1
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Tse V, Chacaltana G, Gutierrez M, Forino NM, Jimenez AG, Tao H, Do PH, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone MD, Sanford JR. An intronic RNA element modulates Factor VIII exon-16 splicing. Nucleic Acids Res 2024; 52:300-315. [PMID: 37962303 PMCID: PMC10783525 DOI: 10.1093/nar/gkad1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Pathogenic variants in the human Factor VIII (F8) gene cause Hemophilia A (HA). Here, we investigated the impact of 97 HA-causing single-nucleotide variants on the splicing of 11 exons from F8. For the majority of F8 exons, splicing was insensitive to the presence of HA-causing variants. However, splicing of several exons, including exon-16, was impacted by variants predicted to alter exonic splicing regulatory sequences. Using exon-16 as a model, we investigated the structure-function relationship of HA-causing variants on splicing. Intriguingly, RNA chemical probing analyses revealed a three-way junction structure at the 3'-end of intron-15 (TWJ-3-15) capable of sequestering the polypyrimidine tract. We discovered antisense oligonucleotides (ASOs) targeting TWJ-3-15 partially rescue splicing-deficient exon-16 variants by increasing accessibility of the polypyrimidine tract. The apical stem loop region of TWJ-3-15 also contains two hnRNPA1-dependent intronic splicing silencers (ISSs). ASOs blocking these ISSs also partially rescued splicing. When used in combination, ASOs targeting both the ISSs and the region sequestering the polypyrimidine tract, fully rescue pre-mRNA splicing of multiple HA-linked variants of exon-16. Together, our data reveal a putative RNA structure that sensitizes F8 exon-16 to aberrant splicing.
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Affiliation(s)
- Victor Tse
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Guillermo Chacaltana
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Martin Gutierrez
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Nicholas M Forino
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Arcelia G Jimenez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Hanzhang Tao
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Phong H Do
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Catherine Oh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Priyanka Chary
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Isabel Quesada
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Antonia Hamrick
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sophie Lee
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jeremy R Sanford
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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2
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Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Cech TR, Rouskin S, Stone MD. Dissecting telomerase RNA structural heterogeneity in living human cells with DMS-MaPseq. bioRxiv 2023:2023.10.04.560962. [PMID: 37873413 PMCID: PMC10592977 DOI: 10.1101/2023.10.04.560962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features required for hTERT binding. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.
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Affiliation(s)
- Nicholas M Forino
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Jia Zheng Woo
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Arthur J Zaug
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | | | - Thomas R Cech
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
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3
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Hentschel J, Badstübner M, Choi J, Bagshaw CR, Lapointe CP, Wang J, Jansson LI, Puglisi JD, Stone MD. Real-time detection of human telomerase DNA synthesis by multiplexed single-molecule FRET. Biophys J 2023; 122:3447-3457. [PMID: 37515327 PMCID: PMC10502476 DOI: 10.1016/j.bpj.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Genomic stability in proliferating cells critically depends on telomere maintenance by telomerase reverse transcriptase. Here we report the development and proof-of-concept results of a single-molecule approach to monitor the catalytic activity of human telomerase in real time and with single-nucleotide resolution. Using zero-mode waveguides and multicolor FRET, we recorded the processive addition of multiple telomeric repeats to individual DNA primers. Unlike existing biophysical and biochemical tools, the novel approach enables the quantification of nucleotide-binding kinetics before nucleotide incorporation. Moreover, it provides a means to dissect the unique translocation dynamics that telomerase must undergo after synthesis of each hexameric DNA repeat. We observed an unexpectedly prolonged binding dwell time of dGTP in the enzyme active site at the start of each repeat synthesis cycle, suggesting that telomerase translocation is composed of multiple rate-contributing sub-steps that evade classical biochemical analysis.
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Affiliation(s)
- Jendrik Hentschel
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California; Department of Structural Biology, Stanford University School of Medicine, Stanford, California
| | - Mareike Badstübner
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California
| | - Linnea I Jansson
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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4
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Hassan N, Gregson CL, Tang H, van der Kamp M, Leo P, McInerney‐Leo AM, Zheng J, Brandi ML, Tang JCY, Fraser W, Stone MD, Grundberg E, Brown MA, Duncan EL, Tobias JH. Rare and Common Variants in GALNT3 May Affect Bone Mass Independently of Phosphate Metabolism. J Bone Miner Res 2023; 38:678-691. [PMID: 36824040 PMCID: PMC10729283 DOI: 10.1002/jbmr.4795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Anabolic treatment options for osteoporosis remain limited. One approach to discovering novel anabolic drug targets is to identify genetic causes of extreme high bone mass (HBM). We investigated a pedigree with unexplained HBM within the UK HBM study, a national cohort of probands with HBM and their relatives. Whole exome sequencing (WES) in a family with HBM identified a rare heterozygous missense variant (NM_004482.4:c.1657C > T, p.Arg553Trp) in GALNT3, segregating appropriately. Interrogation of data from the UK HBM study and the Anglo-Australasian Osteoporosis Genetics Consortium (AOGC) revealed an unrelated individual with HBM with another rare heterozygous variant (NM_004482.4:c.831 T > A, p.Asp277Glu) within the same gene. In silico protein modeling predicted that p.Arg553Trp would disrupt salt-bridge interactions, causing instability of GALNT3, and that p.Asp277Glu would disrupt manganese binding and consequently GALNT3 catalytic function. Bi-allelic loss-of-function GALNT3 mutations alter FGF23 metabolism, resulting in hyperphosphatemia and causing familial tumoral calcinosis (FTC). However, bone mineral density (BMD) in FTC cases, when reported, has been either normal or low. Common variants in the GALNT3 locus show genome-wide significant associations with lumbar, femoral neck, and total body BMD. However, no significant associations with BMD are observed at loci coding for FGF23, its receptor FGFR1, or coreceptor klotho. Mendelian randomization analysis, using expression quantitative trait loci (eQTL) data from primary human osteoblasts and genome-wide association studies data from UK Biobank, suggested increased expression of GALNT3 reduces total body, lumbar spine, and femoral neck BMD but has no effect on phosphate concentrations. In conclusion, rare heterozygous loss-of-function variants in GALNT3 may cause HBM without altering phosphate concentration. These findings suggest that GALNT3 may affect BMD through pathways other than FGF23 regulation, the identification of which may yield novel anabolic drug targets for osteoporosis. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Celia L. Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Haotian Tang
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Paul Leo
- Faculty of Health, Translational Genomics Group, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Aideen M. McInerney‐Leo
