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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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2
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Xu Y. Recent progress in human telomere RNA structure and function. Bioorg Med Chem Lett 2018; 28:2577-2584. [DOI: 10.1016/j.bmcl.2018.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022]
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3
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Gutiérrez I, Garavís M, de Lorenzo S, Villasante A, González C, Arias-Gonzalez JR. Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA. J Phys Chem Lett 2018; 9:2498-2503. [PMID: 29688724 DOI: 10.1021/acs.jpclett.8b00722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
TERRA is an RNA molecule transcribed from human subtelomeric regions toward chromosome ends potentially involved in regulation of heterochromatin stability, semiconservative replication, and telomerase inhibition, among others. TERRA contains tandem repeats of the sequence GGGUUA, with a strong tendency to fold into a four-stranded arrangement known as a parallel G-quadruplex. Here, we demonstrate by using single-molecule force spectroscopy that this potential is limited by the inherent capacity of RNA to self-associate randomly and further condense into entropically more favorable structures. We stretched RNA constructions with more than four and less than eight hexanucleotide repeats, thus unable to form several G-quadruplexes in tandem, flanked by non-G-rich overhangs of random sequence by optical tweezers on a one by one basis. We found that condensed RNA stochastically blocks G-quadruplex folding pathways with a near 20% probability, a behavior that is not found in DNA analogous molecules.
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Affiliation(s)
- Irene Gutiérrez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) , Cantoblanco, 28049 Madrid , Spain
| | - Miguel Garavís
- Instituto de Química Física Rocasolano, CSIC , C/Serrano 119 , 28006 Madrid , Spain
| | - Sara de Lorenzo
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) , Cantoblanco, 28049 Madrid , Spain
| | - Alfredo Villasante
- Centro de Biología Molecular "Severo Ochoa" CSIC-UAM , C/Nicolás Cabrera 1 , 28049 Madrid , Spain
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC , C/Serrano 119 , 28006 Madrid , Spain
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) , Cantoblanco, 28049 Madrid , Spain
- CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología" , Cantoblanco, 28049 Madrid , Spain
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4
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Kar A, Willcox S, Griffith JD. Transcription of telomeric DNA leads to high levels of homologous recombination and t-loops. Nucleic Acids Res 2016; 44:9369-9380. [PMID: 27608724 PMCID: PMC5100571 DOI: 10.1093/nar/gkw779] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022] Open
Abstract
The formation of DNA loops at chromosome ends (t-loops) and the transcription of telomeres producing G-rich RNA (TERRA) represent two central features of telomeres. To explore a possible link between them we employed artificial human telomeres containing long arrays of TTAGGG repeats flanked by the T7 or T3 promoters. Transcription of these DNAs generates a high frequency of t-loops within individual molecules and homologous recombination events between different DNAs at their telomeric sequences. T-loop formation does not require a single strand overhang, arguing that both terminal strands insert into the preceding duplex. The loops are very stable and some RNase H resistant TERRA remains at the t-loop, likely adding to their stability. Transcription of DNAs containing TTAGTG or TGAGTG repeats showed greatly reduced loop formation. While in the cell multiple pathways may lead to t-loop formation, the pathway revealed here does not depend on the shelterins but rather on the unique character of telomeric DNA when it is opened for transcription. Hence, telomeric sequences may have evolved to facilitate their ability to loop back on themselves.
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Affiliation(s)
- Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA
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Bergues-Pupo AE, Arias-Gonzalez JR, Morón MC, Fiasconaro A, Falo F. Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes. Nucleic Acids Res 2015; 43:7638-47. [PMID: 26170233 PMCID: PMC4551928 DOI: 10.1093/nar/gkv690] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022] Open
Abstract
Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of \documentclass[12pt]{minimal}
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}{}$\rm {K}^+$\end{document} central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery.
