1a overexpression inhibits growth; induces a large flattened cell morphology and the expression of senescence-associated β-galactosidase; increases Rb, p16, and cyclin D1 levels; and results in the accumulation of senescence-associated heterochromatic foci. Here we identify ING1a-regulated genes and find that ING1a induces the expression of a disproportionate number of genes whose products encode proteins involved in endocytosis. Intersectin 2 (ITSN2) is most affected by ING1a, being rapidly induced >25-fold. Overexpression of ITSN2 independently induces expression of the p16 and p57KIP2 cyclin-dependent kinase inhibitors, which act to block Rb inactivation, acting as downstream effectors of ING1a. ITSN2 is also induced in normally senescing cells, consistent with elevated levels of ING1a inducing ITSN2 as part of a normal senescence program. Inhibition of endocytosis or altering the stoichiometry of endosome components such as Rab family members similarly induces senescence. Knockdown of ITSN2 also blocks the ability of ING1a to induce a senescent phenotype, confirming that ITSN2 is a major transducer of ING1a-induced senescence signaling. These data identify a pathway by which ING1a induces senescence and indicate that altered endocytosis activates the Rb pathway, subsequently effecting a senescent phenotype. Alternative splicing of several genes including the p16 and p53 tumor suppressors has been reported to increase during replicative senescence of normal diploid cells, but the biological functions of most alternative transcripts are unknown. We have found that a splicing product of the ING1 epigenetic regulator, ING1a, also increases during senescence; moreover, forced expression of ING1a at these levels in otherwise growth-competent cells can induce senescence. In this study we have determined that a major mechanism by which ING1a induces senescence is through inhibiting endocytosis; this subsequently activates the retinoblastoma (Rb) tumor suppressor pathway by increasing Rb levels and preventing its inactivation through multiple mechanisms. Our study also establishes a link between endocytosis and oxidative stress and suggests that multiple mechanisms that induce cellular senescence may do so by inhibiting normal endocytic processes, thereby affecting normal signal transduction pathways including those mitogenic pathways required for cell growth.
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29
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Impact of maternal aging on the molecular signature of human cumulus cells. Fertil Steril 2012; 98:1574-80.e5. [DOI: 10.1016/j.fertnstert.2012.08.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/01/2012] [Accepted: 08/07/2012] [Indexed: 11/20/2022]
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30
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The impact of mRNA turnover and translation on age-related muscle loss. Ageing Res Rev 2012; 11:432-41. [PMID: 22687959 DOI: 10.1016/j.arr.2012.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/25/2012] [Accepted: 05/31/2012] [Indexed: 12/21/2022]
Abstract
The deterioration of skeletal muscle that develops slowly with age, termed sarcopenia, often leads to disability and mortality in the elderly population. As the proportion of elderly citizens continues to increase due to the dramatic rise in life expectancy, there are rising concerns about the healthcare cost and social burden of caring for geriatric patients. Thus, there is a growing need to understand the underlying mechanisms of sarcopenic muscle loss so that more efficacious therapies may be developed. Building evidence suggests that the onset of age-related muscle loss is linked to the age-related changes in gene expression that occur during sarcopenia. In recent work, the posttranscriptional regulation of gene expression by RNA-binding proteins (RBPs) and microRNA (miRNA) involved in the turnover and translation of mRNA were shown as key players believed to be involved in the induction of muscle wasting. Furthermore, posttranscriptional regulation may also be linked to the reduced ability of muscle satellite cells to contribute to muscle mass during ageing, a key contributing factor to sarcopenic progression. Here we highlight how the activation of pathways such as the p38 MAPK and the phosphoinositide 3-kinase (PI3K) pathways alter the ability of RBPs to regulate the expression of their target mRNAs encoding proteins involved in cell cycle (p21 and p16), as well as myogenesis (Pax7, myogenin and MyoD). Further investigation into the role of RBPs and miRNA during sarcopenia may provide new insights into the development and progression of this disorder, which may lead to the development of new treatment options for elderly patients suffering from sarcopenia.