- The Faculty of Medicine, Frazer InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Jie Zheng
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai National Clinical Research Center for metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR ChinaShanghai Jiao Tong University School of MedicineShanghaiChina
- Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | | | - Jonathan C. Y. Tang
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Clinical Biochemistry, Departments of Laboratory MedicineNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - William Fraser
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
- Department of Diabetes, Endocrinology and Clinical BiochemistryNorfolk and Norwich University Hospital NHS Foundation TrustNorwichUK
| | - Michael D. Stone
- University Hospital LlandoughCardiff & Vale University Health BoardCardiffUK
| | - Elin Grundberg
- Genomic Medicine CenterChildren's Mercy Kansas CityKansas CityMissouriUSA
| | | | | | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Jonathan H. Tobias
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- MRC Integrated Epidemiology Unit, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
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5
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Tse V, Chacaltana G, Gutierrez M, Forino NM, Jimenez AG, Tao H, Do PH, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone MD, Sanford JR. Rescue of blood coagulation Factor VIII exon-16 mis-splicing by antisense oligonucleotides. bioRxiv 2023:2023.03.31.535160. [PMID: 37034721 PMCID: PMC10081312 DOI: 10.1101/2023.03.31.535160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The human Factor VIII ( F8 ) protein is essential for the blood coagulation cascade and specific F8 mutations cause the rare bleeding disorder Hemophilia A (HA). Here, we investigated the impact of HA-causing single-nucleotide mutations on F8 pre-mRNA splicing. We found that 14/97 (∼14.4%) coding sequence mutations tested in our study induced exon skipping. Splicing patterns of 4/11 (∼36.4%) F8 exons tested were especially sensitive to the presence of common disease-causing mutations. RNA-chemical probing analyses revealed a three-way junction structure at the 3' end of intron 15 (TWJ-3-15). TWJ-3-15 sequesters the polypyrimidine tract, a key determinant of 3' splice site strength. Using exon-16 of the F8 gene as a model, we designed specific antisense oligonucleotides (ASOs) that target TWJ-3-15 and identified three that promote the splicing of F8 exon-16. Interaction of TWJ-3-15 with ASOs increases accessibility of the polypyrimidine tract and inhibits the binding of hnRNPA1-dependent splicing silencing factors. Moreover, ASOs targeting TWJ-3-15 rescue diverse splicing-sensitive HA-causing mutations, most of which are distal to the 3' splice site being impacted. The TWJ-3-15 structure and its effect on mRNA splicing provide a model for HA etiology in patients harboring specific F8 mutations and provide a framework for precision RNA-based HA therapies.
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6
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Banijamali E, Baronti L, Becker W, Sajkowska-Kozielewicz JJ, Huang T, Palka C, Kosek D, Sweetapple L, Müller J, Stone MD, Andersson ER, Petzold K. RNA:RNA interaction in ternary complexes resolved by chemical probing. RNA 2023; 29:317-329. [PMID: 36617673 PMCID: PMC9945442 DOI: 10.1261/rna.079190.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA regulation can be performed by a second targeting RNA molecule, such as in the microRNA regulation mechanism. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) probes the structure of RNA molecules and can resolve RNA:protein interactions, but RNA:RNA interactions have not yet been addressed with this technique. Here, we apply SHAPE to investigate RNA-mediated binding processes in RNA:RNA and RNA:RNA-RBP complexes. We use RNA:RNA binding by SHAPE (RABS) to investigate microRNA-34a (miR-34a) binding its mRNA target, the silent information regulator 1 (mSIRT1), both with and without the Argonaute protein, constituting the RNA-induced silencing complex (RISC). We show that the seed of the mRNA target must be bound to the microRNA loaded into RISC to enable further binding of the compensatory region by RISC, while the naked miR-34a is able to bind the compensatory region without seed interaction. The method presented here provides complementary structural evidence for the commonly performed luciferase-assay-based evaluation of microRNA binding-site efficiency and specificity on the mRNA target site and could therefore be used in conjunction with it. The method can be applied to any nucleic acid-mediated RNA- or RBP-binding process, such as splicing, antisense RNA binding, or regulation by RISC, providing important insight into the targeted RNA structure.
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Affiliation(s)
- Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lorenzo Baronti
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Walter Becker
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | | | - Ting Huang
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Christina Palka
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - David Kosek
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Lara Sweetapple
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Juliane Müller
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, 17177 Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
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7
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Abstract
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Telomeres are essential
chromosome end capping structures that
safeguard the genome from dangerous DNA processing events. DNA strand
invasion occurs during vital transactions at telomeres, including
telomere length maintenance by the alternative lengthening of telomeres
(ALT) pathway. During telomeric strand invasion, a single-stranded
guanine-rich (G-rich) DNA invades at a complementary duplex telomere
repeat sequence, forming a displacement loop (D-loop) in which the
displaced DNA consists of the same G-rich sequence as the invading
single-stranded DNA. Single-stranded G-rich telomeric DNA readily
folds into stable, compact, structures called G-quadruplexes (GQs)
in vitro and is anticipated to form within the context of a D-loop;
however, evidence supporting this hypothesis is lacking. Here, we
report a magnetic tweezers assay that permits the controlled formation
of telomeric D-loops (TDLs) within uninterrupted duplex human telomere
DNA molecules of physiologically relevant lengths. Our results are
consistent with a model wherein the displaced single-stranded DNA
of a TDL fold into a GQ. This study provides new insight into telomere
structure and establishes a framework for the development of novel
therapeutics designed to target GQs at telomeres in cancer cells.
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Affiliation(s)
- Terren R. Chang
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, United States
| | - Xi Long
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, United States
| | - Shankar Shastry
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, United States
- 10X Genomics, 6230 Stoneridge Mall Rd, Pleasanton, California 94588, United States
| | - Joseph W. Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, United States
- Invitae, 1400 16th St, San Francisco, California 94103, United States
| | - Michael D. Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, United States
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8
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Forino N, Stone MD. Dissection of structural heterogeneity in human telomerase RNA. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Chang T, Draper JM, Van den Bout A, Kephart E, Maul-Newby H, Vasquez Y, Woodbury J, Randi S, Pedersen M, Nave M, La S, Gallagher N, McCabe MM, Dhillon N, Bjork I, Luttrell M, Dang F, MacMillan JB, Green R, Miller E, Kilpatrick AM, Vaske O, Stone MD, Sanford JR. A method for campus-wide SARS-CoV-2 surveillance at a large public university. PLoS One 2021; 16:e0261230. [PMID: 34919584 PMCID: PMC8682906 DOI: 10.1371/journal.pone.0261230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.