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Affiliation(s)
- Ana Elisa Bergues-Pupo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain Departamento de Física, Universidad de Oriente, 90500 Santiago de Cuba, Cuba
| | - J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Cantoblanco, 28049 Madrid, Spain CNB-CSIC-IMDEA Nanociencia Associated Unit 'Unidad de Nanobiotecnología, Madrid, Spain'
| | - María Carmen Morón
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alessandro Fiasconaro
- School of Mathematical Sciences, Queen Mary University of London - Mile End Road, London E1 4NS, UK
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Mariano Esquillor, 50018 Zaragoza, Spain
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Recognition of chelerythrine to human telomeric DNA and RNA G-quadruplexes. Sci Rep 2014; 4:6767. [PMID: 25341562 PMCID: PMC4208030 DOI: 10.1038/srep06767] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/29/2014] [Indexed: 01/25/2023] Open
Abstract
A study on binding of antitumor chelerythrine to human telomeric DNA/RNA G-quadruplexes was performed by using DNA polymerase stop assay, UV-melting, ESI-TOF-MS, UV-Vis absorption spectrophotometry and fluorescent triazole orange displacement assay. Chelerythrine selectively binds to and stabilizes the K(+)-form hybrid-type human telomeric DNA G-quadruplex of biological significance, compared with the Na(+)-form antiparallel-type DNA G-quadruplex. ESI-TOF-MS study showed that chelerythrine possesses a binding strength for DNA G-quadruplex comparable to that of TMPyP4 tetrachloride. Both 1:1 and 2:1 stoichiometries were observed for chelerythrine's binding with DNA and RNA G-quadruplexes. The binding strength of chelerythrine with RNA G-quadruplex is stronger than that with DNA G-quadruplex. Fluorescent triazole orange displacement assay revealed that chelerythrine interacts with human telomeric RNA/DNA G-quadruplexes by the mode of end- stacking. The relative binding strength of chelerythrine for human telomeric RNA and DNA G-quadruplexes obtained from ESI-TOF-MS experiments are respectively 6.0- and 2.5-fold tighter than that with human telomeric double-stranded hairpin DNA. The binding selectivity of chelerythrine for the biologically significant K(+)-form human telomeric DNA G-quadruplex over the Na(+)-form analogue, and binding specificity for human telomeric RNA G-quadruplex established it as a promising candidate in the structure-based design and development of G-quadruplex specific ligands.
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Kim IS, Seo YJ. Probe development for detection of TERRA 1 intramolecular G-quadruplex formation using a fluorescent adenosine derivative. Bioorg Med Chem Lett 2014; 24:1589-91. [PMID: 24513043 DOI: 10.1016/j.bmcl.2014.01.068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/09/2014] [Accepted: 01/22/2014] [Indexed: 01/20/2023]
Abstract
We developed a probing system to detect the intramolecular G-quadruplex of telomeric repeat-containing RNA (TERRA 1). We used a fluorescent adenosine derivative rA(py) as a fluorophore and incorporated it into the dangling position of the parallel-type G-quadruplex sequence of TERRA 1. The rA(py)-modified G-quadruplex structure exhibited a strong fluorescence emission signal, while the emission signals of the single-strand and duplex structures were much lower.
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Affiliation(s)
- In Sun Kim
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea.
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Mathiyalagan P, Keating ST, Du XJ, El-Osta A. Interplay of chromatin modifications and non-coding RNAs in the heart. Epigenetics 2013; 9:101-12. [PMID: 24247090 DOI: 10.4161/epi.26405] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.
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Affiliation(s)
- Prabhu Mathiyalagan
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Samuel T Keating
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia
| | - Xiao-Jun Du
- Experimental Cardiology Laboratory; Baker IDI Heart and Diabetes Institute; Melbourne, VIC Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Epigenomics Profiling Facility; Baker IDI Heart and Diabetes Institute; The Alfred Medical Research and Education Precinct; Melbourne, VIC Australia; Department of Pathology; The University of Melbourne; Melbourne, VIC Australia; Faculty of Medicine; Monash University; Melbourne, VIC Australia
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9
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Martadinata H, Phan AT. Structure of human telomeric RNA (TERRA): stacking of two G-quadruplex blocks in K(+) solution. Biochemistry 2013; 52:2176-83. [PMID: 23445442 DOI: 10.1021/bi301606u] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.
