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Fonseca-Carvalho M, Veríssimo G, Lopes M, Ferreira D, Louzada S, Chaves R. Answering the Cell Stress Call: Satellite Non-Coding Transcription as a Response Mechanism. Biomolecules 2024; 14:124. [PMID: 38254724 PMCID: PMC10813801 DOI: 10.3390/biom14010124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Organisms are often subjected to conditions that promote cellular stress. Cell responses to stress include the activation of pathways to defend against and recover from the stress, or the initiation of programmed cell death to eliminate the damaged cells. One of the processes that can be triggered under stress is the transcription and variation in the number of copies of satellite DNA sequences (satDNA), which are involved in response mechanisms. Satellite DNAs are highly repetitive tandem sequences, mainly located in the centromeric and pericentromeric regions of eukaryotic chromosomes, where they form the constitutive heterochromatin. Satellite non-coding RNAs (satncRNAs) are important regulators of cell processes, and their deregulation has been associated with disease. Also, these transcripts have been associated with stress-response mechanisms in varied eukaryotic species. This review intends to explore the role of satncRNAs when cells are subjected to adverse conditions. Studying satDNA transcription under various stress conditions and deepening our understanding of where and how these sequences are involved could be a key factor in uncovering important facts about the functions of these sequences.
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Affiliation(s)
- Marisa Fonseca-Carvalho
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Gabriela Veríssimo
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Mariana Lopes
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniela Ferreira
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Sandra Louzada
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.F.-C.); (G.V.); (M.L.); (D.F.); (S.L.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
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Kim H, Gomez-Pastor R. HSF1 and Its Role in Huntington's Disease Pathology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1410:35-95. [PMID: 36396925 PMCID: PMC12001818 DOI: 10.1007/5584_2022_742] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PURPOSE OF REVIEW Heat shock factor 1 (HSF1) is the master transcriptional regulator of the heat shock response (HSR) in mammalian cells and is a critical element in maintaining protein homeostasis. HSF1 functions at the center of many physiological processes like embryogenesis, metabolism, immune response, aging, cancer, and neurodegeneration. However, the mechanisms that allow HSF1 to control these different biological and pathophysiological processes are not fully understood. This review focuses on Huntington's disease (HD), a neurodegenerative disease characterized by severe protein aggregation of the huntingtin (HTT) protein. The aggregation of HTT, in turn, leads to a halt in the function of HSF1. Understanding the pathways that regulate HSF1 in different contexts like HD may hold the key to understanding the pathomechanisms underlying other proteinopathies. We provide the most current information on HSF1 structure, function, and regulation, emphasizing HD, and discussing its potential as a biological target for therapy. DATA SOURCES We performed PubMed search to find established and recent reports in HSF1, heat shock proteins (Hsp), HD, Hsp inhibitors, HSF1 activators, and HSF1 in aging, inflammation, cancer, brain development, mitochondria, synaptic plasticity, polyglutamine (polyQ) diseases, and HD. STUDY SELECTIONS Research and review articles that described the mechanisms of action of HSF1 were selected based on terms used in PubMed search. RESULTS HSF1 plays a crucial role in the progression of HD and other protein-misfolding related neurodegenerative diseases. Different animal models of HD, as well as postmortem brains of patients with HD, reveal a connection between the levels of HSF1 and HSF1 dysfunction to mutant HTT (mHTT)-induced toxicity and protein aggregation, dysregulation of the ubiquitin-proteasome system (UPS), oxidative stress, mitochondrial dysfunction, and disruption of the structural and functional integrity of synaptic connections, which eventually leads to neuronal loss. These features are shared with other neurodegenerative diseases (NDs). Currently, several inhibitors against negative regulators of HSF1, as well as HSF1 activators, are developed and hold promise to prevent neurodegeneration in HD and other NDs. CONCLUSION Understanding the role of HSF1 during protein aggregation and neurodegeneration in HD may help to develop therapeutic strategies that could be effective across different NDs.
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Affiliation(s)
- Hyuck Kim
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Rocio Gomez-Pastor
- Department of Neuroscience, School of Medicine, University of Minnesota, Minneapolis, MN, USA.