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Affiliation(s)
- Terren Chang
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jolene M. Draper
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Anouk Van den Bout
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ellen Kephart
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hannah Maul-Newby
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Yvonne Vasquez
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jason Woodbury
- Thirdwave Analytics, San Francisco, California, United States of America
| | - Savanna Randi
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Martina Pedersen
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Maeve Nave
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Scott La
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Natalie Gallagher
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Molly M. McCabe
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Namrita Dhillon
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Isabel Bjork
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael Luttrell
- Business and Accounting Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Frank Dang
- University of California Davis, Davis, California, United States of America
| | - John B. MacMillan
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ralph Green
- University of California Davis, Davis, California, United States of America
| | - Elizabeth Miller
- Student Health Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Auston M. Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Olena Vaske
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael D. Stone
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jeremy R. Sanford
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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10
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Bagshaw CR, Hentschel J, Stone MD. The Processivity of Telomerase: Insights from Kinetic Simulations and Analyses. Molecules 2021; 26:7532. [PMID: 34946615 PMCID: PMC8705835 DOI: 10.3390/molecules26247532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Telomerases are moderately processive reverse transcriptases that use an integral RNA template to extend the 3' end of linear chromosomes. Processivity values, defined as the probability of extension rather than dissociation, range from about 0.7 to 0.99 at each step. Consequently, an average of tens to hundreds of nucleotides are incorporated before the single-stranded sDNA product dissociates. The RNA template includes a six nucleotide repeat, which must be reset in the active site via a series of translocation steps. Nucleotide addition associated with a translocation event shows a lower processivity (repeat addition processivity, RAP) than that at other positions (nucleotide addition processivity, NAP), giving rise to a characteristic strong band every 6th position when the product DNA is analyzed by gel electrophoresis. Here, we simulate basic reaction mechanisms and analyze the product concentrations using several standard procedures to show how the latter can give rise to systematic errors in the processivity estimate. Complete kinetic analysis of the time course of DNA product concentrations following a chase with excess unlabeled DNA primer (i.e., a pulse-chase experiment) provides the most rigorous approach. This analysis reveals that the higher product concentrations associated with RAP arise from a stalling of nucleotide incorporation reaction during translocation rather than an increased rate constant for the dissociation of DNA from the telomerase.
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Affiliation(s)
- Clive R. Bagshaw
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA;
| | - Jendrik Hentschel
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA;
- Element Biosciences, 9880 Campus Point Drive, San Diego, CA 92121, USA
| | - Michael D. Stone
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA;
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11
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Palka C, Forino NM, Hentschel J, Das R, Stone MD. Folding heterogeneity in the essential human telomerase RNA three-way junction. RNA 2020; 26:1787-1800. [PMID: 32817241 PMCID: PMC7668248 DOI: 10.1261/rna.077255.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Telomeres safeguard the genome by suppressing illicit DNA damage responses at chromosome termini. To compensate for incomplete DNA replication at telomeres, most continually dividing cells, including many cancers, express the telomerase ribonucleoprotein (RNP) complex. Telomerase maintains telomere length by catalyzing de novo synthesis of short DNA repeats using an internal telomerase RNA (TR) template. TRs from diverse species harbor structurally conserved domains that contribute to RNP biogenesis and function. In vertebrate TRs, the conserved regions 4 and 5 (CR4/5) fold into a three-way junction (TWJ) that binds directly to the telomerase catalytic protein subunit and is required for telomerase function. We have analyzed the structural properties of the human TR (hTR) CR4/5 domain using a combination of in vitro chemical mapping, secondary structural modeling, and single-molecule structural analysis. Our data suggest the essential P6.1 stem-loop within CR4/5 is not stably folded in the absence of the telomerase reverse transcriptase in vitro. Rather, the hTR CR4/5 domain adopts a heterogeneous ensemble of conformations. Finally, single-molecule FRET measurements of CR4/5 and a mutant designed to stabilize the P6.1 stem demonstrate that TERT binding selects for a structural conformation of CR4/5 that is not the dominant state of the TERT-free in vitro RNA ensemble.
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Affiliation(s)
- Christina Palka
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Nicholas M Forino
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | - Jendrik Hentschel
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, California 94305, USA
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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12
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Ralston SH, Corral-Gudino L, Cooper C, Francis RM, Fraser WD, Gennari L, Guanabens N, Javaid MK, Layfield R, O'Neill TW, Russell RGG, Stone MD, Simpson K, Wilkinson D, Wills R, Zillikens MC, Tuck SP. Clinical Guidelines on Paget's Disease of Bone. J Bone Miner Res 2019; 34:2327-2329. [PMID: 31651997 DOI: 10.1002/jbmr.3873] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/12/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Stuart H Ralston
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Luis Corral-Gudino
- Internal Medicine Department, Hospital Universitario Río Hortega, University of Valladolid, Valladolid, Spain
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | | | - William D Fraser
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK
| | - Luigi Gennari
- Department of Medicine, Surgery and Neurosciences, University of Siena, Policlinico Santa Maria alle Scotte, Siena, Italy
| | - Nuria Guanabens
- Hospital Clinic, IDIBAPS, CiberEHD, University of Barcelona, Barcelona, Spain
| | - M Kassim Javaid
- Botnar Research Centre, NDORMS, University of Oxford, Oxford, UK
| | - Robert Layfield
- University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Terence W O'Neill
- Centre for Epidemiology Versus Arthritis, University of Manchester, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Robert Graham G Russell
- Botnar Research Centre, NDORMS, University of Oxford, Oxford, UK.,The Mellanby Centre for Bone Research, University of Sheffield, Sheffield, UK
| | - Michael D Stone
- Bone Research Unit, University Hospital Llandough, Penarth, UK
| | - Keith Simpson
- Paget's Association, Moorfield House, Manchester, UK
| | | | - Ruth Wills
- International Medical Press, Admiral House, London, UK
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stephen P Tuck
- Department of Rheumatology, The James Cook University Hospital, Middlesbrough, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
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13
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Abstract
The original discovery of enzymes that synthesize DNA using an RNA template appeared to contradict the central dogma of biology, in which information is transferred, in a unidirectional way, from DNA genes into RNA molecules. The paradigm-shifting discovery of RNA-dependent DNA polymerases, also called reverse transcriptases (RTs), reshaped existing views for how cells function; however, the scope of the impact RTs impose on biology had yet to be realized. In the decades of research since the early 1970s, the biomedical and biotechnological significance of retroviral RTs, as well as the evolutionarily related telomerase enzyme, has become exceedingly clear. One common theme that has emerged in the course of RT-related research is the central role of nucleic acid binding and dynamics during enzyme function. However, directly interrogating these dynamic properties is challenging because of the stochastic properties of biological macromolecules. In this review, we describe how the development of single-molecule biophysical techniques has opened new windows through which to observe the dynamic behavior of this remarkable class of enzymes. Specifically, we focus on how the powerful single-molecule Förster resonance energy transfer (FRET) method has been exploited to study the structure and function of the human immunodeficiency virus (HIV) RT and telomerase ribonucleoprotein (RNP) enzymes. These exciting studies have refined our understanding of RT catalysis, have revealed unforeseen structural rearrangements between RTs and their nucleic acid substrates, and have helped to characterize the mode of action of RT-inhibiting drugs. We conclude with a discussion of how the ongoing development of single-molecule technologies will continue to empower researchers to probe RT mechanisms in new and exciting ways.