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31
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Butte MJ, Lee SJ, Jesneck J, Keir ME, Haining WN, Sharpe AH. CD28 costimulation regulates genome-wide effects on alternative splicing. PLoS One 2012; 7:e40032. [PMID: 22768209 PMCID: PMC3386953 DOI: 10.1371/journal.pone.0040032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/03/2012] [Indexed: 12/31/2022] Open
Abstract
CD28 is the major costimulatory receptor required for activation of naïve T cells, yet CD28 costimulation affects the expression level of surprisingly few genes over those altered by TCR stimulation alone. Alternate splicing of genes adds diversity to the proteome and contributes to tissue-specific regulation of genes. Here we demonstrate that CD28 costimulation leads to major changes in alternative splicing during activation of naïve T cells, beyond the effects of TCR alone. CD28 costimulation affected many more genes through modulation of alternate splicing than by modulation of transcription. Different families of biological processes are over-represented among genes alternatively spliced in response to CD28 costimulation compared to those genes whose transcription is altered, suggesting that alternative splicing regulates distinct biological effects. Moreover, genes dependent upon hnRNPLL, a global regulator of splicing in activated T cells, were enriched in T cells activated through TCR plus CD28 as compared to TCR alone. We show that hnRNPLL expression is dependent on CD28 signaling, providing a mechanism by which CD28 can regulate splicing in T cells and insight into how hnRNPLL can influence signal-induced alternative splicing in T cells. The effects of CD28 on alternative splicing provide a newly appreciated means by which CD28 can regulate T cell responses.
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Affiliation(s)
- Manish J. Butte
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sun Jung Lee
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan Jesneck
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America and Division of Pediatric Hematology/Oncology, Children’s Hospital, Boston, Massachusetts, United States of America
| | - Mary E. Keir
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. Nicholas Haining
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America and Division of Pediatric Hematology/Oncology, Children’s Hospital, Boston, Massachusetts, United States of America
| | - Arlene H. Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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Blanco FJ, Bernabéu C. The Splicing Factor SRSF1 as a Marker for Endothelial Senescence. Front Physiol 2012; 3:54. [PMID: 22470345 PMCID: PMC3314196 DOI: 10.3389/fphys.2012.00054] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 02/26/2012] [Indexed: 01/03/2023] Open
Abstract
Aging is the major risk factor per se for the development of cardiovascular diseases. The senescence of the endothelial cells (ECs) that line the lumen of blood vessels is the cellular basis for these age-dependent vascular pathologies, including atherosclerosis and hypertension. During their lifespan, ECs may reach a stage of senescence by two different pathways; a replicative one derived from their preprogrammed finite number of cell divisions; and one induced by stress stimuli. Also, certain physiological stimuli, such as transforming growth factor-β, are able to modulate cellular senescence. Currently, the cellular aging process is being widely studied to identify novel molecular markers whose changes correlate with senescence. This review focuses on the regulation of alternative splicing mediated by the serine-arginine splicing factor 1 (SRSF1, or ASF/SF2) during endothelial senescence, a process that is associated with a differential subcellular localization of SRSF1, which typically exhibits a scattered distribution throughout the cytoplasm. Based on its senescence-dependent involvement in alternative splicing, we postulate that SRSF1 is a key marker of EC senescence, regulating the expression of alternative isoforms of target genes such as endoglin (ENG), vascular endothelial growth factor A (VEGFA), tissue factor (T3), or lamin A (LMNA) that integrate in a common molecular senescence program.