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Combined Assay of rDNA and SatIII Copy Numbers as an Individual Profile of Stress Resistance, Longevity, Fertility and Disease Predisposition. J Pers Med 2022; 12:jpm12101752. [PMID: 36294891 PMCID: PMC9604575 DOI: 10.3390/jpm12101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/08/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
The ribosomal DNA and pericentromeric satellite repeats are two important types of moderately repeated sequences existing in the human genome. They are functionally involved in the universal stress response. There is accumulating evidence that the copy number variation (CNV) of the repeat units is a novel factor modulating the stress response and, thus, has phenotypic manifestations. The ribosomal repeat copy number plays a role in stress resistance, lifespan, in vitro fertilization chances, disease progression and aging, while the dynamics of the satellite copy number are a sort of indicator of the current stress state. Here, we review some facts showing that a combined assay of rDNA and SatII/III abundance can provide valuable individual data ("stress profile") indicating not only the inherited adaptive reserve but also the stress duration and acute or chronic character of the stress. Thus, the repeat count could have applications in personalized medicine in the future.
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A classical revival: Human satellite DNAs enter the genomics era. Semin Cell Dev Biol 2022; 128:2-14. [PMID: 35487859 DOI: 10.1016/j.semcdb.2022.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022]
Abstract
The classical human satellite DNAs, also referred to as human satellites 1, 2 and 3 (HSat1, HSat2, HSat3, or collectively HSat1-3), occur on most human chromosomes as large, pericentromeric tandem repeat arrays, which together constitute roughly 3% of the human genome (100 megabases, on average). Even though HSat1-3 were among the first human DNA sequences to be isolated and characterized at the dawn of molecular biology, they have remained almost entirely missing from the human genome reference assembly for 20 years, hindering studies of their sequence, regulation, and potential structural roles in the nucleus. Recently, the Telomere-to-Telomere Consortium produced the first truly complete assembly of a human genome, paving the way for new studies of HSat1-3 with modern genomic tools. This review provides an account of the history and current understanding of HSat1-3, with a view towards future studies of their evolution and roles in health and disease.
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Chatterjee M, Sengupta S. Human Satellite III long non-coding RNA imparts survival benefits to cancer cells. Cell Biol Int 2022; 46:611-627. [PMID: 35005799 DOI: 10.1002/cbin.11761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 11/06/2021] [Accepted: 12/26/2021] [Indexed: 11/07/2022]
Abstract
Long non-coding RNAs (lncRNAs) are heterogeneous group of transcripts that lack coding potential and have essential roles in gene regulations. Recent days have seen an increasing association of non-coding RNAs with human diseases, especially cancers. One interesting group of non-coding RNAs strongly linked to cancers are heterochromatic repetitive Satellite RNAs. Satellite RNAs are transcribed from pericentromeric heterochromatic region of the human chromosomes. Satellite II RNA, most extensively studied, is upregulated in wide variety of epithelial cancer. Similarly, alpha satellite is over expressed in BRCA1- deficient tumors. Though much is known about alpha satellites and SatII repeats, little is known about Satellite III (SatIII) lncRNAs in human cancers. SatIII repeats, though transcriptionally silent in normal conditions is actively transcribed under condition of stress, mainly heat shock. In the present study, we show that colon and breast cancer cells aberrantly transcribes SatIII, in a Heat shock factor I (HSF1)-independent manner. Our study also reveals that, overexpression of SatIII RNA favours cancer cell survival by overriding chemo drug-induced cell death. Interestingly, knockdown of SatIII sensitizes cells towards chemotherapeutic drugs. This sensitization is possibly mediated by restoration of p53 protein expression that facilitates cell death. Heat shock however helps SatIII to continue with its pro-cell survival function. Our results, therefore suggest SatIII to be an important regulator of human cancers. Induction of SatIII is not only a response to the oncogenic stress but also facilitates cancer progression by a distinct pathway that is different from heat stress pathway. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sonali Sengupta
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India
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Vertii A. Stress as a Chromatin Landscape Architect. Front Cell Dev Biol 2021; 9:790138. [PMID: 34970548 PMCID: PMC8712864 DOI: 10.3389/fcell.2021.790138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
The exponential development of methods investigating different levels of spatial genome organization leads to the appreciation of the chromatin landscape's contribution to gene regulation and cell fate. Multiple levels of 3D chromatin organization include chromatin loops and topologically associated domains, followed by euchromatin and heterochromatin compartments, chromatin domains associated with nuclear bodies, and culminate with the chromosome territories. 3D chromatin architecture is exposed to multiple factors such as cell division and stress, including but not limited to mechanical, inflammatory, and environmental challenges. How exactly the stress exposure shapes the chromatin landscape is a new and intriguing area of research. In this mini-review, the developments that motivate the exploration of this field are discussed.