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Affiliation(s)
- Linnea I Jansson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064.,The Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064
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14
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Collins FL, Stone MD, Turton J, McCabe LR, Wang ECY, Williams AS. Oestrogen-deficiency induces bone loss by modulating CD14 + monocyte and CD4 + T cell DR3 expression and serum TL1A levels. BMC Musculoskelet Disord 2019; 20:326. [PMID: 31299941 PMCID: PMC6626337 DOI: 10.1186/s12891-019-2704-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Background Oestrogen-deficiency induced by menopause is associated with reduced bone density and primary osteoporosis, resulting in an increased risk of fracture. While the exact etiology of menopause-induced primary osteoporotic bone loss is not fully known, members of the tumour necrosis factor super family (TNFSF) are known to play a role. Recent studies have revealed that the TNFSF members death receptor 3 (DR3) and one of its ligands, TNF-like protein 1A (TL1A) have a key role in secondary osteoporosis; enhancing CD14+ peripheral blood mononuclear cell (PBMC) osteoclast formation and bone resorption. Whether DR3 and TL1A contribute towards bone loss in menopause-induced primary osteoporosis however, remains unknown. Methods To investigate this we performed flow cytometry analysis of DR3 expression on CD14+ PBMCs isolated from pre- and early post-menopausal females and late post-menopausal osteoporotic patients. Serum levels of TL1A, CCL3 and total MMP-9 were measured by ELISA. In vitro osteoclast differentiation assays were performed to determine CD14+ monocyte osteoclastogenic potential. In addition, splenic CD4+ T cell DR3 expression was investigated 1 week and 8 weeks post-surgery, using the murine ovariectomy model. Results In contrast to pre-menopausal females, CD14+ monocytes isolated from post-menopausal females were unable to induce DR3 expression. Serum TL1A levels were decreased approx. 2-fold in early post-menopausal females compared to pre-menopausal controls and post-menopausal osteoporotic females; no difference was observed between pre-menopausal and late post-menopausal osteoporotic females. Analysis of in vitro CD14+ monocyte osteoclastogenic potential revealed no significant difference between the post-menopausal and post-menopausal osteoporotic cohorts. Interestingly, in the murine ovariectomy model splenic CD4+ T cell DR3 expression was significantly increased at 1 week but not 8 weeks post-surgery when compared to the sham control. Conclusion Our results reveals for the first time that loss of oestrogen has a significant effect on DR3; decreasing expression on CD14+ monocytes and increasing expression on CD4+ T cells. These data suggest that while oestrogen-deficiency induced changes in DR3 expression do not affect late post-menopausal bone loss they could potentially have an indirect role in early menopausal bone loss through the modulation of T cell activity.
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Affiliation(s)
- Fraser L Collins
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK. .,Department of Physiology, Michigan State University, East Lansing, MI, USA.
| | - Michael D Stone
- University Hospital Llandough, Cardiff & Vale University Health Board, Cardiff, UK
| | - Jane Turton
- University Hospital Llandough, Cardiff & Vale University Health Board, Cardiff, UK
| | - Laura R McCabe
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Eddie C Y Wang
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Anwen S Williams
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
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15
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Ralston SH, Corral-Gudino L, Cooper C, Francis RM, Fraser WD, Gennari L, Guañabens N, Javaid MK, Layfield R, O'Neill TW, Russell RGG, Stone MD, Simpson K, Wilkinson D, Wills R, Zillikens MC, Tuck SP. Diagnosis and Management of Paget's Disease of Bone in Adults: A Clinical Guideline. J Bone Miner Res 2019; 34:579-604. [PMID: 30803025 PMCID: PMC6522384 DOI: 10.1002/jbmr.3657] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 12/21/2022]
Abstract
An evidence-based clinical guideline for the diagnosis and management of Paget's disease of bone (PDB) was developed using GRADE methodology, by a Guideline Development Group (GDG) led by the Paget's Association (UK). A systematic review of diagnostic tests and pharmacological and nonpharmacological treatment options was conducted that sought to address several key questions of clinical relevance. Twelve recommendations and five conditional recommendations were made, but there was insufficient evidence to address eight of the questions posed. The following recommendations were identified as the most important: 1) Radionuclide bone scans, in addition to targeted radiographs, are recommended as a means of fully and accurately defining the extent of metabolically active disease in patients with PDB. 2) Serum total alkaline phosphatase (ALP) is recommended as a first-line biochemical screening test in combination with liver function tests in screening for the presence of metabolically active PDB. 3) Bisphosphonates are recommended for the treatment of bone pain associated with PDB. Zoledronic acid is recommended as the bisphosphonate most likely to give a favorable pain response. 4) Treatment aimed at improving symptoms is recommended over a treat-to-target strategy aimed at normalizing total ALP in PDB. 5) Total hip or knee replacements are recommended for patients with PDB who develop osteoarthritis in whom medical treatment is inadequate. There is insufficient information to recommend one type of surgical approach over another. The guideline was endorsed by the European Calcified Tissues Society, the International Osteoporosis Foundation, the American Society of Bone and Mineral Research, the Bone Research Society (UK), and the British Geriatric Society. The GDG noted that there had been a lack of research on patient-focused clinical outcomes in PDB and identified several areas where further research was needed. © 2019 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals Inc.
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Affiliation(s)
- Stuart H Ralston
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Luis Corral-Gudino
- Internal Medicine Department, Hospital Universitario Río Hortega, University of Valladolid, Valladolid, Spain
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.,Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - William D Fraser
- Norwich Medical School, Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, UK
| | - Luigi Gennari
- Department of Medicine, Surgery, and Neurosciences, University of Siena, Siena, Italy
| | - Núria Guañabens
- Hospital Clinic, IDIBAPS, CiberEHD, University of Barcelona, Barcelona, Spain
| | - M Kassim Javaid
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Robert Layfield
- School of Life Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham, UK
| | - Terence W O'Neill
- Arthritis Research UK Centre for Epidemiology, University of Manchester, Manchester, UK.,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - R Graham G Russell
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK.,The Mellanby Centre for Bone Research, University of Sheffield, Sheffield, UK
| | - Michael D Stone
- Bone Research Unit, University Hospital Llandough, Penarth, UK
| | - Keith Simpson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Diana Wilkinson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - M Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Stephen P Tuck
- Department of Rheumatology, The James Cook University Hospital, Middlesbrough, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
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16
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17
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Shastry S, Steinberg-Neifach O, Lue N, Stone MD. Direct observation of nucleic acid binding dynamics by the telomerase essential N-terminal domain. Nucleic Acids Res 2018; 46:3088-3102. [PMID: 29474579 PMCID: PMC5887506 DOI: 10.1093/nar/gky117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/31/2018] [Accepted: 02/17/2018] [Indexed: 11/12/2022] Open
Abstract
Telomerase is a specialized enzyme that maintains telomere length by adding DNA repeats to chromosome ends. The catalytic protein subunit of telomerase utilizes the integral telomerase RNA to direct telomere DNA synthesis. The telomerase essential N-terminal (TEN) domain is required for enzyme function; however, the precise mechanism of the TEN domain during catalysis is not known. We report a single-molecule study of dynamic TEN-induced conformational changes in its nucleic acid substrates. The TEN domain from the yeast Candida parapsilosis (Cp) exhibits a strong binding preference for double-stranded nucleic acids, with particularly high affinity for an RNA-DNA hybrid mimicking the template-product complex. Surprisingly, the telomere DNA repeat sequence from C. parapsilosis forms a DNA hairpin that also binds CpTEN with high affinity. Mutations to several residues in a putative nucleic acid-binding patch of CpTEN significantly reduced its affinity to the RNA-DNA hybrid and telomere DNA hairpin. Substitution of comparable residues in the related Candida albicans TEN domain caused telomere maintenance defects in vivo and decreased primer extension activity in vitro. Collectively, our results support a working model in which dynamic interactions with telomere DNA and the template-product hybrid underlie the functional requirement for the TEN domain during the telomerase catalytic cycle.
