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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol 2024; 162:65-77. [PMID: 38724854 PMCID: PMC11227451 DOI: 10.1007/s00418-024-02289-7] [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] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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2
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Katsushima K, Joshi K, Yuan M, Romero B, Batish M, Stapleton S, Jallo G, Kolanthai E, Seal S, Saulnier O, Taylor MD, Wechsler-Reya RJ, Eberhart CG, Perera RJ. A therapeutically targetable positive feedback loop between lnc-HLX-2-7, HLX, and MYC that promotes group 3 medulloblastoma. Cell Rep 2024; 43:113938. [PMID: 38460130 DOI: 10.1016/j.celrep.2024.113938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/11/2024] Open
Abstract
Recent studies suggest that long non-coding RNAs (lncRNAs) contribute to medulloblastoma (MB) formation and progression. We have identified an lncRNA, lnc-HLX-2-7, as a potential therapeutic target in group 3 (G3) MBs. lnc-HLX-2-7 RNA specifically accumulates in the promoter region of HLX, a sense-overlapping gene of lnc-HLX-2-7, which activates HLX expression by recruiting multiple factors, including enhancer elements. RNA sequencing and chromatin immunoprecipitation reveal that HLX binds to and activates the promoters of several oncogenes, including TBX2, LIN9, HOXM1, and MYC. Intravenous treatment with cerium-oxide-nanoparticle-coated antisense oligonucleotides targeting lnc-HLX-2-7 (CNP-lnc-HLX-2-7) inhibits tumor growth by 40%-50% in an intracranial MB xenograft mouse model. Combining CNP-lnc-HLX-2-7 with standard-of-care cisplatin further inhibits tumor growth and significantly prolongs mouse survival compared with CNP-lnc-HLX-2-7 monotherapy. Thus, the lnc-HLX-2-7-HLX-MYC axis is important for regulating G3 MB progression, providing a strong rationale for using lnc-HLX-2-7 as a therapeutic target for G3 MBs.
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Affiliation(s)
- Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Kandarp Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19701, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Center, Nanoscience and Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Center, Nanoscience and Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL 32816, USA
| | - Olivier Saulnier
- Genomics and Development of Childhood Cancers, Institut Curie, PSL University, 75005 Paris, France; INSERM U830, Cancer Heterogeneity Instability and Plasticity, Institut Curie, PSL University, 75005 Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, 75005 Paris, France
| | - Michael D Taylor
- Texas Children's Cancer Center, Hematology-Oncology Section, Houston, TX 77004, USA; Department of Pediatrics - Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX 77004, USA
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave., Ross Bldg. 558, Baltimore, MD 21205, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA; Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA.
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. RESEARCH SQUARE 2024:rs.3.rs-3970096. [PMID: 38464289 PMCID: PMC10925428 DOI: 10.21203/rs.3.rs-3970096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
| | | | | | - Tom Misteli
- National Cancer Institute, National Institute of Health
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4
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Manzato C, Larini L, Oss Pegorar C, Dello Stritto MR, Jurikova K, Jantsch V, Cusanelli E. TERRA expression is regulated by the telomere-binding proteins POT-1 and POT-2 in Caenorhabditis elegans. Nucleic Acids Res 2023; 51:10681-10699. [PMID: 37713629 PMCID: PMC10602879 DOI: 10.1093/nar/gkad742] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Several aspects of telomere biology are regulated by the telomeric repeat-containing RNA TERRA. While TERRA expression is conserved through evolution, species-specific mechanisms regulate its biogenesis and function. Here we report on the expression of TERRA in Caenorhabditis elegans. We show that C. elegans TERRA is regulated by the telomere-binding proteins POT-1 and POT-2 which repress TERRA in a telomere-specific manner. C. elegans TERRA transcripts are heterogeneous in length and form discrete nuclear foci, as detected by RNA FISH, in both postmitotic and germline cells; a fraction of TERRA foci localizes to telomeres. Interestingly, in germ cells, TERRA is expressed in all stages of meiotic prophase I, and it increases during pachytene, a stage in meiosis when homologous recombination is ongoing. We used the MS2-GFP system to study the spatiotemporal dynamics of single-telomere TERRA molecules. Single particle tracking revealed different types of motilities, suggesting complex dynamics of TERRA transcripts. Finally, we unveiled distinctive features of C. elegans TERRA, which is regulated by telomere shortening in a telomere-specific manner, and it is upregulated in the telomerase-deficient trt-1; pot-2 double mutant prior to activation of the alternative lengthening mechanism ALT. Interestingly, in these worms TERRA displays distinct dynamics with a higher fraction of fast-moving particles.
