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Bettin N, Querido E, Gialdini I, Grupelli GP, Goretti E, Cantarelli M, Andolfato M, Soror E, Sontacchi A, Jurikova K, Chartrand P, Cusanelli E. TERRA transcripts localize at long telomeres to regulate telomerase access to chromosome ends. SCIENCE ADVANCES 2024; 10:eadk4387. [PMID: 38865460 PMCID: PMC11168465 DOI: 10.1126/sciadv.adk4387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/08/2024] [Indexed: 06/14/2024]
Abstract
The function of TERRA in the regulation of telomerase in human cells is still debated. While TERRA interacts with telomerase, how it regulates telomerase function remains unknown. Here, we show that TERRA colocalizes with the telomerase RNA subunit hTR in the nucleoplasm and at telomeres during different phases of the cell cycle. We report that TERRA transcripts relocate away from chromosome ends during telomere lengthening, leading to a reduced number of telomeric TERRA-hTR molecules and consequent increase in "TERRA-free" telomerase molecules at telomeres. Using live-cell imaging and super-resolution microscopy, we show that upon transcription, TERRA relocates from its telomere of origin to long chromosome ends. Furthermore, TERRA depletion by antisense oligonucleotides promoted hTR localization to telomeres, leading to increased residence time and extended half-life of hTR molecules at telomeres. Overall, our findings indicate that telomeric TERRA transcripts inhibit telomere elongation by telomerase acting in trans, impairing telomerase access to telomeres that are different from their chromosome end of origin.
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Affiliation(s)
- Nicole Bettin
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Emmanuelle Querido
- Department of Biochemistry and Molecular Medicine, University of Montreal, 2900 boul. Edouard Montpetit, H3T1J4 Montreal, Canada
| | - Irene Gialdini
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Glenda Paola Grupelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Elena Goretti
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Marta Cantarelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Marta Andolfato
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Eslam Soror
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Alessandra Sontacchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, University of Montreal, 2900 boul. Edouard Montpetit, H3T1J4 Montreal, Canada
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
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2
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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3
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Catto LFB, Zanelatto LC, Donaires FS, de Carvalho VS, Santana BA, Pinto AL, Fantacini D, de Souza LEB, Fonseca NP, Telho BS, Ayrosa Madeira MI, Barbosa Pagnano KB, Firmato AB, Fagundes EM, Higashi M, Nunes EC, Traina F, Lobo de F. Pontes L, Rego EM, Calado RT. Telomeric repeat-containing RNA is dysregulated in acute myeloid leukemia. Blood Adv 2023; 7:7067-7078. [PMID: 37773887 PMCID: PMC10694524 DOI: 10.1182/bloodadvances.2023010658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
TERRA (telomeric repeat-containing RNA) is a class of long noncoding RNAs transcribed from subtelomeric and telomeric regions. TERRA binds to the subtelomeric and telomeric DNA-forming R-loops (DNA-RNA hybrids), which are involved in telomere maintenance and telomerase function, but the role of TERRA in human cells is not well characterized. Here, we comprehensively investigated for the first time TERRA expression in primary human hematopoietic cells from an exploratory cohort of patients with acute myeloid leukemia (AML), patients with acute lymphoblastic leukemia (ALL), patients with telomere biology disorder (TBD), and healthy subjects. TERRA expression was repressed in primary human hematopoietic cells, including healthy donors, patients with ALL, and patients with TBD, irrespective of their telomere length, except for AML. A second cohort comprising 88 patients with AML showed that TERRA was overexpressed in an AML subgroup also characterized by higher R-loop formation, low TERT and RNAseH2 expression, and a paucity of somatic splicing factor mutations. Telomere length did not correlate with TERRA expression levels. To assess the role of TERRA R-loops in AML, we induced R-loop depletion by increasing RNAseH1 expression in 2 AML cell lines. Decreased TERRA R-loops in AML cell lines resulted in increased chemosensitivity to cytarabine. Our findings indicate that TERRA is uniformly repressed in primary human hematopoietic cells but abnormally expressed in an AML subset with low telomerase.
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Affiliation(s)
- Luiz Fernando B. Catto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Leonardo C. Zanelatto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Flavia S. Donaires
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Vinicius S. de Carvalho
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Bárbara A. Santana
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - André L. Pinto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Daianne Fantacini
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Lucas Eduardo B. de Souza
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Natasha P. Fonseca
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Bruno S. Telho
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Maria Isabel Ayrosa Madeira
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | | | | | | | - Fabiola Traina
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Lorena Lobo de F. Pontes
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Eduardo M. Rego
- Department of Internal Medicine, University of São Paulo Medical School, São Paulo, Brazil
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Regional Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [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: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
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Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
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5
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Rivosecchi J, Cusanelli E. TERRA beyond cancer: the biology of telomeric repeat-containing RNAs in somatic and germ cells. FRONTIERS IN AGING 2023; 4:1224225. [PMID: 37636218 PMCID: PMC10448526 DOI: 10.3389/fragi.2023.1224225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023]
Abstract
The telomeric noncoding RNA TERRA is a key component of telomeres and it is widely expressed in normal as well as cancer cells. In the last 15 years, several publications have shed light on the role of TERRA in telomere homeostasis and cell survival in cancer cells. However, only few studies have investigated the regulation or the functions of TERRA in normal tissues. A better understanding of the biology of TERRA in non-cancer cells may provide unexpected insights into how these lncRNAs are transcribed and operate in cells, and their potential role in physiological processes, such as aging, age-related pathologies, inflammatory processes and human genetic diseases. In this review we aim to discuss the findings that have advanced our understanding of the biology of TERRA using non-cancer mammalian cells as a model system.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, Trento, Italy
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6
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Gong Y, Liu Y. R-Loops at Chromosome Ends: From Formation, Regulation, and Cellular Consequence. Cancers (Basel) 2023; 15:cancers15072178. [PMID: 37046839 PMCID: PMC10093737 DOI: 10.3390/cancers15072178] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair.