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Affiliation(s)
- Francisco Javier Blanco
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas and Centro de Investigación Biomédica en Red de Enfermedades Raras Madrid, Spain
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Hippocampal microRNA-132 mediates stress-inducible cognitive deficits through its acetylcholinesterase target. Brain Struct Funct 2012; 218:59-72. [PMID: 22246100 PMCID: PMC3535403 DOI: 10.1007/s00429-011-0376-z] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/29/2011] [Indexed: 10/28/2022]
Abstract
Diverse stress stimuli induce long-lasting cognitive deficits, but the underlying molecular mechanisms are still incompletely understood. Here, we report three different stress models demonstrating that stress-inducible increases in microRNA-132 (miR-132) and consequent decreases in its acetylcholinesterase (AChE) target are causally involved. In a mild model of predator scent-induced anxiety, we demonstrate long-lasting hippocampal elevation of miR-132, accompanied by and associated with reduced AChE activity. Using lentiviral-mediated suppression of "synaptic" AChE-S mRNA, we quantified footshock stress-inducible changes in miR-132 and AChE and its corresponding cognitive damages. Stressed mice showed long-lasting impairments in the Morris water maze. In contrast, pre-stress injected AChE-suppressing lentivirus, but not a control virus, reduced hippocampal levels of both miR-132 and AChE and maintained similar cognitive performance to that of naïve, non-stressed mice. To dissociate between miR-132 and synaptic AChE-S as potential causes for stress-inducible cognitive deficits, we further used engineered TgR mice with enforced over-expression of the soluble "readthrough" AChE-R variant without the 3'-untranslated region binding site for miR-132. TgR mice displayed excess AChE-R in hippocampal neurons, enhanced c-fos labeling and correspondingly intensified reaction to the cholinergic agonist pilocarpine. They further showed excessive hippocampal expression of miR-132, accompanied by reduced host AChE-S mRNA and the GTPase activator p250GAP target of miR-132. At the behavioral level, TgR mice showed abnormal nocturnal locomotion patterns and serial maze mal-performance in spite of their reduced AChE-S levels. Our findings attribute stress-inducible cognitive impairments to cholinergic-mediated induction of miR-132 and consequently suppressed ACHE-S, opening venues for intercepting these miR-132-mediated damages.
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Blanco FJ, Bernabeu C. Alternative splicing factor or splicing factor-2 plays a key role in intron retention of the endoglin gene during endothelial senescence. Aging Cell 2011; 10:896-907. [PMID: 21668763 DOI: 10.1111/j.1474-9726.2011.00727.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing involving intron retention plays a key role in the regulation of gene expression. We previously reported that the alternatively spliced short isoform of endoglin (S-endoglin) is induced during the aging or senescence of endothelial cells by a mechanism of intron retention. In this work, we demonstrate that the alternative splicing factor or splicing factor-2 (ASF/SF2) is involved in the synthesis of endoglin. Overexpression of ASF/SF2 in endothelial cells switched the balance between the two endoglin isoforms, favoring the synthesis of S-endoglin. Using a minigene reporter vector and RNA immunoprecipitation experiments, it was shown that ASF/SF2 interacts with the nucleotide sequence of the endoglin minigene, suggesting the direct involvement of ASF/SF2. Accordingly, the sequence recognized by ASF/SF2 in the endoglin gene was identified inside the retained intron near the consensus branch point. Finally, the ASF/SF2 subcellular localization during endothelial senescence showed a preferential scattered distribution throughout the cytoplasm, where it interferes with the activity of the minor spliceosome, leading to an increased expression of S-endoglin mRNA. In summary, we report for the first time the molecular mechanisms by which ASF/SF2 regulates the alternative splicing of endoglin in senescent endothelial cells, as well as the involvement of ASF/SF2 in the minor spliceosome.
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MESH Headings
- Alternative Splicing
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Base Sequence
- Blotting, Western
- Cellular Senescence
- Conserved Sequence
- Cytoplasm/genetics
- Cytoplasm/metabolism
- Endoglin
- Genetic Vectors/genetics
- Genetic Vectors/metabolism
- HEK293 Cells
- Human Umbilical Vein Endothelial Cells
- Humans
- Immunoprecipitation/methods
- Introns
- Microscopy, Fluorescence
- Mutagenesis, Site-Directed
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA
- Serine-Arginine Splicing Factors
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Francisco J Blanco
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, and Centro de Investigación Biomédica en Red de Enfermedades Raras, c/Ramiro de Maeztu 9, Madrid, Spain.