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Affiliation(s)
- Anastassiia Vertii
- Department of Molecular, Cellular and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
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The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model. Genes (Basel) 2021; 12:genes12101524. [PMID: 34680920 PMCID: PMC8535310 DOI: 10.3390/genes12101524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 12/18/2022] Open
Abstract
The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.
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Leo L, Marchetti M, Giunta S, Fanti L. Epigenetics as an Evolutionary Tool for Centromere Flexibility. Genes (Basel) 2020; 11:genes11070809. [PMID: 32708654 PMCID: PMC7397245 DOI: 10.3390/genes11070809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022] Open
Abstract
Centromeres are the complex structures responsible for the proper segregation of chromosomes during cell division. Structural or functional alterations of the centromere cause aneuploidies and other chromosomal aberrations that can induce cell death with consequences on health and survival of the organism as a whole. Because of their essential function in the cell, centromeres have evolved high flexibility and mechanisms of tolerance to preserve their function following stress, whether it is originating from within or outside the cell. Here, we review the main epigenetic mechanisms of centromeres’ adaptability to preserve their functional stability, with particular reference to neocentromeres and holocentromeres. The centromere position can shift in response to altered chromosome structures, but how and why neocentromeres appear in a given chromosome region are still open questions. Models of neocentromere formation developed during the last few years will be hereby discussed. Moreover, we will discuss the evolutionary significance of diffuse centromeres (holocentromeres) in organisms such as nematodes. Despite the differences in DNA sequences, protein composition and centromere size, all of these diverse centromere structures promote efficient chromosome segregation, balancing genome stability and adaptability, and ensuring faithful genome inheritance at each cellular generation.
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Affiliation(s)
- Laura Leo
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Marcella Marchetti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
| | - Simona Giunta
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Laura Fanti
- Istituto Pasteur Italia, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy; (L.L.); (M.M.); (S.G.)
- Correspondence:
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Ferreira D, Escudeiro A, Adega F, Anjo SI, Manadas B, Chaves R. FA-SAT ncRNA interacts with PKM2 protein: depletion of this complex induces a switch from cell proliferation to apoptosis. Cell Mol Life Sci 2020; 77:1371-1386. [PMID: 31346634 PMCID: PMC11104958 DOI: 10.1007/s00018-019-03234-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 01/11/2023]
Abstract
FA-SAT is a highly conserved satellite DNA sequence transcribed in many Bilateria species. To disclose the cellular and functional profile of FA-SAT non-coding RNAs, a comprehensive experimental approach, including the transcripts location in the cell and in the cell cycle, the identification of its putative protein interactors, and silencing/ectopic expression phenotype analysis, was performed. FA-SAT non-coding RNAs play a nuclear function at the G1 phase of the cell cycle and the interactomic assay showed that the PKM2 protein is the main interactor. The disruption of the FA-SAT non-coding RNA/PKM2 protein complex, by the depletion of either FA-SAT or PKM2, results in the same phenotype-apoptosis, and the ectopic overexpression of FA-SAT did not affect the cell-cycle progression, but promotes the PKM2 nuclear accumulation. Overall, our data first describe the importance of this ribonucleoprotein complex in apoptosis and cell-cycle progression, what foresees a promising novel candidate molecular target for cancer therapy and diagnosis.
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Affiliation(s)
- Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Sandra I Anjo
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisbon, Portugal.