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Affiliation(s)
- Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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7
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Poondi Krishnan V, Morone B, Toubiana S, Krzak M, Fioriniello S, Della Ragione F, Strazzullo M, Angelini C, Selig S, Matarazzo MR. The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory. Genome Res 2023; 33:169-183. [PMID: 36828588 PMCID: PMC10069469 DOI: 10.1101/gr.276986.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/12/2023] [Indexed: 02/26/2023]
Abstract
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to immunodeficiency, centromeric instability, facial anomalies syndrome, type 1 (ICF1). Although several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-derived induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9-corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome. Hypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1 patient peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are premarked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions reacquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increases in H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persists, and hypomethylation remains uncorrected. Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
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Affiliation(s)
- Varsha Poondi Krishnan
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Barbara Morone
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Shir Toubiana
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Monika Krzak
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy.,IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli, Isernia 86077, Italy
| | - Maria Strazzullo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy;
| | - Claudia Angelini
- Institute for Applied Computing (IAC) "Mauro Picone", CNR, Naples 80131 Italy;
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel; .,Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics Adriano Buzzati Traverso, (IGB-ABT) CNR, Naples 80131, Italy
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8
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Allison T, Langerman J, Sabri S, Otero-Garcia M, Lund A, Huang J, Wei X, Samarasinghe RA, Polioudakis D, Mody I, Cobos I, Novitch BG, Geschwind DH, Plath K, Lowry WE. Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysis. Stem Cell Reports 2021; 16:2548-2564. [PMID: 34506726 PMCID: PMC8514853 DOI: 10.1016/j.stemcr.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/19/2023] Open
Abstract
The specification of inhibitory neurons has been described for the mouse and human brain, and many studies have shown that pluripotent stem cells (PSCs) can be used to create interneurons in vitro. It is unclear whether in vitro methods to produce human interneurons generate all the subtypes found in brain, and how similar in vitro and in vivo interneurons are. We applied single-nuclei and single-cell transcriptomics to model interneuron development from human cortex and interneurons derived from PSCs. We provide a direct comparison of various in vitro interneuron derivation methods to determine the homogeneity achieved. We find that PSC-derived interneurons capture stages of development prior to mid-gestation, and represent a minority of potential subtypes found in brain. Comparison with those found in fetal or adult brain highlighted decreased expression of synapse-related genes. These analyses highlight the potential to tailor the method of generation to drive formation of particular subtypes.
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Affiliation(s)
- Thomas Allison
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Justin Langerman
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Shan Sabri
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Bioinformatics PhD Program, UCLA, Los Angeles, CA, USA
| | - Marcos Otero-Garcia
- Center for Autism Research and Treatment, Semel Institute, UCLA, Los Angeles, CA, USA
| | - Andrew Lund
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, CA, USA
| | - John Huang
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xiaofei Wei
- Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA
| | - Ranmal A. Samarasinghe
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Department of Neurobiology, UCLA, Los Angeles, CA, USA,Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Damon Polioudakis
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Istvan Mody
- Department of Neurology, David Geffen School of Medicine UCLA, Los Angeles, CA, USA
| | - Inma Cobos
- Department of Pathology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Bennett G. Novitch
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Department of Neurobiology, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Daniel H. Geschwind
- Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Center for Autism Research and Treatment, Semel Institute, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA
| | - Kathrin Plath
- Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Molecular Biology Institute, UCLA, Los Angeles, CA, USA,Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Bioinformatics PhD Program, UCLA, Los Angeles, CA, USA,Corresponding author
| | - William E. Lowry
- Department of Molecular Cell and Developmental Biology, UCLA, Los Angeles, CA, USA,Broad Stem Cell Center for Regenerative Medicine, UCLA, Los Angeles, CA, USA,Molecular Biology Institute, UCLA, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA,Intellectual and Developmental Disabilities Research Center, UCLA, Los Angeles, CA, USA,Corresponding author
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9
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Toubiana S, Larom G, Smoom R, Duszynski RJ, Godley LA, Francastel C, Velasco G, Selig S. Regulation of telomeric function by DNA methylation differs between humans and mice. Hum Mol Genet 2020; 29:3197-3210. [PMID: 32916696 DOI: 10.1093/hmg/ddaa206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 11/13/2022] Open
Abstract
The most distal 2 kb region in the majority of human subtelomeres contains CpG-rich promoters for TERRA, a long non-coding RNA. When the function of the de novo DNA methyltransferase DNMT3B is disrupted, as in ICF1 syndrome, subtelomeres are abnormally hypomethylated, subtelomeric heterochromatin acquires open chromatin characteristics, TERRA is highly expressed, and telomeres shorten rapidly. In this study, we explored whether the regulation of subtelomeric epigenetic characteristics by DNMT3B is conserved between humans and mice. Studying the DNA sequence of the distal 30 kb of the majority of murine q-arm subtelomeres indicated that these regions are relatively CpG-poor and do not contain TERRA promoters similar to those present in humans. Despite the lack of human-like TERRA promoters, we clearly detected TERRA expression originating from at least seven q-arm subtelomeres, and at higher levels in mouse pluripotent stem cells in comparison with mouse embryonic fibroblasts (MEFs). However, these differences in TERRA expression could not be explained by differential methylation of CpG islands present in the TERRA-expressing murine subtelomeres. To determine whether Dnmt3b regulates the expression of TERRA in mice, we characterized subtelomeric methylation and associated telomeric functions in cells derived from ICF1 model mice. Littermate-derived WT and ICF1 MEFs demonstrated no significant differences in subtelomeric DNA methylation, chromatin modifications, TERRA expression levels, telomere sister chromatid exchange or telomere length. We conclude that the epigenetic characteristics of murine subtelomeres differ substantially from their human counterparts and that TERRA transcription in mice is regulated by factors others than Dnmt3b.