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Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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Abstract
UPF1 (up-frameshift 1) is a protein conserved in all eukaryotes that is necessary for NMD (nonsense-mediated mRNA decay). UPF1 mainly localizes to the cytoplasm and, via mechanisms that are linked to translation termination but not yet well understood, stimulates rapid destruction of mRNAs carrying a PTC (premature translation termination codon). However, some studies have indicated that in human cells UPF1 has additional roles, possibly unrelated to NMD, which are carried out in the nucleus. These might involve telomere maintenance, cell cycle progression and DNA replication. In the present paper, we review the available experimental evidence implicating UPF1 in nuclear functions. The unexpected view that emerges from this literature is that the nuclear functions primarily stem from UPF1 having an important role in DNA replication, rather than NMD affecting the expression of proteins involved in these processes. Our bioinformatics survey of the interaction network of UPF1 with other human proteins, however, highlights that UPF1 also interacts with proteins associated with nuclear RNA degradation and transcription termination; therefore suggesting involvement in processes that could also impinge on DNA replication indirectly.
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Sana J, Faltejskova P, Svoboda M, Slaby O. Novel classes of non-coding RNAs and cancer. J Transl Med 2012; 10:103. [PMID: 22613733 PMCID: PMC3434024 DOI: 10.1186/1479-5876-10-103] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 05/21/2012] [Indexed: 12/12/2022] Open
Abstract
For the many years, the central dogma of molecular biology has been that RNA functions mainly as an informational intermediate between a DNA sequence and its encoded protein. But one of the great surprises of modern biology was the discovery that protein-coding genes represent less than 2% of the total genome sequence, and subsequently the fact that at least 90% of the human genome is actively transcribed. Thus, the human transcriptome was found to be more complex than a collection of protein-coding genes and their splice variants. Although initially argued to be spurious transcriptional noise or accumulated evolutionary debris arising from the early assembly of genes and/or the insertion of mobile genetic elements, recent evidence suggests that the non-coding RNAs (ncRNAs) may play major biological roles in cellular development, physiology and pathologies. NcRNAs could be grouped into two major classes based on the transcript size; small ncRNAs and long ncRNAs. Each of these classes can be further divided, whereas novel subclasses are still being discovered and characterized. Although, in the last years, small ncRNAs called microRNAs were studied most frequently with more than ten thousand hits at PubMed database, recently, evidence has begun to accumulate describing the molecular mechanisms by which a wide range of novel RNA species function, providing insight into their functional roles in cellular biology and in human disease. In this review, we summarize newly discovered classes of ncRNAs, and highlight their functioning in cancer biology and potential usage as biomarkers or therapeutic targets.
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Affiliation(s)
- Jiri Sana
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, Brno, Czech Republic, Europe
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic, Europe
| | - Petra Faltejskova
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, Brno, Czech Republic, Europe
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic, Europe
| | - Marek Svoboda
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, Brno, Czech Republic, Europe
| | - Ondrej Slaby
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, Brno, Czech Republic, Europe
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic, Europe
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Zluty kopec 7, 656 53, Brno, Czech Republic, Europe
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Xu Y, Komiyama M. Structure, function and targeting of human telomere RNA. Methods 2012; 57:100-5. [PMID: 22425636 DOI: 10.1016/j.ymeth.2012.02.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/26/2012] [Accepted: 02/28/2012] [Indexed: 11/18/2022] Open
Abstract
Human telomeres play an important role in critical processes underlying genome stability, cancer, and aging. For a long time, telomeres have been considered transcriptionally silent. A recent finding demonstrated that telomere DNA is transcribed into telomeric repeat-containing RNA (referred to as TERRA) in mammalian cells. The existence of TERRA RNA may reveal a new level of regulation and protection of chromosome ends that could promote valuable insight into fundamental biological processes such as cancer and aging. Revealing the structure and function of telomere RNA will be essential for understanding telomere biology and telomere-related diseases. NMR and X-ray crystallography have demonstrated that human telomere RNA forms G-quadruplex structures. More recently, human telomere RNA is suggested to form a G-quadruplex dimer in the living cells by employing a light-switching probe. The proposed structures may be a valuable target for anticancer agents directed against telomeres. This review highlights the structures and topologies for telomere RNA G-quadruplex and recent efforts in the design of telomere RNA G-quadruplex ligands. The future challenges in the field are outlined.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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Abstract
Structural studies have shown that four G-tracts along a DNA strand are the minimal requirement for intramolecular G-quadruplex formation. Longer DNA sequences containing multiples of four G-tracts could, in principle, form higher-order structures based on multiple G-quadruplex blocks. This latter condition is abundantly verified for the telomeric single-stranded overhang (~200 nt) consisting of tens of TTAGGG repeats, thus opening new interesting questions about the structure of the "real" telomeric DNA. How many quadruplex units form in the human telomeric overhang? Which type of quadruplex topologies? Do they interact or not? What about their binding properties? Although many of these questions are still unanswered, recent experimental and computational studies have begun to address them. The existence and relevance of these higher-order quadruplex structures in the human genome is now an interesting and stimulating research topic in the quadruplex field. The recent results, the unsolved problems, and the future prospects for understanding higher-order telomeric quadruplex structures are the main topics of this review. Other studies on long telomeric RNA sequences and on other intramolecular (non telomeric) DNA higher order quadruplex structures are also presented.