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Affiliation(s)
- Caterina Manzato
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Luca Larini
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Claudio Oss Pegorar
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
| | - Maria Rosaria Dello Stritto
- Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter 1030, Vienna, Austria
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina 84215, Bratislava, Slovakia
| | - Verena Jantsch
- Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter 1030, Vienna, Austria
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, 38123, Trento, Italy
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Greenberg E, Hochberg-Laufer H, Blanga S, Kinor N, Shav-Tal Y. Cytoplasmic DNA can be detected by RNA fluorescence in situ hybridization. Nucleic Acids Res 2019; 47:e109. [PMID: 31340014 PMCID: PMC6765201 DOI: 10.1093/nar/gkz645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 06/26/2019] [Accepted: 07/15/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) can be used for the intracellular detection of DNA or RNA molecules. The detection of DNA sequences by DNA FISH requires the denaturation of the DNA double helix to allow the hybridization of the fluorescent probe with DNA in a single stranded form. These hybridization conditions require high temperature and low pH that can damage RNA, and therefore RNA is not typically detectable by DNA FISH. In contrast, RNA FISH does not require a denaturation step since RNA is single stranded, and therefore DNA molecules are not detectable by RNA FISH. Hence, DNA FISH and RNA FISH are mutually exclusive. In this study, we show that plasmid DNA transiently transfected into cells is readily detectable in the cytoplasm by RNA FISH without need for denaturation, shortly after transfection and for several hours. The plasmids, however, are usually not detectable in the nucleus except when the plasmids are efficiently directed into the nucleus, which may imply a more open packaging state for DNA after transfection. This detection of plasmid DNA in the cytoplasm has implications for RNA FISH experiments and opens a window to study conditions when DNA is present in the cytoplasm.
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Affiliation(s)
- Eliraz Greenberg
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Hodaya Hochberg-Laufer
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shalev Blanga
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 5290002, Israel
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The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability. Cells 2019; 8:cells8030246. [PMID: 30875900 PMCID: PMC6468625 DOI: 10.3390/cells8030246] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
The finding that transcription occurs at chromosome ends has opened new fields of study on the roles of telomeric transcripts in chromosome end maintenance and genome stability. Indeed, the ends of chromosomes are required to be protected from activation of DNA damage response and DNA repair pathways. Chromosome end protection is achieved by the activity of specific proteins that associate with chromosome ends, forming telomeres. Telomeres need to be constantly maintained as they are in a heterochromatic state and fold into specific structures (T-loops), which may hamper DNA replication. In addition, in the absence of maintenance mechanisms, chromosome ends shorten at every cell division due to limitations in the DNA replication machinery, which is unable to fully replicate the extremities of chromosomes. Altered telomere structure or critically short chromosome ends generate dysfunctional telomeres, ultimately leading to replicative senescence or chromosome instability. Telomere biology is thus implicated in multiple human diseases, including cancer. Emerging evidence indicates that a class of long noncoding RNAs transcribed at telomeres, known as TERRA for “TElomeric Repeat-containing RNA,” actively participates in the mechanisms regulating telomere maintenance and chromosome end protection. However, the molecular details of TERRA activities remain to be elucidated. In this review, we discuss recent findings on the emerging roles of TERRA in telomere maintenance and genome stability and their implications in human diseases.
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Abstract
A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.
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Affiliation(s)
- Lan-Tian Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhenyu Meng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore.
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Cusanelli E, Chartrand P. Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity. Front Genet 2015; 6:143. [PMID: 25926849 PMCID: PMC4396414 DOI: 10.3389/fgene.2015.00143] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/25/2015] [Indexed: 12/15/2022] Open
Abstract
Telomeres are dynamic nucleoprotein structures that protect the ends of chromosomes from degradation and activation of DNA damage response. For this reason, telomeres are essential to genome integrity. Chromosome ends are enriched in heterochromatic marks and proper organization of telomeric chromatin is important to telomere stability. Despite their heterochromatic state, telomeres are transcribed giving rise to long noncoding RNAs (lncRNA) called TERRA (telomeric repeat-containing RNA). TERRA molecules play critical roles in telomere biology, including regulation of telomerase activity and heterochromatin formation at chromosome ends. Emerging evidence indicate that TERRA transcripts form DNA-RNA hybrids at chromosome ends which can promote homologous recombination among telomeres, delaying cellular senescence and sustaining genome instability. Intriguingly, TERRA RNA-telomeric DNA hybrids are involved in telomere length homeostasis of telomerase-negative cancer cells. Furthermore, TERRA transcripts play a role in the DNA damage response (DDR) triggered by dysfunctional telomeres. We discuss here recent developments on TERRA's role in telomere biology and genome integrity, and its implication in cancer.