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Affiliation(s)
- Shir Toubiana
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Gal Larom
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
| | - Riham Smoom
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Robert J Duszynski
- Department of Medicine, Section of Hematology Oncology, The University of Chicago, Chicago 60637, USA
| | - Lucy A Godley
- Department of Medicine, Section of Hematology Oncology, The University of Chicago, Chicago 60637, USA
| | - Claire Francastel
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris 75013, France
| | - Guillaume Velasco
- Université de Paris, Epigénétique et Destin Cellulaire, CNRS, Paris 75013, France
| | - Sara Selig
- Department of Genetics, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
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10
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Ziv A, Werner L, Konnikova L, Awad A, Jeske T, Hastreiter M, Mitsialis V, Stauber T, Wall S, Kotlarz D, Klein C, Snapper SB, Tzfati Y, Weiss B, Somech R, Shouval DS. An RTEL1 Mutation Links to Infantile-Onset Ulcerative Colitis and Severe Immunodeficiency. J Clin Immunol 2020; 40:1010-1019. [PMID: 32710398 DOI: 10.1007/s10875-020-00829-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
PURPOSE More than 50 different monogenic disorders causing inflammatory bowel disease (IBD) have been identified. Our goal was to characterize the clinical phenotype, genetic workup, and immunologic alterations in an Ashkenazi Jewish patient that presented during infancy with ulcerative colitis and unique clinical manifestations. METHODS Immune workup and whole-exome sequencing were performed, along with Sanger sequencing for confirmation. Next-generation sequencing of the TCRB and IgH was conducted for immune repertoire analysis. Telomere length was evaluated by in-gel hybridization assay. Mass cytometry was performed on patient's peripheral blood mononuclear cells, and compared with control subjects and patients with UC. RESULTS The patient presented in infancy with failure to thrive and dysmorphic features, consistent with a diagnosis of dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. Severe ulcerative colitis manifested in the first year of life and proceeded to the development of a primary immunodeficiency, presenting as Pneumocystis jiroveci pneumonia and hypogammaglobulinemia. Genetic studies identified a deleterious homozygous C.3791G>A missense mutation in the helicase regulator of telomere elongation 1 (RTEL1), leading to short telomeres in the index patient. Immune repertoire studies showed polyclonal T and B cell receptor distribution, while mass cytometry analysis demonstrated marked immunological alterations, including a predominance of naïve T cells, paucity of B cells, and a decrease in various innate immune subsets. CONCLUSIONS RTEL1 mutations are associated with significant alterations in immune landscape and can manifest with infantile-onset IBD. A high index of suspicion is required in Ashkenazi Jewish families where the carriage rate of the C.3791G>A variant is high.
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Affiliation(s)
- Alma Ziv
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aya Awad
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tim Jeske
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Hastreiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tali Stauber
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Sarah Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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11
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Awad A, Glousker G, Lamm N, Tawil S, Hourvitz N, Smoom R, Revy P, Tzfati Y. Full length RTEL1 is required for the elongation of the single-stranded telomeric overhang by telomerase. Nucleic Acids Res 2020; 48:7239-7251. [PMID: 32542379 PMCID: PMC7367169 DOI: 10.1093/nar/gkaa503] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Telomeres cap the ends of eukaryotic chromosomes and distinguish them from broken DNA ends to suppress DNA damage response, cell cycle arrest and genomic instability. Telomeres are elongated by telomerase to compensate for incomplete replication and nuclease degradation and to extend the proliferation potential of germ and stem cells and most cancers. However, telomeres in somatic cells gradually shorten with age, ultimately leading to cellular senescence. Hoyeraal-Hreidarsson syndrome (HHS) is characterized by accelerated telomere shortening and diverse symptoms including bone marrow failure, immunodeficiency, and neurodevelopmental defects. HHS is caused by germline mutations in telomerase subunits, factors essential for its biogenesis and recruitment to telomeres, and in the helicase RTEL1. While diverse phenotypes were associated with RTEL1 deficiency, the telomeric role of RTEL1 affected in HHS is yet unknown. Inducible ectopic expression of wild-type RTEL1 in patient fibroblasts rescued the cells, enabled telomerase-dependent telomere elongation and suppressed the abnormal cellular phenotypes, while silencing its expression resulted in gradual telomere shortening. Our observations reveal an essential role of the RTEL1 C-terminus in facilitating telomerase action at the telomeric 3' overhang. Thus, the common etiology for HHS is the compromised telomerase action, resulting in telomere shortening and reduced lifespan of telomerase positive cells.