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Martadinata H, Heddi B, Lim KW, Phan AT. Structure of Long Human Telomeric RNA (TERRA): G-Quadruplexes Formed by Four and Eight UUAGGG Repeats Are Stable Building Blocks. Biochemistry 2011; 50:6455-61. [DOI: 10.1021/bi200569f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
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15
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Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, Rinn JL. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol 2011; 12:R56. [PMID: 21689454 PMCID: PMC3218844 DOI: 10.1186/gb-2011-12-6-r56] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 04/27/2011] [Accepted: 06/20/2011] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling. We therefore set out to investigate putative roles for lncRNAs in P. falciparum transcriptional regulation. RESULTS We used a high-resolution DNA tiling microarray to survey transcriptional activity across 22.6% of the P. falciparum strain 3D7 genome. We identified 872 protein-coding genes and 60 putative P. falciparum lncRNAs under developmental regulation during the parasite's pathogenic human blood stage. Further characterization of lncRNA candidates led to the discovery of an intriguing family of lncRNA telomere-associated repetitive element transcripts, termed lncRNA-TARE. We have quantified lncRNA-TARE expression at 15 distinct chromosome ends and mapped putative transcriptional start and termination sites of lncRNA-TARE loci. Remarkably, we observed coordinated and stage-specific expression of lncRNA-TARE on all chromosome ends tested, and two dominant transcripts of approximately 1.5 kb and 3.1 kb transcribed towards the telomere. CONCLUSIONS We have characterized a family of 22 telomere-associated lncRNAs in P. falciparum. Homologous lncRNA-TARE loci are coordinately expressed after parasite DNA replication, and are poised to play an important role in P. falciparum telomere maintenance, virulence gene regulation, and potentially other processes of parasite chromosome end biology. Further study of lncRNA-TARE and other promising lncRNA candidates may provide mechanistic insight into P. falciparum transcriptional regulation.
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Affiliation(s)
- Kate M Broadbent
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Daniel Park
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Ashley R Wolf
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Daria Van Tyne
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Jennifer S Sims
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Sarah Volkman
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
- School of Nursing and Health Sciences, Simmons College, 300 The Fenway, Boston, MA 02115, USA
| | - Manoj Duraisingh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Dyann Wirth
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston, MA 02115, USA
| | - Pardis C Sabeti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - John L Rinn
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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Diotti R, Loayza D. Shelterin complex and associated factors at human telomeres. Nucleus 2011; 2:119-35. [PMID: 21738835 PMCID: PMC3127094 DOI: 10.4161/nucl.2.2.15135] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 12/17/2022] Open
Abstract
The processes regulating telomere function have major impacts on fundamental issues in human cancer biology. First, active telomere maintenance is almost always required for full oncogenic transformation of human cells, through cellular immortalization by endowment of an infinite replicative potential. Second, the attrition that telomeres undergo upon replication is responsible for the finite replicative life span of cells in culture, a process called senescence, which is of paramount importance for tumor suppression in vivo. The process of telomere-based senescence is intimately coupled to the induction of a DNA damage response emanating from telomeres, which can be elicited by both the ATM and ATR dependent pathways. At telomeres, the shelterin complex is constituted by a group of six proteins which assembles quantitatively along the telomere tract, and imparts both telomere maintenance and telomere protection. Shelterin is known to regulate the action of telomerase, and to prevent inappropriate DNA damage responses at chromosome ends, mostly through inhibition of ATM and ATR. The roles of shelterin have increasingly been associated with transient interactions with downstream factors that are not associated quantitatively or stably with telomeres. Here, some of the important known interactions between shelterin and these associated factors and their interplay to mediate telomere functions are reviewed.