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35
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Harries LW, Hernandez D, Henley W, Wood AR, Holly AC, Bradley-Smith RM, Yaghootkar H, Dutta A, Murray A, Frayling TM, Guralnik JM, Bandinelli S, Singleton A, Ferrucci L, Melzer D. Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing. Aging Cell 2011; 10:868-78. [PMID: 21668623 PMCID: PMC3173580 DOI: 10.1111/j.1474-9726.2011.00726.x] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aging is a major risk factor for chronic disease in the human population, but there are little human data on gene expression alterations that accompany the process. We examined human peripheral blood leukocyte in-vivo RNA in a large-scale transcriptomic microarray study (subjects aged 30-104 years). We tested associations between probe expression intensity and advancing age (adjusting for confounding factors), initially in a discovery set (n= 58), following-up findings in a replication set (n=240). We confirmed expression of key results by real-time PCR. Of 16,571 expressed probes, only 295 (2%) were robustly associated with age. Just six probes were required for a highly efficient model for distinguishing between young and old (area under the curve in replication set; 95%). The focused nature of age-related gene expression may therefore provide potential biomarkers of aging. Similarly, only 7 of 1065 biological or metabolic pathways were age-associated, in gene set enrichment analysis, notably including the processing of messenger RNAs (mRNAs); [P<0.002, false discovery rate (FDR) q<0.05]. This is supported by our observation of age-associated disruption to the balance of alternatively expressed isoforms for selected genes, suggesting that modification of mRNA processing may be a feature of human aging.
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Affiliation(s)
- Lorna W Harries
- Institute of Biomedical and Clinical Sciences, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK.
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36
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Dellago H, Löscher M, Ajuh P, Ryder U, Kaisermayer C, Grillari-Voglauer R, Fortschegger K, Gross S, Gstraunthaler A, Borth N, Eisenhaber F, Lamond AI, Grillari J. Exo70, a subunit of the exocyst complex, interacts with SNEV(hPrp19/hPso4) and is involved in pre-mRNA splicing. Biochem J 2011; 438:81-91. [PMID: 21639856 PMCID: PMC3708444 DOI: 10.1042/bj20110183] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Cdc5L (cell division cycle 5-like) complex is a spliceosomal subcomplex that also plays a role in DNA repair. The complex contains the splicing factor hPrp19, also known as SNEV or hPso4, which is involved in cellular life-span regulation and proteasomal breakdown. In a recent large-scale proteomics analysis for proteins associated with this complex, proteins involved in transcription, cell-cycle regulation, DNA repair, the ubiquitin-proteasome system, chromatin remodelling, cellular aging, the cytoskeleton and trafficking, including four members of the exocyst complex, were identified. In the present paper we report that Exo70 interacts directly with SNEV(hPrp19/hPso4) and shuttles to the nucleus, where it associates with the spliceosome. We mapped the interaction site to the N-terminal 100 amino acids of Exo70, which interfere with pre-mRNA splicing in vitro. Furthermore, Exo70 influences the splicing of a model substrate as well as of its own pre-mRNA in vivo. In addition, we found that Exo70 is alternatively spliced in a cell-type- and cell-age- dependent way. These results suggest a novel and unexpected role of Exo70 in nuclear mRNA splicing, where it might signal membrane events to the splicing apparatus.
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Affiliation(s)
- Hanna Dellago
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Marlies Löscher
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Paul Ajuh
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Ursula Ryder
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Christian Kaisermayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Klaus Fortschegger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stefan Gross
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Anna Gstraunthaler
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597
- School of Computater Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553
| | - Angus I. Lamond
- Department of Gene Expression and Regulation, University of Dundee, Dundee, Scotland, U.K
| | - Johannes Grillari
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Kohman RA, Rodriguez-Zas SL, Southey BR, Kelley KW, Dantzer R, Rhodes JS. Voluntary wheel running reverses age-induced changes in hippocampal gene expression. PLoS One 2011; 6:e22654. [PMID: 21857943 PMCID: PMC3152565 DOI: 10.1371/journal.pone.0022654] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 06/27/2011] [Indexed: 12/18/2022] Open
Abstract
Normal aging alters expression of numerous genes within the brain. Some of these transcription changes likely contribute to age-associated cognitive decline, reduced neural plasticity, and the higher incidence of neuropathology. Identifying factors that modulate brain aging is crucial for improving quality of life. One promising intervention to counteract negative effects of aging is aerobic exercise. Aged subjects that exercise show enhanced cognitive performance and increased hippocampal neurogenesis and synaptic plasticity. Currently, the mechanisms behind the anti-aging effects of exercise are not understood. The present study conducted a microarray on whole hippocampal samples from adult (3.5-month-old) and aged (18-month-old) male BALB/c mice that were individually housed with or without running wheels for 8 weeks. Results showed that aging altered genes related to chromatin remodeling, cell growth, immune activity, and synapse organization compared to adult mice. Exercise was found to modulate many of the genes altered by aging, but in the opposite direction. For example, wheel running increased expression of genes related to cell growth and attenuated expression of genes involved in immune function and chromatin remodeling. Collectively, findings show that even late-onset exercise may attenuate age-related changes in gene expression and identifies possible pathways through which exercise may exert its beneficial effects.