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Ershova ES, Agafonova ON, Zakharova NV, Bravve LV, Jestkova EM, Golimbet VE, Lezheiko TV, Morozova AY, Martynov AV, Veiko RV, Umriukhin PE, Kostyuk GP, Kutsev SI, Veiko NN, Kostyuk SV. Copy Number Variation of Satellite III (1q12) in Patients With Schizophrenia. Front Genet 2019; 10:1132. [PMID: 31850056 PMCID: PMC6902095 DOI: 10.3389/fgene.2019.01132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022] Open
Abstract
Introduction: It was shown that copy number variations (CNVs) of human satellite III (1q12) fragment (f-SatIII) reflects the human cells response to stress of different nature and intensity. Patients with schizophrenia (SZ) experience chronic stress. The major research question: What is the f-SatIII CNVs in human leukocyte as a function of SZ? Materials and Methods: Biotinylated pUC1.77 probe was used for f-SatIII quantitation in leukocyte DNA by the non-radioactive quantitative hybridization for SZ patients (N = 840) and healthy control (HC, N = 401). SZ-sample included four groups. Two groups: first-episode drug-naïve patients [SZ (M-)] and medicated patients [SZ (M+)]. The medical history of these patients did not contain reliable confirmed information about fetal hypoxia and obstetric complications (H/OCs). Two other groups: medicated patients with documented H/OCs [hypoxia group (H-SZ (M+)] and medicated patients with documented absence of H/OCs [non-hypoxia group (NH-SZ (M+)]. The content of f-SatIII was also determined in eight post-mortem brain tissues of one SZ patient. Results: f-SatIII in human leukocyte varies between 5.7 to 44 pg/ng DNA. f-SatIII CNVs in SZ patients depends on the patient’s history of H/OCs. f-SatIII CN in NH-SZ (M+)-group was significantly reduced compared to H-SZ (M+)-group and HC-group (p < 10-30). f-SatIII CN in SZ patients negatively correlated with the index reflecting the seriousness of the disease (Positive and Negative Syndrome Scale). Antipsychotic therapy increases f-SatIII CN in the untreated SZ patients with a low content of the repeat and reduces the f-SatIII CN in SZ patients with high content of the repeat. In general, the SZ (M+) and SZ (M-) groups do not differ in the content of f-SatIII, but significantly differ from the HC-group by lower values of the repeat content. f-SatIII CN in the eight regions of the brain of the SZ patient varies significantly. Conclusion: The content of f-SatIII repeat in leukocytes of the most patients with SZ is significantly reduced compared to the HC. Two hypotheses were put forward: (1) the low content of the repeat is a genetic feature of SZ; and/or (2) the genomes of the SZ patients respond to chronic oxidative stress reducing the repeats copies number.
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Affiliation(s)
- Elizaveta S Ershova
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Oksana N Agafonova
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia
| | - Natalia V Zakharova
- Moscow Healthcare Department, N. A. Alexeev Clinical Psychiatric Hospital №1, Moscow, Russia
| | - Lidia V Bravve
- Moscow Healthcare Department, N. A. Alexeev Clinical Psychiatric Hospital №1, Moscow, Russia
| | - Elizaveta M Jestkova
- Moscow Healthcare Department, P.B. Ganushkin Clinical Psychiatric Hospital №4, Moscow, Russia
| | - Vera E Golimbet
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Tatiana V Lezheiko
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Anna Y Morozova
- Department of Basic and Applied Neurobiology, V. Serbsky National Medical Research Center for Psychiatry and Narcology, Moscow, Russia
| | - Andrey V Martynov
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia
| | - Roman V Veiko
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia
| | - Pavel E Umriukhin
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia.,P.K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | - Georgiy P Kostyuk
- Moscow Healthcare Department, N. A. Alexeev Clinical Psychiatric Hospital №1, Moscow, Russia
| | - Sergey I Kutsev
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia
| | - Natalia N Veiko
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia
| | - Svetlana V Kostyuk
- Department of Molecular Biology, Research Centre for Medical Genetics, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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Ershova ES, Malinovskaya EM, Konkova MS, Veiko RV, Umriukhin PE, Martynov AV, Kutsev SI, Veiko NN, Kostyuk SV. Copy Number Variation of Human Satellite III (1q12) With Aging. Front Genet 2019; 10:704. [PMID: 31447880 PMCID: PMC6692473 DOI: 10.3389/fgene.2019.00704] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022] Open
Abstract