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Affiliation(s)
- Raffaella Diotti
- Department of Biological Sciences, Hunter College, New York, NY, USA
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17
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Abstract
Telomeric repeat-containing RNA (referred to as TERRA), a noncoding RNA molecule, has recently been found in mammalian cells. The detailed structural features and function of the TERRA RNA at human chromosome ends remain unclear, although this RNA molecule may be a key component of the telomere machinery. In the present studies, we investigated the structural features of human TERRA RNA in living cells. Using a light-switching pyrene probe, we found that human TERRA RNA forms a parallel G-quadruplex structure in living cells, providing the in vivo evidence for the presence of the G-quadruplex in human TERRA RNA. Furthermore, imaging experiments clearly show that TERRA RNA G-quadruplex localizes to telomere DNA at cell nuclei. These results provide valuable information to allow understanding of the structure and function of human TERRA RNA.
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Abstract
Chromosome termini form a specialized type of heterochromatin that is important for chromosome stability. The recent discovery of telomeric RNA transcripts in yeast and vertebrates raised the question of whether RNA-based mechanisms are involved in the formation of telomeric heterochromatin. In this study, we performed detailed analysis of chromatin structure and RNA transcription at chromosome termini in Arabidopsis. Arabidopsis telomeres display features of intermediate heterochromatin that does not extensively spread to subtelomeric regions which encode transcriptionally active genes. We also found telomeric repeat-containing transcripts arising from telomeres and centromeric loci, a portion of which are processed into small interfering RNAs. These telomeric siRNAs contribute to the maintenance of telomeric chromatin through promoting methylation of asymmetric cytosines in telomeric (CCCTAAA)(n) repeats. The formation of telomeric siRNAs and methylation of telomeres relies on the RNA-dependent DNA methylation pathway. The loss of telomeric DNA methylation in rdr2 mutants is accompanied by only a modest effect on histone heterochromatic marks, indicating that maintenance of telomeric heterochromatin in Arabidopsis is reinforced by several independent mechanisms. In conclusion, this study provides evidence for an siRNA-directed mechanism of chromatin maintenance at telomeres in Arabidopsis.
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Abstract
Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies.
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Affiliation(s)
- Anh Tuân Phan
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore.
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20
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Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS. A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res 2009; 38:608-17. [PMID: 19864253 PMCID: PMC2811010 DOI: 10.1093/nar/gkp895] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense–antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology, ZMBE, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
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21
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Tsai YC, Qi H, Lin CP, Lin RK, Kerrigan JE, Rzuczek SG, LaVoie EJ, Rice JE, Pilch DS, Lyu YL, Liu LF. A G-quadruplex stabilizer induces M-phase cell cycle arrest. J Biol Chem 2009; 284:22535-43. [PMID: 19531483 PMCID: PMC2755660 DOI: 10.1074/jbc.m109.020230] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 06/14/2009] [Indexed: 11/06/2022] Open
Abstract
G-quadruplex stabilizers such as telomestatin and HXDV bind with exquisite specificity to G-quadruplexes, but not to triplex, duplex, or single-stranded DNAs. Studies have suggested that the antiproliferative and possibly anti-tumor activities of these compounds are linked to their inhibitory effect on telomerase and/or telomere function. In the current studies, we show that HXDV, a synthetic analog of telomestatin, exhibits antiproliferative activity against both telomerase-positive and -negative cells and induces robust apoptosis within 16 h of treatment, suggesting a mode of action independent of telomerase. HXDV was also shown to inhibit cell cycle progression causing M-phase cell cycle arrest, as evidenced by accumulation of cells with 4 n DNA content, increased mitotic index, separated centrosomes, elevated histone H3 phosphorylation at Ser-10 (an M-phase marker), and defective chromosome alignment and spindle fiber assembly (revealed by time-lapse microscopy). The M-phase arrest caused by HXDV paralleled with reduction in the expression level of the major M-phase checkpoint regulator Aurora A. All these cellular effects appear to depend on the G-quadruplex binding activity of HXDV as its non-G-quadruplex binding analog, TXTLeu, is completely devoid of all these effects. In the aggregate, our results suggest that HXDV, which exhibits anti-proliferative and apoptotic activities, is also a novel M-phase blocker, with a mode of action dependent on its G-quadruplex binding activity.