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Affiliation(s)
- Aya Awad
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Galina Glousker
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Noa Lamm
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Shadi Tawil
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Noa Hourvitz
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Riham Smoom
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer and Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
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12
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Human subtelomeric DNA methylation: regulation and roles in telomere function. Curr Opin Genet Dev 2020; 60:9-16. [PMID: 32109830 DOI: 10.1016/j.gde.2020.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/21/2020] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Subtelomeres are the regions at chromosome ends, immediately adjacent to the terminal telomeric repeats. The majority of human subtelomeres are CpG-rich in their distal two kilobases, and are methylated during early embryonic development by the de novo DNA methyltransferase DNMT3B. The biological relevance of subtelomeric DNA methylation is highlighted by the presence of promoters for the long non-coding TERRA transcripts in these CpG-rich regions. Indeed, deviant subtelomeric methylation has been linked with abnormal telomeric phenotypes, as most strikingly found in ICF syndrome. Here we review recent studies that explore new aspects of subtelomeric methylation regulation and demonstrate the significance of maintaining proper DNA methylation at the extreme distal human subtelomeric regions.
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13
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Lalonde M, Chartrand P. TERRA, a Multifaceted Regulator of Telomerase Activity at Telomeres. J Mol Biol 2020; 432:4232-4243. [PMID: 32084415 DOI: 10.1016/j.jmb.2020.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023]
Abstract
In eukaryotes, telomeres are repetitive sequences at the end of chromosomes, which are maintained in a constitutive heterochromatin state. It is now known that telomeres can be actively transcribed, leading to the production of a telomeric repeat-containing noncoding RNA called TERRA. Due to its sequence complementarity to the telomerase template, it was suggested early on that TERRA could be an inhibitor of telomerase. Since then, TERRA has been shown to be involved in heterochromatin formation at telomeres, to invade telomeric dsDNA and form R-loops, and even to promote telomerase recruitment at short telomeres. All these functions depend on the diverse capacities of this lncRNA to bind various cofactors, act as a scaffold, and promote higher-order complexes in cells. In this review, it will be highlighted as to how these properties of TERRA work together to regulate telomerase activity at telomeres.
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Affiliation(s)
- Maxime Lalonde
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Quebec, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Quebec, Canada.
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14
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Vukic M, Daxinger L. DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome. Essays Biochem 2019; 63:773-783. [PMID: 31724723 PMCID: PMC6923317 DOI: 10.1042/ebc20190035] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation is an epigenetic modification essential for normal mammalian development. Initially associated with gene silencing, more diverse roles for DNA methylation in the regulation of gene expression patterns are increasingly being recognized. Some of these insights come from studying the function of genes that are mutated in human diseases characterized by abnormal DNA methylation landscapes. The first disorder to be associated with congenital defects in DNA methylation was Immunodeficiency, Centromeric instability, Facial anomalies syndrome (ICF). The hallmark of this syndrome is hypomethylation of pericentromeric satellite repeats, with mutations in four genes: DNMT3B, ZBTB24, CDCA7 and HELLS, being linked to the disease. Here, we discuss recent progress in understanding the molecular interactions between these genes and consider current evidence for how aberrant DNA methylation may contribute to the abnormal phenotype present in ICF syndrome patients.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
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15
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Toubiana S, Gagliardi M, Papa M, Manco R, Tzukerman M, Matarazzo MR, Selig S. Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction. eLife 2019; 8:e47859. [PMID: 31738163 PMCID: PMC6897513 DOI: 10.7554/elife.47859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/17/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methyltransferase 3B (DNMT3B) is the major DNMT that methylates mammalian genomes during early development. Mutations in human DNMT3B disrupt genome-wide DNA methylation patterns and result in ICF syndrome type 1 (ICF1). To study whether normal DNA methylation patterns may be restored in ICF1 cells, we corrected DNMT3B mutations in induced pluripotent stem cells from ICF1 patients. Focusing on repetitive regions, we show that in contrast to pericentromeric repeats, which reacquire normal methylation, the majority of subtelomeres acquire only partial DNA methylation and, accordingly, the ICF1 telomeric phenotype persists. Subtelomeres resistant to de novo methylation were characterized by abnormally high H3K4 trimethylation (H3K4me3), and short-term reduction of H3K4me3 by pharmacological intervention partially restored subtelomeric DNA methylation. These findings demonstrate that the abnormal epigenetic landscape established in ICF1 cells restricts the recruitment of DNMT3B, and suggest that rescue of epigenetic diseases with genome-wide disruptions will demand further manipulation beyond mutation correction.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
| | | | | | - Roberta Manco
- Institute of Genetics and Biophysics, ABT CNRNaplesItaly
| | - Maty Tzukerman
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
| | | | - Sara Selig
- Molecular Medicine LaboratoryRappaport Faculty of Medicine, TechnionHaifaIsrael
- Rambam Health Care CampusHaifaIsrael
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16
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Dion C, Roche S, Laberthonnière C, Broucqsault N, Mariot V, Xue S, Gurzau AD, Nowak A, Gordon CT, Gaillard MC, El-Yazidi C, Thomas M, Schlupp-Robaglia A, Missirian C, Malan V, Ratbi L, Sefiani A, Wollnik B, Binetruy B, Salort Campana E, Attarian S, Bernard R, Nguyen K, Amiel J, Dumonceaux J, Murphy JM, Déjardin J, Blewitt ME, Reversade B, Robin JD, Magdinier F. SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite. Nucleic Acids Res 2019; 47:2822-2839. [PMID: 30698748 PMCID: PMC6451109 DOI: 10.1093/nar/gkz005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS). By investigating why germline SMCHD1 mutations lead to these two different diseases, we uncovered a role for this factor in de novo methylation at the pluripotent stage. SMCHD1 is required for the dynamic methylation of the D4Z4 macrosatellite upon reprogramming but seems dispensable for methylation maintenance. We find that FSHD and BAMS patient's cells carrying SMCHD1 mutations are both permissive for DUX4 expression, a transcription factor whose regulation has been proposed as the main trigger for FSHD. These findings open new questions as to what is the true aetiology for FSHD, the epigenetic events associated with the disease thus calling the current model into question and opening new perspectives for understanding repetitive DNA sequences regulation.