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Affiliation(s)
- Shankar Shastry
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Olga Steinberg-Neifach
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Neal Lue
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
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18
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Long X, Chang T, Shastry S, Parks JW, Stone MD. Direct Measurement of Torque Induced Telomere Strand Invasion using Magnetic Tweezers. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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19
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Musgrove C, Jansson LI, Stone MD. New perspectives on telomerase RNA structure and function. Wiley Interdiscip Rev RNA 2017; 9. [PMID: 29124890 DOI: 10.1002/wrna.1456] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/08/2017] [Accepted: 09/18/2017] [Indexed: 12/20/2022]
Abstract
Telomerase is an ancient ribonucleoprotein (RNP) that protects the ends of linear chromosomes from the loss of critical coding sequences through repetitive addition of short DNA sequences. These repeats comprise the telomere, which together with many accessory proteins, protect chromosomal ends from degradation and unwanted DNA repair. Telomerase is a unique reverse transcriptase (RT) that carries its own RNA to use as a template for repeat addition. Over decades of research, it has become clear that there are many diverse, crucial functions played by telomerase RNA beyond simply acting as a template. In this review, we highlight recent findings in three model systems: ciliates, yeast and vertebrates, that have shifted the way the field views the structural and mechanistic role(s) of RNA within the functional telomerase RNP complex. Viewed in this light, we hope to demonstrate that while telomerase RNA is just one example of the myriad functional RNA in the cell, insights into its structure and mechanism have wide-ranging impacts. WIREs RNA 2018, 9:e1456. doi: 10.1002/wrna.1456 This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Cherie Musgrove
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Linnea I Jansson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.,Center for Molecular Biology of RNA, University of California, Santa Cruz, CA, USA
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20
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Collins FL, Williams JO, Bloom AC, Singh RK, Jordan L, Stone MD, McCabe LR, Wang ECY, Williams AS. CCL3 and MMP-9 are induced by TL1A during death receptor 3 (TNFRSF25)-dependent osteoclast function and systemic bone loss. Bone 2017; 97:94-104. [PMID: 28062298 PMCID: PMC5378198 DOI: 10.1016/j.bone.2017.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/23/2016] [Accepted: 01/03/2017] [Indexed: 12/11/2022]
Abstract
Reduced bone density and secondary osteoporosis, resulting in increased risk of fracture, is a significant complicating factor in the inflammatory arthritides. While the exact etiology of systemic bone loss is not fully elucidated, recent insights into the tumor necrosis factor super family (TNFSF) revealed a potential role for death receptor 3 (DR3/TNFRSF25) and one of its ligands, TNF-like protein 1A (TL1A/TNFSF15). The mechanisms by which DR3/TL1A signalling modulates bone loss are unclear. We investigated the effect of DR3/TL1A signalling upon osteoclast-dependent chemokine and MMP production to unravel novel mechanisms whereby this pathway regulates OC formation and OC-dependent bone resorption. Collagen induced arthritis (CIA) was established in DR3wt and DR3ko mice, joints were sectioned and analysed histologically for bone damage while systemic trabecular bone loss distal to the affected joints was compared by micro-CT. Ablation of DR3 protected DBA/1 mice against the development and progression of CIA. In DR3ko, joints of the ankle and mid-foot were almost free of bone erosions and long bones of mice with CIA were protected against systemic trabecular bone loss. In vitro, expression of DR3 was confirmed on primary human CD14+ osteoclast precursors by flow cytometry. These cells were treated with TL1A in osteoclast differentiation medium and TRAP+ osteoclasts, bone resorption, levels of osteoclast-associated chemokines (CCL3, CCL2 and CXCL8) and MMP-9 measured. TL1A intensified human osteoclast differentiation and bone resorption and increased osteoclast-associated production of CCL3 and MMP-9. Our data reveals the DR3 pathway as an attractive therapeutic target to combat adverse bone pathology associated with inflammatory arthritis. We demonstrate that DR3 is critical in the pathogenesis of murine CIA and associated secondary osteoporosis. Furthermore, we identify a novel mechanism by which the DR3/TL1A pathway directly enhances human OC formation and resorptive activity, controlling expression and activation of CCL3 and MMP-9.
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Affiliation(s)
- Fraser L Collins
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom; Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Jessica O Williams
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Anja C Bloom
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Ravinder K Singh
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Lauren Jordan
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael D Stone
- University Hospital Llandough, Cardiff & Vale University Health Board, Cardiff, United Kingdom
| | - Laura R McCabe
- Department of Physiology, Michigan State University, East Lansing, MI, USA; Department of Radiology, Michigan State University, East Lansing, MI, USA; Biomedical Imaging Research Centre, Michigan State University, East Lansing, MI, USA
| | - Eddie C Y Wang
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.