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Affiliation(s)
- Rachel A Kohman
- Department of Psychology, Beckman Institute, University of Illinois, Urbana, Illinois, United States of America.
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38
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Aberrant Single Exon Skipping is not Altered by Age in Exons of NF1, RABAC1, AATF or PCGF2 in Human Blood Cells and Fibroblasts. Genes (Basel) 2011; 2:562-77. [PMID: 24710210 PMCID: PMC3927615 DOI: 10.3390/genes2030562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 11/17/2022] Open
Abstract
In human pre-mRNA splicing, infrequent errors occur resulting in erroneous splice products as shown in a genome-wide approach. One characteristic subgroup consists of products lacking one cassette exon. The noise in the splicing process, represented by those misspliced products, can be increased by cold shock treatment or by inhibiting the nonsense mediated decay. Here, we investigated whether the splicing noise frequency increases with age in vivo in peripheral bloods cells or in vitro in cultured and aged fibroblasts from healthy donors. Splicing noise frequency was measured for four erroneously skipped NF1 exons and one exon of RABAC1, AATF and PCGF2 by RT-qPCR. Measurements were validated in cultured fibroblasts treated with cold shock or puromycin. Intragenic but not interpersonal differences were detected in splicing noise frequencies in vivo in peripheral blood cells of 11 healthy donors (15 y–85 y) and in in vitro senescent fibroblasts from three further donors. No correlation to the age of the donors was found in the splicing noise frequencies. Our data demonstrates that splicing error frequencies are not altered by age in peripheral blood cells or in vitro aged fibroblasts in the tested exons of the four investigated genes, indicating a high importance of correct splicing in these proliferating aged cells.
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van Tijn P, Kamphuis W, Marlatt MW, Hol EM, Lucassen PJ. Presenilin mouse and zebrafish models for dementia: focus on neurogenesis. Prog Neurobiol 2010; 93:149-64. [PMID: 21056616 DOI: 10.1016/j.pneurobio.2010.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/27/2010] [Accepted: 10/31/2010] [Indexed: 01/18/2023]
Abstract
Autosomal dominant mutations in the presenilin gene PSEN cause familial Alzheimer's disease (AD), a neurological disorder pathologically characterized by intraneuronal accumulation and extracellular deposition of amyloid-β in plaques and intraneuronal, hyperphosphorylated tau aggregation in neurofibrillary tangles. Presenilins (PS/PSENs) are part of the proteolytic γ-secretase complex, which cleaves substrate proteins within the membrane. Cleavage of the amyloid precursor protein (APP) by γ-secretase releases amyloid-β peptides. Besides its role in the processing of APP and other transmembrane proteins, presenilin plays an important role in neural progenitor cell maintenance and neurogenesis. In this review, we discuss the role of presenilin in relation to neurogenesis and neurodegeneration and review the currently available presenilin animal models. In addition to established mouse models, zebrafish are emerging as an attractive vertebrate model organism to study the role of presenilin during the development of the nervous system and in neurodegenerative disorders involving presenilin. Zebrafish is a suitable model organism for large-scale drug screening, making this a valuable model to identify novel therapeutic targets for AD.
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Affiliation(s)
- Paula van Tijn
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands.