Introduction: Human satellite DNA is organized in long arrays in peri/centromeric heterochromatin. There is little information about satellite copy number variants (CNVs) in aging and replicative cell senescence (RS). Materials and Methods: Biotinylated pUC1.77 probe was used for the satellite III (f-SatIII) quantitation in leukocyte DNA by the non-radioactive quantitative hybridization for 557 subjects between 2 and 91 years old. The effect of RS and genotoxic stress (GS, 4 or 6 µM of K2CrO4) on the f-SatIII CNV was studied on the cultured human skin fibroblast (HSF) lines of five subjects. Results: f-SatIII in leukocyte and HSFs varies between 5.7 and 40 pg/ng of DNA. During RS, the f-SatIII content in HSFs increased. During GS, HSFs may increase or decrease f-SatIII content. Cells with low f-SatIII content have the greatest proliferative potential. F-SatIII CNVs in different individuals belonging to the different generations depend on year of their birth. Children (born in 2005-2015 years) differed significantly from the other age groups by low content and low coefficient of variation of f-SatIII. In the individuals born in 1912-1925 and living in unfavorable social conditions (FWW, the Revolution and the Russian Civil War, SWW), there is a significant disproportion in the content of f-SatIII. The coefficient of variation reaches the maximum values than in individuals born in the period from 1926 to 1975. In the group of people born in 1990-2000 (Chernobyl disaster, the collapse of the Soviet Union, and a sharp decline in the population living standard), again, there is a significant disproportion of individuals in the content of f-SatIII. A similar disproportion was observed in the analysis of a group of individuals born in 1926-1975 who in their youth worked for a long time in high-radioactive environment. Conclusion: In generations that were born and who lived in childhood in a period of severe social perturbations or in conditions of environmental pollution, we found a significant increase in leukocyte DNA f-SatIII variability. It is hypothesized that the change of the f-SatIII content in the blood cells reflects the body response to stress of different nature and intensity.
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Affiliation(s)
- Elizaveta S. Ershova
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | - Roman V. Veiko
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
| | - Pavel E. Umriukhin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
- P.K. Anokhin Institute of Normal Physiology, Moscow, Russia
| | | | | | | | - Svetlana V. Kostyuk
- Research Centre for Medical Genetics (RCMG), Moscow, Russia
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Chatterjee M, Dass J. FP, Sengupta S. Nuclear stress bodies: Interaction of its components in oncogenic regulation. J Cell Biochem 2019; 120:14700-14710. [DOI: 10.1002/jcb.28731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
| | - Febin Prabhu Dass J.
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
| | - Sonali Sengupta
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore India
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Podgornaya OI, Ostromyshenskii DI, Enukashvily NI. Who Needs This Junk, or Genomic Dark Matter. BIOCHEMISTRY (MOSCOW) 2018; 83:450-466. [PMID: 29626931 DOI: 10.1134/s0006297918040156] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC). TRs comprise ~70% of ChrmC occupying the first place. Non-LTR (-long terminal repeat) retroposons (mainly LINE, long interspersed nuclear element) are the next (~11%), and endogenous retroviruses (ERV; LTR-containing) are in the third position (~9%). HChr is not enriched with ERV in comparison with the whole genome, but there are differences in distribution of certain elements: while MaLR-like elements (ERV3) are dominant in the whole genome, intracisternal A-particles and corresponding LTR (ERV2) are prevalent in HChr. Most of LINE in ChrmC is represented by the 2-kb fragment at the end of the 2nd open reading frame and its flanking regions. Almost all tandem repeats classified as CEN or periCEN are contained in ChrmC. Our previous classification revealed 60 new mouse TR families with 29 of them being absent in ChrmC, which indicates their location on chromosome arms. TR transcription is necessary for maintenance of heterochromatic status of the HChr genome part. A burst of TR transcription is especially important in embryogenesis and other cases of radical changes in the cell program, including carcinogenesis. The recently discovered mechanism of epigenetic regulation with noncoding sequences transcripts, long noncoding RNA, and its role in embryogenesis and pluripotency maintenance is discussed.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
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15
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Abstract
The importance of noncoding genome has become more evident in recent years. Before genome sequencing, the most well studied portion of our genome was protein coding genes. Interestingly, this coding portion accounted only for 1.5% of the genome, the rest being the noncoding sequences. Noncoding RNAs (ncRNAs) are involved in normal cell physiology, stress, and disease states. A class of small ncRNAs and miRNAs has gained much importance because of its involvement in human diseases such as cancer. Involvement of long ncRNAs have also been acknowledged in other human diseases, especially in neurodegenerative diseases. Neurodegenerative diseases are characterized by the presence of abnormally folded proteins that are toxic to the cell. Several studies from model organisms suggest upregulation of pathways that clear this toxic protein may provide protection against neurodegeneration. In this review, I summarize the importance of ncRNAs in protein quality control system of cell that is implicated in this fatal group of neurodegenerative diseases.