| | - Anwen S Williams
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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21
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Abstract
Telomeres are specialized chromatin structures that protect chromosome ends from dangerous processing events. In most tissues, telomeres shorten with each round of cell division, placing a finite limit on cell growth. In rapidly dividing cells, including the majority of human cancers, cells bypass this growth limit through telomerase-catalyzed maintenance of telomere length. The dynamic properties of telomeres and telomerase render them difficult to study using ensemble biochemical and structural techniques. This review describes single-molecule approaches to studying how individual components of telomeres and telomerase contribute to function. Single-molecule methods provide a window into the complex nature of telomeres and telomerase by permitting researchers to directly visualize and manipulate the individual protein, DNA, and RNA molecules required for telomere function. The work reviewed in this article highlights how single-molecule techniques have been utilized to investigate the function of telomeres and telomerase.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Center for Molecular Biology of RNA, Santa Cruz, California 95064
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22
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Parks JW, Kappel K, Das R, Stone MD. Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. RNA 2017; 23:175-188. [PMID: 28096444 PMCID: PMC5238793 DOI: 10.1261/rna.058743.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein. FRET-guided modeling places the essential pseudoknot fold distal to the active site on a protein surface comprising the C-terminal element, a domain that shares structural homology with canonical polymerase thumb domains. An independently solved medium-resolution structure of Tetrahymena telomerase provides a blind test of our modeling methodology and sheds light on the structural homology of this domain across diverse organisms. Our smFRET-Rosetta models reveal nanometer-scale rearrangements within the RNA core domain during catalysis. Taken together, our FRET data and pseudoatomic molecular models permit us to propose a possible mechanism for how RNA core domain rearrangement is coupled to template hybrid elongation.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, California 94305, USA
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
- Department of Physics, Stanford University, Stanford, California 94305, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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Long X, Parks JW, Stone MD. Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Methods 2016; 105:16-25. [PMID: 27320203 DOI: 10.1016/j.ymeth.2016.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 02/02/2023] Open
Abstract
Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph W Parks
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA; Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
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Beattie JR, Cummins NM, Caraher C, O’Driscoll OM, Bansal AT, Eastell R, Ralston SH, Stone MD, Pearson G, Towler MR. Raman Spectroscopic Analysis of Fingernail Clippings Can Help Differentiate Between Postmenopausal Women Who Have and Have Not Suffered a Fracture. Clin Med Insights Arthritis Musculoskelet Disord 2016; 9:109-16. [PMID: 27429561 PMCID: PMC4939848 DOI: 10.4137/cmamd.s38493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 11/23/2022]
Abstract
Raman spectroscopy was applied to nail clippings from 633 postmenopausal British and Irish women, from six clinical sites, of whom 42% had experienced a fragility fracture. The objective was to build a prediction algorithm for fracture using data from four sites (known as the calibration set) and test its performance using data from the other two sites (known as the validation set). Results from the validation set showed that a novel algorithm, combining spectroscopy data with clinical data, provided area under the curve (AUC) of 74% compared to an AUC of 60% from a reduced QFracture score (a clinically accepted risk calculator) and 61% from the dual-energy X-ray absorptiometry T-score, which is in current use for the diagnosis of osteoporosis. Raman spectroscopy should be investigated further as a noninvasive tool for the early detection of enhanced risk of fragility fracture.
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Affiliation(s)
| | - Niamh M. Cummins
- Centre for Interventions in Infection, Inflammation and Immunity (4i), Graduate Entry Medical School, University of Limerick, Limerick, Ireland
| | | | - Olive M. O’Driscoll
- Medical Engineering Design & Innovation Centre, Cork Institute of Technology, Cork, Ireland
| | | | - Richard Eastell
- Academic Unit of Bone Metabolism, Metabolic Bone Centre, Northern General Hospital, Sheffield, UK
| | - Stuart H. Ralston
- School of Molecular and Clinical Medicine, Western General Hospital, Edinburgh, UK
| | | | - Gill Pearson
- Osteoporosis Centre, University Hospital Southampton Foundation Trust, Southampton, UK
| | - Mark R. Towler
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur, Malaysia
- Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, Canada
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Jansson LI, Akiyama BM, Ooms A, Lu C, Rubin SM, Stone MD. Structural basis of template-boundary definition in Tetrahymena telomerase. Nat Struct Mol Biol 2015; 22:883-8. [PMID: 26436828 PMCID: PMC4654688 DOI: 10.1038/nsmb.3101] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/02/2015] [Indexed: 01/07/2023]
Abstract
Telomerase is required to maintain repetitive G-rich telomeric DNA sequences at chromosome ends. To do so, the telomerase reverse transcriptase (TERT) subunit reiteratively uses a small region of the integral telomerase RNA (TER) as a template. An essential feature of telomerase catalysis is the strict definition of the template boundary to determine the precise TER nucleotides to be reverse transcribed by TERT. We report the 3-Å crystal structure of the Tetrahymena TERT RNA-binding domain (tTRBD) bound to the template boundary element (TBE) of TER. tTRBD is wedged into the base of the TBE RNA stem-loop, and each of the flanking RNA strands wraps around opposite sides of the protein domain. The structure illustrates how the tTRBD establishes the template boundary by positioning the TBE at the correct distance from the TERT active site to prohibit copying of nontemplate nucleotides.
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Affiliation(s)
- Linnea I Jansson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Ben M Akiyama
- Department of Chemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, Colorado, USA
| | - Alexandra Ooms
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cheng Lu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
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Al-Azzani WAK, Evans L, Speight L, Lea-Davies M, Stone MD, Lau D, Ketchell RI, Duckers J. Hyperpharmacotherapy in ageing cystic fibrosis patients: The first report of an atypical hip fracture. Respir Med Case Rep 2015; 16:148-50. [PMID: 26744685 PMCID: PMC4682004 DOI: 10.1016/j.rmcr.2015.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 09/29/2015] [Indexed: 11/28/2022] Open
Abstract
Cystic fibrosis (CF) is a common autosomal recessive disorder in Caucasian populations with respiratory, gastrointestinal and endocrine manifestations. Thanks to recent advances in medical therapies and infection control, life expectancy of a patient with CF has significantly increased from less than 5 years in the mid-1900s to almost 50 years nowadays. However, as CF patients are living longer, multimorbidity and Hyperpharmacotherapy are becoming more common. This case illustrates a cascade of problems that ensued from medication side-effects, highlighting the increasing challenge of managing an ageing CF population.
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Affiliation(s)
- W A K Al-Azzani
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - L Evans
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - L Speight
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - M Lea-Davies
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - M D Stone
- Bone Unit, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - D Lau
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - R I Ketchell
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
| | - J Duckers
- All Wales Adult Cystic Fibrosis Centre, University Hospital Llandough, Cardiff, CF64 2XX, United Kingdom
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Akiyama BM, Parks JW, Stone MD. The telomerase essential N-terminal domain promotes DNA synthesis by stabilizing short RNA-DNA hybrids. Nucleic Acids Res 2015; 43:5537-49. [PMID: 25940626 PMCID: PMC4477650 DOI: 10.1093/nar/gkv406] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/15/2015] [Indexed: 01/11/2023] Open
Abstract
Telomerase is an enzyme that adds repetitive DNA sequences to the ends of chromosomes and consists of two main subunits: the telomerase reverse transcriptase (TERT) protein and an associated telomerase RNA (TER). The telomerase essential N-terminal (TEN) domain is a conserved region of TERT proposed to mediate DNA substrate interactions. Here, we have employed single molecule telomerase binding assays to investigate the function of the TEN domain. Our results reveal telomeric DNA substrates bound to telomerase exhibit a dynamic equilibrium between two states: a docked conformation and an alternative conformation. The relative stabilities of the docked and alternative states correlate with the number of basepairs that can be formed between the DNA substrate and the RNA template, with more basepairing favoring the docked state. The docked state is further buttressed by the TEN domain and mutations within the TEN domain substantially alter the DNA substrate structural equilibrium. We propose a model in which the TEN domain stabilizes short RNA–DNA duplexes in the active site of the enzyme, promoting the docked state to augment telomerase processivity.