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Affiliation(s)
- Camille Dion
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | | | - Natacha Broucqsault
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Agnieszka Nowak
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Claire El-Yazidi
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Morgane Thomas
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Andrée Schlupp-Robaglia
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France.,Centre de ressources biologiques, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Chantal Missirian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Valérie Malan
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Liham Ratbi
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Campus Göttingen, 37073 Göttingen, Germany
| | - Bernard Binetruy
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Jérôme Déjardin
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore.,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.,Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
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17
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Hu H, Chen C, Shi S, Li B, Duan S. The gene mutations and subtelomeric DNA methylation in immunodeficiency, centromeric instability and facial anomalies syndrome. Autoimmunity 2019; 52:192-198. [PMID: 31476899 DOI: 10.1080/08916934.2019.1657846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disorder, which is characteristic of a severe impairment of immunity. In the genetic aspect, ICF is featured with mutations primarily located in the specific genes (DNMT3B for ICF1, ZBTB24 for ICF2, CDCA7 for ICF3, and HELLS for ICF4). The subtelomeric region is defined as 500 kb at the terminal of each autosomal arm. And subtelomeric DNA fragments can partially regulate key biological activities, including chromosome movement and localization in the nucleus. In this review, we updated and summarized gene mutations in ICF based on the previous review. In addition, we focused on the correlation between subtelomeric DNA methylation and ICF. The relationship between subtelomeric methylation and telomere length in ICF was also summarized.
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Affiliation(s)
- Haochang Hu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Chujia Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shanping Shi
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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18
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Cubiles MD, Barroso S, Vaquero-Sedas MI, Enguix A, Aguilera A, Vega-Palas MA. Epigenetic features of human telomeres. Nucleic Acids Res 2019; 46:2347-2355. [PMID: 29361030 PMCID: PMC5861411 DOI: 10.1093/nar/gky006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/09/2018] [Indexed: 01/02/2023] Open
Abstract
Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, different human cell lines might carry diverse epigenetic marks at telomeres. We have developed a reliable procedure to study the chromatin structure of human telomeres independently of subtelomeres and ITSs. This procedure is based on the statistical analysis of multiple ChIP-seq experiments. We have found that human telomeres are not enriched in the heterochromatic H3K9me3 mark in most of the common laboratory cell lines, including embryonic stem cells. Instead, they are labeled with H4K20me1 and H3K27ac, which might be established by p300. These results together with previously published data argue that subtelomeric heterochromatin might control human telomere functions. Interestingly, U2OS cells that exhibit alternative lengthening of telomeres have heterochromatic levels of H3K9me3 in their telomeres.
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Affiliation(s)
- María D Cubiles
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
| | - Alicia Enguix
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Avd. Américo Vespucio s/n, 41092 Seville, Spain
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Avd. Américo Vespucio n° 49, 41092 Seville, Spain
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19
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Targeting Cancer through the Epigenetic Features of Telomeric Regions. Trends Cell Biol 2019; 29:281-290. [PMID: 30660503 DOI: 10.1016/j.tcb.2018.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/16/2022]
Abstract
The integrity of the chromatin associated with telomeric regions, which include telomeres and subtelomeres, is essential for telomeres function and cell viability. Whereas human subtelomeres are heterochromatic, telomeres are labeled with euchromatic marks like H4K20me1 and H3K27ac in most commonly studied human cell lines. The epigenetic marks of human telomeric regions influence oncogenic processes. Indeed, different drugs that decrease their genome-wide levels are currently being used or tested in specific cancer therapies. These drugs can challenge cancer by altering the function of key cellular proteins. However, they should also compromise oncogenic processes by modifying the epigenetic landscape of telomeric regions. We believe that studies of telomeric chromatin structure and telomeres dysfunction should help to design epigenetic therapies for cancer treatment.