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Affiliation(s)
- Sonali Sengupta
- Division of Biomolecules and Genetics, School of Biosciences and Technology, VIT University, Vellore 632 014, India.
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16
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Miga KH. The Promises and Challenges of Genomic Studies of Human Centromeres. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:285-304. [PMID: 28840242 DOI: 10.1007/978-3-319-58592-5_12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human centromeres are genomic regions that act as sites of kinetochore assembly to ensure proper chromosome segregation during mitosis and meiosis. Although the biological importance of centromeres in genome stability, and ultimately, cell viability are well understood, the complete sequence content and organization in these multi-megabase-sized regions remains unknown. The lack of a high-resolution reference assembly inhibits standard bioinformatics protocols, and as a result, sequence-based studies involving human centromeres lag far behind the advances made for the non-repetitive sequences in the human genome. In this chapter, I introduce what is known about the genomic organization in the highly repetitive regions spanning human centromeres, and discuss the challenges these sequences pose for assembly, alignment, and data interpretation. Overcoming these obstacles is expected to issue a new era for centromere genomics, which will offer new discoveries in basic cell biology and human biomedical research.
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Affiliation(s)
- Karen H Miga
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA.
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Goenka A, Sengupta S, Pandey R, Parihar R, Mohanta GC, Mukerji M, Ganesh S. Human satellite-III non-coding RNAs modulate heat-shock-induced transcriptional repression. J Cell Sci 2016; 129:3541-3552. [PMID: 27528402 DOI: 10.1242/jcs.189803] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/10/2016] [Indexed: 12/31/2022] Open
Abstract
The heat shock response is a conserved defense mechanism that protects cells from physiological stress, including thermal stress. Besides the activation of heat-shock-protein genes, the heat shock response is also known to bring about global suppression of transcription; however, the mechanism by which this occurs is poorly understood. One of the intriguing aspects of the heat shock response in human cells is the transcription of satellite-III (Sat3) long non-coding RNAs and their association with nuclear stress bodies (nSBs) of unknown function. Besides association with the Sat3 transcript, the nSBs are also known to recruit the transcription factors HSF1 and CREBBP, and several RNA-binding proteins, including the splicing factor SRSF1. We demonstrate here that the recruitment of CREBBP and SRSF1 to nSBs is Sat3-dependent, and that loss of Sat3 transcripts relieves the heat-shock-induced transcriptional repression of a few target genes. Conversely, forced expression of Sat3 transcripts results in the formation of nSBs and transcriptional repression even without a heat shock. Our results thus provide a novel insight into the regulatory role for the Sat3 transcripts in heat-shock-dependent transcriptional repression.
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Affiliation(s)
- Anshika Goenka
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sonali Sengupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit - TRISUTRA, CSIR - Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Rashmi Parihar
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Girish Chandra Mohanta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Mitali Mukerji
- CSIR Ayurgenomics Unit - TRISUTRA, CSIR - Institute of Genomics and Integrative Biology (IGIB), Mathura Road, New Delhi 110025, India
| | - Subramaniam Ganesh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
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18
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Altemose N, Miga KH, Maggioni M, Willard HF. Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Comput Biol 2014; 10:e1003628. [PMID: 24831296 PMCID: PMC4022460 DOI: 10.1371/journal.pcbi.1003628] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 03/26/2014] [Indexed: 01/24/2023] Open
Abstract
The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb) and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations. At least 5–10% of the human genome remains unassembled, unmapped, and poorly characterized. The reference assembly annotates these missing regions as multi-megabase heterochromatic gaps, found primarily near centromeres and on the short arms of the acrocentric chromosomes. This missing fraction of the genome consists predominantly of long arrays of near-identical tandem repeats called satellite DNA. Due to the repetitive nature of satellite DNA, sequence assembly algorithms cannot uniquely align overlapping sequence reads, and thus satellite-rich domains have been omitted from the reference assembly and from most genome-wide studies of variation and function. Existing methods for analyzing some satellite DNAs cannot be easily extended to a large portion of satellites whose repeat structures are complex and largely uncharacterized, such as Human Satellites 2 and 3 (HSat2,3). Here we characterize HSat2,3 using a novel approach that does not depend on having a well-defined repeat structure. By classifying genome-wide HSat2,3 sequences into subfamilies and localizing them to chromosomes, we have generated an initial HSat2,3 genomic reference, which serves as a critical foundation for future studies of variation and function in these regions. This approach should be generally applicable to other classes of satellite DNA, in both the human genome and other complex genomes.