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Affiliation(s)
- Benjamin M Akiyama
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
| | - Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064, USA
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Long X, Stone MD. Mechanical Properties and Strand Invasion of Duplex Telomere DNA Probed using Magnetic Tweezers. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.1926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Falcone TE, Stein DJ, Jumaily JS, Pearce EN, Holick MF, McAneny DB, Jalisi S, Grillone GA, Stone MD, Devaiah AK, Noordzij JP. Correlating pre-operative vitamin D status with post-thyroidectomy hypocalcemia. Endocr Pract 2014; 21:348-54. [PMID: 25536969 DOI: 10.4158/ep14264.or] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To examine the relationship between pre-operative vitamin D status and post-thyroidectomy hypocalcemia. METHODS Retrospective study examining 264 total and completion thyroidectomies conducted between 2007 and 2011. Subjects included had a recorded 25-hydroxyvitamin D (25[OH]D) level within 21 days prior to or 1 day following surgery, did not have a primary parathyroid gland disorder, and were not taking 1,25-dihydroxyvitamin D3 (calcitriol) prior to surgery. Some subjects were repleted with vitamin D pre-operatively if a low 25(OH)D level (typically below 20 ng/mL) was identified. Pre-operative 25(OH)D, concurrent neck dissection, integrity of parathyroid glands, final pathology, postoperative parathyroid hormone (PTH), calcium nadir and repletion, and length of stay were examined. RESULTS The mean pre-operative 25(OH)D for all subjects was 25 ng/mL, and the overall rate of post-operative hypocalcemia was 37.5%. Lower pre-operative 25(OH)D did not predict postoperative hypocalcemia (P = .96); however, it did predict the need for postoperative 1,25-dihydroxyvitamin D3 administration (P = .01). Lower postoperative PTH levels (P = .001) were associated with postoperative hypocalcemia. CONCLUSION Pre-operative 25(OH)D did not predict a postoperative decrease in serum calcium, although it did predict the need for 1,25-dihydroxyvitamin D3 therapy in hypocalcemic subjects. We recommend that 25(OH)D be assessed and, if indicated, repleted pre-operatively in patients undergoing total thyroidectomy.
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Evans BAJ, James TW, James K, Cox A, Farr L, Paisey SJ, Dempster DW, Stone MD, Griffiths PA, Hugtenburg RP, Brady SM, Wells T. Preclinical assessment of a new magnetic resonance-based technique for determining bone quality by characterization of trabecular microarchitecture. Calcif Tissue Int 2014; 95:506-20. [PMID: 25380571 DOI: 10.1007/s00223-014-9922-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/17/2014] [Indexed: 10/24/2022]
Abstract
The utility of HR-CT to study longitudinal changes in bone microarchitecture is limited by subject radiation exposure. Although MR is not subject to this limitation, it is limited both by patient movement that occurs during prolonged scanning at distal sites, and by the signal-to-noise ratio that is achievable for high-resolution images in a reasonable scan time at proximal sites. Recently, a novel MR-based technique, fine structure analysis (FSA) (Chase et al. Localised one-dimensional magnetic resonance spatial frequency spectroscopy. PCT/US2012/068284 2012, James and Chase Magnetic field gradient structure characteristic assessment using one-dimensional (1D) spatial frequency distribution analysis. 7932720 B2, 2011) has been developed which provides both high-resolution and fast scan times, but which generates at a designated set of spatial positions (voxels) a one-dimensional signal of spatial frequencies. Appendix 1 provides a brief introduction to FSA. This article describes an initial exploration of FSA for the rapid, non-invasive characterization of trabecular microarchitecture in a preclinical setting. For L4 vertebrae of sham and ovariectomized (OVX) rats, we compared FSA-generated metrics with those from CT datasets and from CT-derived histomorphometry parameters, trabecular number (Tb.N), bone volume density (BV/TV), trabecular thickness (Tb.Th) and trabecular separation (Tb.Sp). OVX caused a reduction of the higher frequency structures that correspond to a denser trabecular lattice, while increasing the preponderance of lower frequency structures, which correspond to a more open lattice. As one example measure, the centroid of the FSA spectrum (which we refer to as fSAcB) showed strong correlation in the same region with CT-derived histomorphometry values: Tb.Sp: r -0.63, p < 0.001; Tb.N: r 0.71, p < 0.001; BV/TV: r 0.64, p < 0.001, Tb.Th: r 0.44, p < 0.05. Furthermore, we found a 17.5% reduction in fSAcB in OVX rats (p < 0.0001). In a longitudinal study, FSA showed that the age-related increase in higher frequency structures was abolished in OVX rats, being replaced with a 78-194% increase in lower frequency structures (2.4-2.8 objects/mm range), indicating a more sparse trabecular lattice (p < 0.05). The MR-based fine structure analysis enables high-resolution, radiation-free, rapid quantification of bone structures in one dimension (the specific point and direction being chosen by the clinician) of the spine.
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Affiliation(s)
- B A J Evans
- Institute of Molecular and Experimental Medicine, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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Parks JW, Stone MD. Coordinated DNA dynamics during the human telomerase catalytic cycle. Nat Commun 2014; 5:4146. [PMID: 24923681 PMCID: PMC4107311 DOI: 10.1038/ncomms5146] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/15/2014] [Indexed: 11/09/2022] Open
Abstract
The human telomerase reverse transcriptase (hTERT) utilizes a template within the integral RNA subunit (hTR) to direct extension of telomeres. Telomerase exhibits repeat addition processivity (RAP) and must therefore translocate the nascent DNA product into a new RNA:DNA hybrid register to prime each round of telomere repeat synthesis. Here we use single-molecule FRET and nuclease protection assays to monitor telomere DNA structure and dynamics during the telomerase catalytic cycle. DNA translocation during RAP proceeds through a previously uncharacterized kinetic sub-step during which the 3′-end of the DNA substrate base pairs downstream within the hTR template. The rate constant for DNA primer re-alignment reveals this step is not rate-limiting for RAP, suggesting a second slow conformational change repositions the RNA:DNA hybrid into the telomerase active site and drives the extrusion of the 5′-end of the DNA primer out of the enzyme complex.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - Michael D Stone
- 1] Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA [2] Center for Molecular Biology of RNA, University of California, 1156 High Street, Santa Cruz, California 95064, USA
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Long X, Parks JW, Bagshaw CR, Stone MD. Mechanical Unfolding of Human Telomere G-Quadruplex DNA Probed by Integrated Fluorescence and Magnetic Tweezers Spectroscopy. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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33
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Akiyama BM, Stone MD. Direct Visualization of DNA Dynamics During the Telomerase Catalytic Cycle Reveals the Function of a Conserved Telomerase Domain. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Abstract