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Affiliation(s)
- Emilio Cusanelli
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna Vienna, Austria
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal Montréal, QC, Canada
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Basu R, Lai LT, Meng Z, Wu J, Shao F, Zhang LF. Using amino-labeled nucleotide probes for simultaneous single molecule RNA-DNA FISH. PLoS One 2014; 9:e107425. [PMID: 25226542 PMCID: PMC4167323 DOI: 10.1371/journal.pone.0107425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/07/2014] [Indexed: 01/17/2023] Open
Abstract
Using amino-labeled oligonucleotide probes, we established a simple, robust and low-noise method for simultaneous detection of RNA and DNA by fluorescence in situ hybridization, a highly useful tool to study the large pool of long non-coding RNAs being identified in the current research. With probes either chemically or biologically synthesized, we demonstrate that the method can be applied to study a wide range of RNA and DNA targets at the single-cell and single-molecule level in cellular contexts.
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Affiliation(s)
- Reelina Basu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lan-Tian Lai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhenyu Meng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jun Wu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (FS); (L-FZ)
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (FS); (L-FZ)
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López CS, Sloan R, Cylinder I, Kozak SL, Kabat D, Barklis E. RRE-dependent HIV-1 Env RNA effects on Gag protein expression, assembly and release. Virology 2014; 462-463:126-34. [PMID: 24971705 DOI: 10.1016/j.virol.2014.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/16/2014] [Accepted: 05/17/2014] [Indexed: 12/14/2022]
Abstract
The HIV-1 Gag proteins are translated from the full-length HIV-1 viral RNA (vRNA), whereas the envelope (Env) protein is translated from incompletely spliced Env mRNAs. Nuclear export of vRNAs and Env mRNAs is mediated by the Rev accessory protein which binds to the rev-responsive element (RRE) present on these RNAs. Evidence has shown there is a direct or indirect interaction between the Gag protein, and the cytoplasmic tail (CT) of the Env protein. Our current work shows that env gene expression impacts HIV-1 Gag expression and function in two ways. At the protein level, full-length Env expression altered Gag protein expression, while Env CT-deletion proteins did not. At the RNA level, RRE-containing Env mRNA expression reduced Gag expression, processing, and virus particle release from cells. Our results support models in which Gag is influenced by the Env CT, and Env mRNAs compete with vRNAs for nuclear export.
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Affiliation(s)
- Claudia S López
- Departments of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States.
| | - Rachel Sloan
- Departments of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Isabel Cylinder
- Departments of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Susan L Kozak
- Biochemistry and Molecular Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - David Kabat
- Biochemistry and Molecular Biology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Eric Barklis
- Departments of Molecular Microbiology and Immunology, Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States.
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Cusanelli E, Chartrand P. Telomeric noncoding RNA: telomeric repeat-containing RNA in telomere biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:407-19. [PMID: 24523222 DOI: 10.1002/wrna.1220] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Telomeres are nucleoprotein structures that cap the ends of eukaryotic chromosomes, protecting them from degradation and activation of DNA damage response. For this reason, functional telomeres are vital to genome stability. For years, telomeres were assumed to be transcriptionally silent, because of their heterochromatic state. It was only recently shown that, in several organisms, telomeres are transcribed, giving rise to a long noncoding RNA (lncRNA) called telomeric repeat-containing RNA (TERRA). Several lines of evidence now indicate that TERRA molecules play crucial roles in telomere homeostasis and telomere functions. Recent studies have shown that the expression and regulation of TERRA are dynamically controlled by each chromosome end. TERRA has been involved in the regulation of telomere length, telomerase activity, and heterochromatin formation at telomeres. The correct regulation of the telomeric transcripts may be essential to genome stability, and altered TERRA levels associate with tumorigenesis and cellular senescence. Thus, the study of the molecular mechanisms of TERRA biogenesis and function may advance the understanding of telomere-related diseases, including cancer and aging.
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Affiliation(s)
- Emilio Cusanelli
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Canada
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12
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Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres. Mol Cell 2013; 51:780-91. [PMID: 24074956 DOI: 10.1016/j.molcel.2013.08.029] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/05/2013] [Accepted: 08/19/2013] [Indexed: 11/20/2022]
Abstract
Elongation of a short telomere depends on the action of multiple telomerase molecules, which are visible as telomerase RNA foci or clusters associated with telomeres in yeast and mammalian cells. How several telomerase molecules act on a single short telomere is unknown. Herein, we report that the telomeric noncoding RNA TERRA is involved in the nucleation of telomerase molecules into clusters prior to their recruitment at a short telomere. We find that telomere shortening induces TERRA expression, leading to the accumulation of TERRA molecules into a nuclear focus. Simultaneous time-lapse imaging of telomerase RNA and TERRA reveals spontaneous events of telomerase nucleation on TERRA foci in early S phase, generating TERRA-telomerase clusters. This cluster is subsequently recruited to the short telomere from which TERRA transcripts originate during S phase. We propose that telomere shortening induces noncoding RNA expression to coordinate the recruitment and activity of telomerase molecules at short telomeres.
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