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20
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Toubiana S, Velasco G, Chityat A, Kaindl AM, Hershtig N, Tzur-Gilat A, Francastel C, Selig S. Subtelomeric methylation distinguishes between subtypes of Immunodeficiency, Centromeric instability and Facial anomalies syndrome. Hum Mol Genet 2018; 27:3568-3581. [PMID: 30010917 DOI: 10.1093/hmg/ddy265] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Human telomeres and adjacent subtelomeres are packaged as heterochromatin. Subtelomeric DNA undergoes methylation during development by DNA methyltransferase 3B (DNMT3B), including the CpG-rich promoters of the long non-coding RNA (TERRA) embedded in these regions. The factors that direct DNMT3B methylation to human subtelomeres and maintain this methylation throughout lifetime are yet unknown. The importance of subtelomeric methylation is manifested through the abnormal telomeric phenotype in Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome type 1 patients carrying mutations in DNMT3B. Patient cells demonstrate subtelomeric hypomethylation, accompanied by elevated TERRA transcription, accelerated telomere shortening and premature senescence of fibroblasts. ICF syndrome can arise due to mutations in at least three additional genes, ZBTB24 (ICF2), CDCA7 (ICF3) and HELLS (ICF4). While pericentromeric repeat hypomethylation is evident in all ICF syndrome subtypes, the status of subtelomeric DNA methylation had not been described for patients of subtypes 2-4. Here we explored the telomeric phenotype in cells derived from ICF2-4 patients with the aim to determine whether ZBTB24, CDCA7 and HELLS also play a role in establishing and/or maintaining human subtelomeric methylation. We found normal subtelomeric methylation in ICF2-4 and accordingly low TERRA levels and unperturbed telomere length. Moreover, depleting the ICF2-4-related proteins in normal fibroblasts did not influence subtelomeric methylation. Thus, these gene products are not involved in establishing or maintaining subtelomeric methylation. Our findings indicate that human subtelomeric heterochromatin has specialized methylation regulation and highlight the telomeric phenotype as a characteristic that distinguishes ICF1 from ICF2-4.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Guillaume Velasco
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Adi Chityat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Center for Chronically Sick Children, Institute of Cell Biology and Neurobiology, Augustenburger Platz 1, Berlin, Germany
| | | | - Aya Tzur-Gilat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS, Paris Cedex, France
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
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21
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Toubiana S, Selig S. DNA:RNA hybrids at telomeres - when it is better to be out of the (R) loop. FEBS J 2018; 285:2552-2566. [PMID: 29637701 DOI: 10.1111/febs.14464] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/11/2018] [Accepted: 04/03/2018] [Indexed: 01/31/2023]
Abstract
R-loops (RLs) are three-stranded nucleic acid structures that contain a DNA:RNA hybrid and a displaced DNA strand. Genomic regions with GC skew and a G-rich transcript are particularly prone to form RLs. RLs play important physiological roles in cells; however, when present at abnormally high levels, they may threaten genome stability. The perfect GC skew of telomeric repeats and the discovery of telomeric repeat-containing RNA (TERRA), a long noncoding transcript that consists of the G-rich telomeric sequence, make telomeric sequences the perfect candidates for generating RLs. Indeed, in the past 5 years, telomere R-loops (TRLs) have been demonstrated in Saccharomyces cerevisiae, Trypanosoma brucei, and human cells. The presence of TRLs in normal human cells that transcribe low levels of TERRA, suggests a physiological role for these nucleic structures in telomere maintenance. Abnormally enhanced TERRA transcription, as found in several human pathological conditions, leads to high TRL levels and various cellular outcomes, depending on the recombinogenic capabilities of the cells. Study of TRLs in various organisms highlights the necessity for tight regulation of these structures, which can switch from beneficial to detrimental under different conditions. Here, we review the current state of knowledge on TRLs, describe several means by which TRLs are regulated, and discuss how findings from yeast are relevant to human pathological scenarios in which TRLs are deregulated.
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Affiliation(s)
- Shir Toubiana
- Molecular Medicine Laboratory, Rappaport Faculty of Medicine, Rambam Health Care Campus, Technion, Haifa, Israel
| | - Sara Selig
- Molecular Medicine Laboratory, Rappaport Faculty of Medicine, Rambam Health Care Campus, Technion, Haifa, Israel
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22
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Wanat JJ, Logsdon GA, Driskill JH, Deng Z, Lieberman PM, Johnson FB. TERRA and the histone methyltransferase Dot1 cooperate to regulate senescence in budding yeast. PLoS One 2018; 13:e0195698. [PMID: 29649255 PMCID: PMC5896980 DOI: 10.1371/journal.pone.0195698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 01/27/2023] Open
Abstract
The events underlying senescence induced by critical telomere shortening are not fully understood. Here we provide evidence that TERRA, a non-coding RNA transcribed from subtelomeres, contributes to senescence in yeast lacking telomerase (tlc1Δ). Levels of TERRA expressed from multiple telomere ends appear elevated at senescence, and expression of an artificial RNA complementary to TERRA (anti-TERRA) binds TERRA in vivo and delays senescence. Anti-TERRA acts independently from several other mechanisms known to delay senescence, including those elicited by deletions of EXO1, TEL1, SAS2, and genes encoding RNase H enzymes. Further, it acts independently of the senescence delay provided by RAD52-dependent recombination. However, anti-TERRA delays senescence in a fashion epistatic to inactivation of the conserved histone methyltransferase Dot1. Dot1 associates with TERRA, and anti-TERRA disrupts this interaction in vitro and in vivo. Surprisingly, the anti-TERRA delay is independent of the C-terminal methyltransferase domain of Dot1 and instead requires only its N-terminus, which was previously found to facilitate release of telomeres from the nuclear periphery. Together, these data suggest that TERRA and Dot1 cooperate to drive senescence.