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Affiliation(s)
- Yuan-Chin Tsai
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - Haiyan Qi
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - Chao-Po Lin
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - Ren-Kuo Lin
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - John E. Kerrigan
- the Cancer Institute of New Jersey, New Brunswick, New Jersey 08903-2681, and
| | - Suzanne G. Rzuczek
- the Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020
| | - Edmond J. LaVoie
- the Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020
| | - Joseph E. Rice
- the Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020
| | - Daniel S. Pilch
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - Yi Lisa Lyu
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
| | - Leroy F. Liu
- From the Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635
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22
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Cao F, Li X, Hiew S, Brady H, Liu Y, Dou Y. Dicer independent small RNAs associate with telomeric heterochromatin. RNA (NEW YORK, N.Y.) 2009; 15:1274-81. [PMID: 19460867 PMCID: PMC2704082 DOI: 10.1261/rna.1423309] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/06/2009] [Indexed: 05/25/2023]
Abstract
Small RNAs play important roles in the establishment and maintenance of heterochromatin structures. We show the presence of telomere specific small RNAs (tel-sRNAs) in mouse embryonic stem cells that are approximately 24 nucleotides in length, Dicer-independent, and 2'-O-methylated at the 3' terminus. The tel-sRNAs are asymmetric with specificity toward telomere G-rich strand, and evolutionarily conserved from protozoan to mammalian cells. Furthermore, tel-sRNAs are up-regulated in cells that carry null mutation of H3K4 methyltransferase MLL (Mll((-/-))) and down-regulated in cells that carry null mutations of histone H3K9 methyltransferase SUV39H (Suv39h1/h2((-/-))), suggesting that they are subject to epigenetic regulation. These results support that tel-sRNAs are heterochromatin associated pi-like small RNAs.
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Affiliation(s)
- Fang Cao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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23
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Martadinata H, Phan AT. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution. J Am Chem Soc 2009; 131:2570-8. [PMID: 19183046 DOI: 10.1021/ja806592z] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
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Affiliation(s)
- Herry Martadinata
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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24
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Luke B, Panza A, Redon S, Iglesias N, Li Z, Lingner J. The Rat1p 5' to 3' exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol Cell 2009; 32:465-77. [PMID: 19026778 DOI: 10.1016/j.molcel.2008.10.019] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/21/2008] [Accepted: 10/28/2008] [Indexed: 10/21/2022]
Abstract
Vertebrate telomeres are transcribed into telomeric repeat-containing RNA (TERRA) that associates with telomeres and may be important for telomere function. Here, we demonstrate that telomeres are also transcribed in Saccharomyces cerevisiae by RNA polymerase II (RNAPII). Yeast TERRA is polyadenylated and stabilized by Pap1p and regulated by the 5' to 3' exonuclease, Rat1p. rat1-1 mutant cells accumulate TERRA and harbor short telomeres because of defects in telomerase-mediated telomere elongation. Overexpression of RNaseH overcomes telomere elongation defects in rat1-1 cells, indicating that RNA/DNA hybrids inhibit telomerase function at chromosome ends in these mutants. Thus, telomeric transcription combined with Rat1p-dependent TERRA degradation is important for regulating telomerase in yeast. Telomere transcription is conserved in different kingdoms of the eukaryotic domain.
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Affiliation(s)
- Brian Luke
- Ecole Polytechnique Fédérale de Lausanne, Swiss Institute for Experimental Cancer Research (ISREC), CH-1066 Epalinges, Switzerland
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Simple telomeres in a simple animal: absence of subtelomeric repeat regions in the placozoan Trichoplax adhaerens. Genetics 2008; 181:323-5. [PMID: 18984569 DOI: 10.1534/genetics.108.096289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Simple telomeres were identified in the genome assembly of the basal placozoan animal Trichoplax adhaerens. They have 1-2 kb of TTAGGG telomeric repeats, which are preceded by a subtelomeric region of 1.5-13 kb. Unlike subtelomeric regions in most animals examined, these subtelomeric regions are unique to each telomere.
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