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Affiliation(s)
- Nicolas Altemose
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Karen H. Miga
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Mauro Maggioni
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - Huntington F. Willard
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
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Enukashvily NI, Ponomartsev NV. Mammalian satellite DNA: a speaking dumb. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 90:31-65. [PMID: 23582201 DOI: 10.1016/b978-0-12-410523-2.00002-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The tandemly organized highly repetitive satellite DNA is the main DNA component of centromeric/pericentromeric constitutive heterochromatin. For almost a century, it was considered as "junk DNA," only a small portion of which is used for kinetochore formation. The current review summarizes recent data about satellite DNA transcription. The possible functions of the transcripts are discussed.
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20
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Lakhotia SC. Long non-coding RNAs coordinate cellular responses to stress. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:779-96. [PMID: 22976942 DOI: 10.1002/wrna.1135] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Following the initial discovery of the heat shock RNA omega (hsrω) gene of Drosophila melanogaster to be non-coding (nc) and also inducible by cell stress, other stress-inducible long non-coding RNAs (lncRNA) have been described in diverse organisms. In view of the rapid sequence divergence of lncRNAs, present knowledge of stress trasncriptome is limited and fragmented. Several known stress-related lncRNAs, associated with specific nuclear speckled domains or nucleolus, provide structural base for sequestering diverse RNA-processing/regulatory proteins. Others have roles in transcriptional or translational inhibition during stress or in signaling pathways; functions of several other lncRNAs are not yet known. Most stress-related lncRNAs act primarily by modulating activity of the proteins to which they bind or by sequestering specific sets of proteins away from the active pool. A common emerging theme is that a given lncRNA targets one or more protein/s with key role/s in the cascade of events triggered by the stress and therefore has a widespread integrative effect. Since proteins associate with RNA through short sequence motifs, the overall base sequence of functionally similar ncRNAs is often not conserved except for specific motifs. The rapid evolvability of ncRNA sequences provides elegant modules for adaptability to changing environment as binding of one or the other protein to ncRNA can alter its structure and functions in distinct ways. Thus the stress-related lncRNAs act as hubs in the cellular networks to coordinate activities of the members within and between different networks to maintain cellular homeostasis for survival or to trigger cell death.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.
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21
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Miyagawa R, Mizuno R, Watanabe K, Ijiri K. Formation of tRNA granules in the nucleus of heat-induced human cells. Biochem Biophys Res Commun 2012; 418:149-55. [PMID: 22244871 DOI: 10.1016/j.bbrc.2011.12.150] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 12/30/2011] [Indexed: 10/14/2022]
Abstract
The stress response, which can trigger various physiological phenomena, is important for living organisms. For instance, a number of stress-induced granules such as P-body and stress granule have been identified. These granules are formed in the cytoplasm under stress conditions and are associated with translational inhibition and mRNA decay. In the nucleus, there is a focus named nuclear stress body (nSB) that distinguishes these structures from cytoplasmic stress granules. Many splicing factors and long non-coding RNA species localize in nSBs as a result of stress. Indeed, tRNAs respond to several kinds of stress such as heat, oxidation or starvation. Although nuclear accumulation of tRNAs occurs in starved Saccharomyces cerevisiae, this phenomenon is not found in mammalian cells. We observed that initiator tRNA(Met) (Meti) is actively translocated into the nucleus of human cells under heat stress. During this study, we identified unique granules of Meti that overlapped with nSBs. Similarly, elongator tRNA(Met) was translocated into the nucleus and formed granules during heat stress. Formation of tRNA granules is closely related to the translocation ratio. Then, all tRNAs may form the specific granules.