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40
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Newman M, Verdile G, Martins RN, Lardelli M. Zebrafish as a tool in Alzheimer's disease research. Biochim Biophys Acta Mol Basis Dis 2010; 1812:346-52. [PMID: 20920580 DOI: 10.1016/j.bbadis.2010.09.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
Alzheimer's disease is the most prevalent form of neurodegenerative disease. Despite many years of intensive research our understanding of the molecular events leading to this pathology is far from complete. No effective treatments have been defined and questions surround the validity and utility of existing animal models. The zebrafish (and, in particular, its embryos) is a malleable and accessible model possessing a vertebrate neural structure and genome. Zebrafish genes orthologous to those mutated in human familial Alzheimer's disease have been defined. Work in zebrafish has permitted discovery of unique characteristics of these genes that would have been difficult to observe with other models. In this brief review we give an overview of Alzheimer's disease and transgenic animal models before examining the current contribution of zebrafish to this research area. This article is part of a Special Issue entitled Zebrafish Models of Neurological Diseases.
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Affiliation(s)
- Morgan Newman
- Discipline of Genetics, The University of Adelaide, SA 5005, Australia
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41
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Avila J, Wandosell F, Hernández F. Role of glycogen synthase kinase-3 in Alzheimer's disease pathogenesis and glycogen synthase kinase-3 inhibitors. Expert Rev Neurother 2010; 10:703-10. [PMID: 20420491 DOI: 10.1586/ern.10.40] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Glycogen synthase kinase (GSK)-3 has been proposed as the link between the two histopathological hallmarks of Alzheimer's disease, the extracellular senile plaques composed of beta-amyloid and the intracellular neurofibrillary tangles formed from hyperphosphorylated tau. Thus, GSK-3 is one of the main tau kinases and it modifies several sites of the tau protein present in neurofibrillary tangles. Furthermore, GSK-3 is able to modulate the generation of amyloid-beta, as well as to respond to this peptide. In several transgenic models, overexpression of GSK-3 has been associated with neuronal death, tau hyperphosphorylation and a decline in cognitive performance. Lithium, a widely used drug for affective disorders, inhibits GSK-3 at therapeutically relevant concentrations and it has been demonstrated that this is able to prevent tau phosphorylation. In the present review, we summarize all these data and discuss the potential of GSK-3 inhibitors for Alzheimer's disease therapy, as well as some of their potential problems.
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Affiliation(s)
- Jesús Avila
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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42
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Pre-mRNA processing is partially impaired in satellite cell nuclei from aged muscles. J Biomed Biotechnol 2010; 2010:410405. [PMID: 20490357 PMCID: PMC2872765 DOI: 10.1155/2010/410405] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 02/03/2010] [Indexed: 01/25/2023] Open
Abstract
Satellite cells are responsible for the capacity of mature mammalian skeletal muscles to repair and maintain mass. During aging, skeletal muscle mass as well as the muscle strength and endurance progressively decrease, leading to a condition termed sarcopenia. The causes of sarcopenia are manifold and remain to be completely elucidated. One of them could be the remarkable decline in the efficiency of muscle regeneration; this has been associated with decreasing amounts of satellite cells, but also to alterations in their activation, proliferation, and/or differentiation. In this study, we investigated the satellite cell nuclei of biceps and quadriceps muscles from adult and old rats; morphometry and immunocytochemistry at light and electron microscopy have been combined to assess the organization of the nuclear RNP structural constituents involved in different steps of mRNA formation. We demonstrated that in satellite cells the RNA pathways undergo alterations during aging, possibly hampering their responsiveness to muscle damage.