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Affiliation(s)
- Jennifer J. Wanat
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Washington College, Department of Biology, Chestertown, Maryland, United States of America
| | - Glennis A. Logsdon
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jordan H. Driskill
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Zhong Deng
- The Wistar Institute, Gene Expression and Regulation, Philadelphia, Pennsylvania, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Gene Expression and Regulation, Philadelphia, Pennsylvania, United States of America
| | - F. Brad Johnson
- University of Pennsylvania School of Medicine, Pathology and Laboratory Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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23
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Sagie S, Edni O, Weinberg J, Toubiana S, Kozlovski T, Frostig T, Katzin N, Bar-Am I, Selig S. Non-random length distribution of individual telomeres in immunodeficiency, centromeric instability and facial anomalies syndrome, type I. Hum Mol Genet 2017; 26:4244-4256. [PMID: 28973513 DOI: 10.1093/hmg/ddx313] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in the de novo DNA methyltransferase DNMT3B lead to Immunodeficiency, Centromeric Instability and Facial anomalies (ICF) syndrome, type I. This syndrome is characterized, among other hypomethylated genomic loci, by severe subtelomeric hypomethylation that is associated with abnormally short telomere length. While it was demonstrated that the mean telomere length is significantly shorter in ICF type I cells, it is unknown whether all telomeres are equally vulnerable to shortening. To study this question we determined by combined telomere-FISH and spectral karyotyping the relative length of each individual telomere in lymphoblastoid cell lines (LCLs) generated from multiple ICF syndrome patients and control individuals. Here we confirm the short telomere lengths, and demonstrate that telomere length variance in the ICF patient group is much larger than in the control group, suggesting that not all telomeres shorten in a uniform manner. We identified a subgroup of telomeres whose relatively short lengths can distinguish with a high degree of certainty between a control and an ICF metaphase, proposing that in ICF syndrome cells, certain individual telomeres are consistently at greater risk to shorten than others. The majority of these telomeres display high sequence identity at the distal 2 kb of their subtelomeres, suggesting that the attenuation in DNMT3B methylation capacity affects individual telomeres to different degrees based, at least in part, on the adjacent subtelomeric sequence composition.
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Omer Edni
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Joseph Weinberg
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Tal Kozlovski
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Tzviel Frostig
- Department of Statistics and Operations Research, The Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Nirit Katzin
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Irit Bar-Am
- Applied Spectral Imaging Ltd., Yokneam 2069200, Israel
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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24
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Regulated expression of the lncRNA TERRA and its impact on telomere biology. Mech Ageing Dev 2017; 167:16-23. [PMID: 28888705 DOI: 10.1016/j.mad.2017.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/21/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022]
Abstract
The telomere protects against genomic instability by minimizing the accelerated end resection of the genetic material, a phenomenon that results in severe chromosome instability that could favor the transformation of a cell by enabling the emergence of tumor-promoting mutations. Some mechanisms that avoid this fate, such as capping and loop formation, have been very well characterized; however, telomeric non-coding transcripts, such as long non-coding RNAs (lncRNAs), should also be considered in this context because they play roles in the organization of telomere dynamics, involving processes such as replication, degradation, extension, and heterochromatin stabilization. Although the mechanism through which the expression of telomeric transcripts regulates telomere dynamics is not yet clear, a non-coding RNA component opens the research options in telomere biology and the impact that it can have on telomere-associated diseases such as cancer.