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Affiliation(s)
- Ryu Miyagawa
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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22
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Sengupta S, Badhwar I, Upadhyay M, Singh S, Ganesh S. Malin and laforin are essential components of a protein complex that protects cells from thermal stress. J Cell Sci 2011; 124:2277-86. [PMID: 21652633 DOI: 10.1242/jcs.082800] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heat-shock response is a conserved cellular process characterized by the induction of a unique group of proteins known as heat-shock proteins. One of the primary triggers for this response, at least in mammals, is heat-shock factor 1 (HSF1)--a transcription factor that activates the transcription of heat-shock genes and confers protection against stress-induced cell death. In the present study, we investigated the role of the phosphatase laforin and the ubiquitin ligase malin in the HSF1-mediated heat-shock response. Laforin and malin are defective in Lafora disease (LD), a neurodegenerative disorder associated with epileptic seizures. Using cellular models, we demonstrate that these two proteins, as a functional complex with the co-chaperone CHIP, translocate to the nucleus upon heat shock and that all the three members of this complex are required for full protection against heat-shock-induced cell death. We show further that laforin and malin interact with HSF1 and contribute to its activation during stress by an unknown mechanism. HSF1 is also required for the heat-induced nuclear translocation of laforin and malin. This study demonstrates that laforin and malin are key regulators of HSF1 and that defects in the HSF1-mediated stress response pathway might underlie some of the pathological symptoms in LD.
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Affiliation(s)
- Sonali Sengupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
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23
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Vourc'h C, Biamonti G. Transcription of Satellite DNAs in Mammals. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:95-118. [PMID: 21287135 DOI: 10.1007/978-3-642-16502-3_5] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Centromeric and pericentric regions have long been regarded as transcriptionally inert portions of chromosomes. A number of studies in the past 10 years disproved this dogma and provided convincing evidence that centromeric and pericentric sequences are transcriptionally active in several biological contexts.In this chapter, we provide a comprehensive picture of the various contexts (cell growth and differentiation, stress, effect of chromatin organization) in which these sequences are expressed in mouse and human cells and discuss the possible functional implications of centromeric and pericentric sequences activation and/or of the resulting noncoding RNAs. Moreover, we provide an overview of the molecular mechanisms underlying the activation of centromeric and pericentromeric sequences as well as the structural features of encoded RNAs.
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Affiliation(s)
- Claire Vourc'h
- INSERM U823; Institut Albert Bonniot, Université Joseph Fourier-Grenoble, La Tronche BP170, 38042, Grenoble cedex 9, France,
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24
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Abstract
Nuclear stress bodies (nSBs) are unique subnuclear organelles which form in response to heat shock. They are initiated through a direct interaction between heat shock transcription factor 1 (HSF1) and pericentric tandem repeats of satellite III sequences and correspond to active transcription sites for noncoding satellite III transcripts. Given their unusual features, nSBs are distinct from other known transcription sites. In stressed cells, they are thought to participate in rapid, transient, and global reprogramming of gene expression through different types of mechanisms including chromatin remodeling and trapping of transcription and splicing factors. The analysis of these atypical and intriguing structures uncovers new facets of the relationship between nuclear organization and nuclear function.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, Pavia, Italy.
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St Laurent G, Savva YA, Reenan R. Enhancing non-coding RNA information content with ADAR editing. Neurosci Lett 2009; 466:89-98. [PMID: 19751800 DOI: 10.1016/j.neulet.2009.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/02/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
Abstract
The depth and complexity of the non-coding transcriptome in nervous system tissues provides a rich substrate for adenosine de-amination acting on RNA (ADAR). Non-coding RNAs (ncRNAs) serve diverse regulatory and computational functions, coupling signal flow from the environment to evolutionarily coded analog and digital information elements within the transcriptome. We present a perspective of ADARs interaction with the non-coding transcriptome as a computational matrix, enhancing the information processing power of the cell, adding flexibility, rapid response, and fine tuning to critical pathways. Dramatic increases in ADAR activity during stress response and inflammation result in powerful information processing events that change the functional state of the cell. This review examines the pathways and mechanisms of ADAR interaction with the non-coding transcriptome, and their functional consequences for information processing in nervous system tissues.
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Affiliation(s)
- Georges St Laurent
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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