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43
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Malatesta M, Biggiogera M, Cisterna B, Balietti M, Bertoni-Freddari C, Fattoretti P. Perichromatin fibrils accumulation in hepatocyte nuclei reveals alterations of pre-mRNA processing during aging. DNA Cell Biol 2010; 29:49-57. [PMID: 20025533 DOI: 10.1089/dna.2009.0880] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We previously described an unusual accumulation of perichromatin fibrils (PF)-the in situ form of pre-mRNA transcription and early splicing-in hepatocyte nuclei of old rats. Here we have investigated, by immunoelectron microscopy, the nature of such PF, analyzing the presence of transcription, splicing and cleavage factors, polyadenylated RNA, and the incorporation of bromouridine in adult and old rats. Our observations revealed alterations in amount and/or distribution of pre-mRNA transcription, splicing and cleavage factors, as well as of polyadenylated RNA, together with lower bromouridine incorporation in newly transcribed RNA in the hepatocyte nucleoplasm of old rats. Therefore, our data indicate both a decrease in pre-mRNA transcription and a slow down of PF processing and transport during aging.
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Affiliation(s)
- Manuela Malatesta
- 1 Department of Morphological and Biomedical Sciences, Anatomy and Histology Section, University of Verona, Verona, Italy
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44
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Compromise in mRNA processing machinery in senescent human fibroblasts: implications for a novel potential role of Phospho-ATR (ser428). Biogerontology 2010; 11:421-36. [PMID: 20084458 DOI: 10.1007/s10522-010-9261-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 01/03/2010] [Indexed: 01/30/2023]
Abstract
Ataxia-Telangiectasia and Rad3 related kinase (ATR) is a major gatekeeper of genomic stability and has been the subject of exhaustive study in the context of cell cycle progression and senescence as a DNA damage-induced response. Conditional knockout of the kinase in adult mice results in accelerated aging phenomena, such as such hair graying, alopecia, kyphosis, osteoporosis, thymic involution, fibrosis, and other abnormalities. In addition to that, recent reports strongly implicate signaling mediated by this kinase in the regulation of alternative splicing of certain, mostly cancer-associated transcripts. Interest to the function of mRNA synthesis and processing is constantly increasing as severe degenerative diseases, such as cancer, cystic fibrosis and Hutchinson-Gilford progeria syndrome are at least partly attributed to these abnormalities. In light of the above, we investigate the RNA processing machinery in senescent fibroblasts as opposed to young, either exponentially proliferating or quiescent, further focusing on the distribution and localization of active, phosphorylated ATR at ser428. This study implicates the spatiotemporal presence of the phosphorylated kinase in the regulation of mRNA splicing and polyadenylation. This function appears perturbed in senescent cells, accompanied by a distinct pattern of phospho-ATR in the senescent nucleus.
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45
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MicroRNA-132 potentiates cholinergic anti-inflammatory signaling by targeting acetylcholinesterase. Immunity 2009; 31:965-73. [PMID: 20005135 DOI: 10.1016/j.immuni.2009.09.019] [Citation(s) in RCA: 324] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 06/18/2009] [Accepted: 09/24/2009] [Indexed: 01/12/2023]
Abstract
MicroRNAs (miRNAs) contribute to both neuronal and immune cell fate, but their involvement in intertissue communication remained unexplored. The brain, via vagal secretion of acetylcholine (ACh), suppresses peripheral inflammation by intercepting cytokine production; therefore, we predicted that microRNAs targeting acetylcholinesterase (AChE) can attenuate inflammation. Here, we report that inflammatory stimuli induced leukocyte overexpression of the AChE-targeting miR-132. Injected locked nucleic acid (LNA)-modified anti-miR-132 oligonucleotide depleted miR-132 amounts while elevating AChE in mouse circulation and tissues. In transfected cells, a mutated 3'UTR miR-132 binding site increased AChE mRNA expression, whereas cells infected with a lentivirus expressing pre-miR-132 showed suppressed AChE. Transgenic mice overexpressing 3'UTR null AChE showed excessive inflammatory mediators and impaired cholinergic anti-inflammatory regulation, in spite of substantial miR-132 upregulation in brain and bone marrow. Our findings identify the AChE mRNA-targeting miR-132 as a functional regulator of the brain-to-body resolution of inflammation, opening avenues for study and therapeutic manipulations of the neuro-immune dialog.