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25
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Sagie S, Toubiana S, Hartono SR, Katzir H, Tzur-Gilat A, Havazelet S, Francastel C, Velasco G, Chédin F, Selig S. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat Commun 2017; 8:14015. [PMID: 28117327 PMCID: PMC5286223 DOI: 10.1038/ncomms14015] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
DNA:RNA hybrids, nucleic acid structures with diverse physiological functions, can disrupt genome integrity when dysregulated. Human telomeres were shown to form hybrids with the lncRNA TERRA, yet the formation and distribution of these hybrids among telomeres, their regulation and their cellular effects remain elusive. Here we predict and confirm in several human cell types that DNA:RNA hybrids form at many subtelomeric and telomeric regions. We demonstrate that ICF syndrome cells, which exhibit short telomeres and elevated TERRA levels, are enriched for hybrids at telomeric regions throughout the cell cycle. Telomeric hybrids are associated with high levels of DNA damage at chromosome ends in ICF cells, which are significantly reduced with overexpression of RNase H1. Our findings suggest that abnormally high TERRA levels in ICF syndrome lead to accumulation of telomeric hybrids that, in turn, can result in telomeric dysfunction. ICF syndrome cells exhibit shortened telomeres and elevated levels of the noncoding RNA TERRA. Here the authors show this is associated with high levels of DNA damage, suggesting an increase in telomere dysfunction due to the formation of DNA: RNA hybrids
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Affiliation(s)
- Shira Sagie
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Hagar Katzir
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Aya Tzur-Gilat
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Shany Havazelet
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
| | - Claire Francastel
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS UMR7216, Paris Cedex 75205, France
| | - Guillaume Velasco
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, CNRS UMR7216, Paris Cedex 75205, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, California 95616, USA
| | - Sara Selig
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa 31096, Israel
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26
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Simon AJ, Lev A, Zhang Y, Weiss B, Rylova A, Eyal E, Kol N, Barel O, Cesarkas K, Soudack M, Greenberg-Kushnir N, Rhodes M, Wiest DL, Schiby G, Barshack I, Katz S, Pras E, Poran H, Reznik-Wolf H, Ribakovsky E, Simon C, Hazou W, Sidi Y, Lahad A, Katzir H, Sagie S, Aqeilan HA, Glousker G, Amariglio N, Tzfati Y, Selig S, Rechavi G, Somech R. Mutations in STN1 cause Coats plus syndrome and are associated with genomic and telomere defects. J Exp Med 2016; 213:1429-40. [PMID: 27432940 PMCID: PMC4986528 DOI: 10.1084/jem.20151618] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 06/10/2016] [Indexed: 12/18/2022] Open
Abstract
The analysis of individuals with telomere defects may shed light on the delicate interplay of factors controlling genome stability, premature aging, and cancer. We herein describe two Coats plus patients with telomere and genomic defects; both harbor distinct, novel mutations in STN1, a member of the human CTC1-STN1-TEN1 (CST) complex, thus linking this gene for the first time to a human telomeropathy. We characterized the patients' phenotype, recapitulated it in a zebrafish model and rescued cellular and clinical aspects by the ectopic expression of wild-type STN1 or by thalidomide treatment. Interestingly, a significant lengthy control of the gastrointestinal bleeding in one of our patients was achieved by thalidomide treatment, exemplifying a successful bed-to-bench-and-back approach.
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Affiliation(s)
- Amos J Simon
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Division of Haematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Atar Lev
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Batia Weiss
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Pediatric Gastroenterology and Nutrition Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Anna Rylova
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Eyal
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nitzan Kol
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ortal Barel
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Keren Cesarkas
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michalle Soudack
- Imaging Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noa Greenberg-Kushnir
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Michele Rhodes
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Ginette Schiby
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Department of Pathology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shulamit Katz
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hana Poran
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Haike Reznik-Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elena Ribakovsky
- Division of Haematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Carlos Simon
- Division of Gastroenterology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Wadi Hazou
- Department of Internal Medicine C, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yechezkel Sidi
- Department of Internal Medicine C, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Avishay Lahad
- Pediatric Gastroenterology and Nutrition Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hagar Katzir
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 8875361, Israel
| | - Shira Sagie
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 8875361, Israel
| | - Haifa A Aqeilan
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Galina Glousker
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Ninette Amariglio
- Division of Haematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel The Everard and Mina Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Sara Selig
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 8875361, Israel
| | - Gideon Rechavi
- The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Raz Somech
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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27
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Avior Y, Sagi I, Benvenisty N. Pluripotent stem cells in disease modelling and drug discovery. Nat Rev Mol Cell Biol 2016; 17:170-82. [DOI: 10.1038/nrm.2015.27] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Samuelov L, Sarig O, Goldsmith T, Pavlovsky M, Goldberg I, Sagie S, Selig S, Sprecher E. A case for diagnosis. Clin Exp Dermatol 2015; 40:697-9. [PMID: 25703141 DOI: 10.1111/ced.12599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2014] [Indexed: 11/28/2022]
Affiliation(s)
- L Samuelov
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - O Sarig
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - T Goldsmith
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - M Pavlovsky
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - I Goldberg
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - S Sagie
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel
| | - S Selig
- Laboratory of Molecular Medicine, Rambam Health Care Campus and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa, Israel
| | - E Sprecher
- Department of Dermatology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat-Aviv, Israel
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Wang C, Zhao L, Lu S. Role of TERRA in the regulation of telomere length. Int J Biol Sci 2015; 11:316-23. [PMID: 25678850 PMCID: PMC4323371 DOI: 10.7150/ijbs.10528] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/25/2014] [Indexed: 01/08/2023] Open
Abstract
Telomere dysfunction is closely associated with human diseases such as cancer and ageing. Inappropriate changes in telomere length and/or structure result in telomere dysfunction. Telomeres have been considered to be transcriptionally silent, but it was recently demonstrated that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA). TERRA, a long non-coding RNA, participates in the regulation of telomere length, telomerase activity and heterochromatinization. The correct regulation of telomere length may be crucial to telomeric homeostasis and functions. Here, we summarize recent advances in our understanding of the crucial role of TERRA in the maintenance of telomere length, with focus on the variety of mechanisms by which TERRA is involved in the regulation of telomere length. This review aims to enable further understanding of how TERRA-targeted drugs can target telomere-related diseases.
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Affiliation(s)
- Caiqin Wang
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, China, Women's Hospital, School of Medicine, Zhejiang University, Xueshi Road 1#, Hangzhou 310006, China
| | - Li Zhao
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, China, Women's Hospital, School of Medicine, Zhejiang University, Xueshi Road 1#, Hangzhou 310006, China
| | - Shiming Lu
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, China, Women's Hospital, School of Medicine, Zhejiang University, Xueshi Road 1#, Hangzhou 310006, China
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