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46
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Aging defined by a chronologic–replicative protein network in Saccharomyces cerevisiae: An interactome analysis. Mech Ageing Dev 2009; 130:444-60. [DOI: 10.1016/j.mad.2009.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 04/20/2009] [Accepted: 04/30/2009] [Indexed: 11/18/2022]
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47
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Shaked I, Zimmerman G, Soreq H. Stress-induced Alternative Splicing Modulations in Brain and Periphery. Ann N Y Acad Sci 2008; 1148:269-81. [DOI: 10.1196/annals.1410.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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48
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Abstract
In the present review we discuss recent findings showing that, in addition to the canonical estrogen receptor-alpha (ERalpha), the level of various ERalpha splice variants is changed in the human brain in aging and Alzheimer's disease (AD) at both the mRNA and protein level and that they should be considered for the understanding of estrogen effects on the brain and estrogen therapy pitfalls. Indeed, the expression pattern of certain splice forms is brain area-specific. Thus, the major isoform found in the mamillary body (MB) appeared to be del.7 (deletion of exon 7), while in the hippocampus del.4 (exon 4 omitted) was expressed at the highest level. Furthermore, while transcripts missing exons 7 and 2 declined with aging in the MB of patients >60 years old, no age-related alterations were determined for a number of splice variants in the hippocampus. A novel MB1 isoform with a 168-bp deletion within the transactivation function 1 of ERalpha turned out to accumulate in the histaminergic tuberomamillary nucleus of postmenopausal women. Finally, the level of alternatively spliced ERalpha may also change in AD in a brain area-specific manner and so affect the sensitivity to estrogen therapy.
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Affiliation(s)
- Tatjana A Ishunina
- Department of Histology and Embryology, Kursk State Medical University, Kursk, Russia.
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49
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Disher K, Skandalis A. Evidence of the modulation of mRNA splicing fidelity in humans by oxidative stress and p53. Genome 2008; 50:946-53. [PMID: 18059557 DOI: 10.1139/g07-074] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The majority of human genes generate mRNA splice variants and while there is little doubt that alternative splicing is an important biological phenomenon, it has also become apparent that some splice variants are associated with disease. To elucidate the molecular mechanisms responsible for generating aberrant splice variants, we have investigated alternative splicing of the human genes HPRT and POLB following oxidative stress in different genetic backgrounds. Our study revealed that splicing fidelity is sensitive to oxidative stress. Following treatment of cells with H2O2, the overall frequency of aberrant, unproductive splice variants increased in both loci. At least in POLB, splicing fidelity is p53 dependent. In the absence of p53, the frequency of POLB splice variants is elevated but oxidative stress does not further increase the frequency of splice variants. Our data indicate that mis-splicing following oxidative stress represents a novel and significant genotoxic outcome and that it is not simply DNA lesions induced by oxidative stress that lead to mis-splicing but changes in the alternative splicing machinery itself.
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Affiliation(s)
- Kim Disher
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON L2S 3A1, Canada
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50
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Biggiogera M, Cisterna B, Spedito A, Vecchio L, Malatesta M. Perichromatin fibrils as early markers of transcriptional alterations. Differentiation 2008; 76:57-65. [PMID: 17697125 DOI: 10.1111/j.1432-0436.2007.00211.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Perichromatin fibrils represent the morphological expression of transcription and co-transcriptional processing of pre-mRNA. They can be considered, hence, an example of work in progress. High resolution techniques such as electron microscopy demonstrate that perichromatin fibrils play a role as early markers of transcriptional alterations. In this paper, we review some experimental and physiological conditions impairing or modulating transcription as well as their effects on perichromatin fibrils. In all the situations reported, perichromatin fibrils show modifications in their amount and/or their associated proteins. Their movements are also affected, as well as their export or their intra-nuclear storage forms. Perichromatin fibrils therefore represent highly sensitive markers not only for monitoring transcriptional and processing rate but also for identifying the maturation level of pre-mRNA/mRNA occurring in the cell nucleus and the functional correlation with the cellular metabolic state.
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Affiliation(s)
- Marco Biggiogera
- Dipartimento di Biologia Animale, Laboratorio di Biologia Cellulare e Neurobiologia, University of Pavia, and Istituto di Genetica Molecolare del C.N.R., Piazza botta 10, 27100 Pavia, Italy.
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