Telomeres are specialized chromatin structures found at the end of chromosomes and are crucial to the maintenance of eukaryotic genome stability. Human telomere DNA is comprised of the repeating sequence (T2AG3)n, which is predominantly double-stranded but terminates with a 3’ single-stranded tail. The guanine-rich tail can fold into secondary structures known as a G-quadruplexes (GQs) that may exist as a polymorphic mixture of anti-parallel, parallel, and several hybrid topological isomers. Using single-molecule Förster resonance energy transfer (smFRET), we have reconstructed distributions of telomere DNA GQ conformations generated by an in situ refolding protocol commonly employed in single-molecule studies of GQ structure, or using a slow cooling DNA annealing protocol typically used in the preparation of GQ samples for ensemble biophysical analyses. We find the choice of GQ folding protocol has a marked impact on the observed distributions of DNA conformations under otherwise identical buffer conditions. A detailed analysis of the kinetics of GQ folding over timescales ranging from minutes to hours revealed the distribution of GQ structures generated by in situ refolding gradually equilibrates to resemble the distribution generated by the slow cooling DNA annealing protocol. Interestingly, conditions of low ionic strength, which promote transient GQ unfolding, permit the fraction of folded DNA molecules to partition into a distribution that more closely approximates the thermodynamic folding equilibrium. Our results are consistent with a model in which kinetic partitioning occurs during in situ folding at room temperature in the presence of K+ ions, producing a long-lived non-equilibrium distribution of GQ structures in which the parallel conformation predominates on the timescale of minutes. These results suggest that telomere DNA GQ folding kinetics, and not just thermodynamic stability, likely contributes to the physiological ensemble GQ structures.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael D. Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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Akiyama BM, Gomez A, Stone MD. A conserved motif in Tetrahymena thermophila telomerase reverse transcriptase is proximal to the RNA template and is essential for boundary definition. J Biol Chem 2013; 288:22141-9. [PMID: 23760279 DOI: 10.1074/jbc.m113.452425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The ends of linear chromosomes are extended by telomerase, a ribonucleoprotein complex minimally consisting of a protein subunit called telomerase reverse transcriptase (TERT) and the telomerase RNA (TER). TERT functions by reverse transcribing a short template region of TER into telomeric DNA. Proper assembly of TERT and TER is essential for telomerase activity; however, a detailed understanding of how TERT interacts with TER is lacking. Previous studies have identified an RNA binding domain (RBD) within TERT, which includes three evolutionarily conserved sequence motifs: CP2, CP, and T. Here, we used site-directed hydroxyl radical probing to directly identify sites of interaction between the TERT RBD and TER, revealing that the CP2 motif is in close proximity to a conserved region of TER known as the template boundary element (TBE). Gel shift assays on CP2 mutants confirmed that the CP2 motif is an RNA binding determinant. Our results explain previous work that established that mutations to the CP2 motif of TERT and to the TBE of TER both permit misincorporation of nucleotides into the growing DNA strand beyond the canonical template. Taken together, these results suggest a model in which the CP2 motif binds the TBE to strictly define which TER nucleotides can be reverse transcribed.
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Affiliation(s)
- Benjamin M Akiyama
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA
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37
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Welton JL, Morgan MP, Martí S, Stone MD, Moser B, Sewell AK, Turton J, Eberl M. Monocytes and γδ T cells control the acute-phase response to intravenous zoledronate: insights from a phase IV safety trial. J Bone Miner Res 2013; 28:464-71. [PMID: 23074158 DOI: 10.1002/jbmr.1797] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 10/02/2012] [Accepted: 10/08/2012] [Indexed: 11/11/2022]
Abstract
Aminobisphosphonates (NBPs) are used widely against excessive bone resorption in osteoporosis and Paget's disease as well as in metastatic bone disease and multiple myeloma. Intravenous NBP administration often causes mild to severe acute-phase responses (APRs) that may require intervention with analgesics and antipyretics and lead to treatment noncompliance and nonadherence. We here undertook a phase IV safety trial in patients with osteoporosis to investigate the APR of otherwise healthy individuals to first-time intravenous treatment with the NBP zoledronate. This study provides unique insight into sterile acute inflammatory responses in vivo, in the absence of confounding factors such as infection or cancer. Our data show that both peripheral γδ T cells and monocytes become rapidly activated after treatment with zoledronate, which ultimately determines the clinical severity of the APR. Our study highlights a key role for IFN-γ in the zoledronate-induced APR and identifies pretreatment levels of monocytes and central/memory Vγ9/Vδ2 T cells as well as their responsiveness to zoledronate in vitro as predictive risk factors for the occurrence of subclinical and clinical symptoms. These findings have diagnostic and prognostic implications for patients with and without malignancy and are relevant for Vγ9/Vδ2 T-cell-based immunotherapy approaches.
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Affiliation(s)
- Joanne L Welton
- Cardiff Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Long X, Parks JW, Bagshaw CR, Stone MD. Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy. Nucleic Acids Res 2013; 41:2746-55. [PMID: 23303789 PMCID: PMC3575832 DOI: 10.1093/nar/gks1341] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-molecule techniques facilitate analysis of mechanical transitions within nucleic acids and proteins. Here, we describe an integrated fluorescence and magnetic tweezers instrument that permits detection of nanometer-scale DNA structural rearrangements together with the application of a wide range of stretching forces to individual DNA molecules. We have analyzed the force-dependent equilibrium and rate constants for telomere DNA G-quadruplex (GQ) folding and unfolding, and have determined the location of the transition state barrier along the well-defined DNA-stretching reaction coordinate. Our results reveal the mechanical unfolding pathway of the telomere DNA GQ is characterized by a short distance (<1 nm) to the transition state for the unfolding reaction. This mechanical unfolding response reflects a critical contribution of long-range interactions to the global stability of the GQ fold, and suggests that telomere-associated proteins need only disrupt a few base pairs to destabilize GQ structures. Comparison of the GQ unfolded state with a single-stranded polyT DNA revealed the unfolded GQ exhibits a compacted non-native conformation reminiscent of the protein molten globule. We expect the capacity to interrogate macromolecular structural transitions with high spatial resolution under conditions of low forces will have broad application in analyses of nucleic acid and protein folding.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Affiliation(s)
- Michael D Stone
- Department of Chemistry and Biochemistry and the Center for Molecular Biology of RNA, University of California Santa Cruz, CA 95064, USA.
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Hengesbach M, Kim NK, Feigon J, Stone MD. Single-molecule FRET reveals the folding dynamics of the human telomerase RNA pseudoknot domain. Angew Chem Int Ed Engl 2012; 51:5876-9. [PMID: 22544760 DOI: 10.1002/anie.201200526] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/10/2012] [Indexed: 12/30/2022]
Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Hengesbach M, Kim NK, Feigon J, Stone MD. Single-Molecule FRET Reveals the Folding Dynamics of the Human Telomerase RNA Pseudoknot Domain. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Akiyama BM, Loper J, Najarro K, Stone MD. The C-terminal domain of Tetrahymena thermophila telomerase holoenzyme protein p65 induces multiple structural changes in telomerase RNA. RNA 2012; 18:653-60. [PMID: 22315458 PMCID: PMC3312553 DOI: 10.1261/rna.031377.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The unique cellular activity of the telomerase reverse transcriptase ribonucleoprotein (RNP) requires proper assembly of protein and RNA components into a functional complex. In the ciliate model organism Tetrahymena thermophila, the La-domain protein p65 is required for in vivo assembly of telomerase. Single-molecule and biochemical studies have shown that p65 promotes efficient RNA assembly with the telomerase reverse transcriptase (TERT) protein, in part by inducing a bend in the conserved stem IV region of telomerase RNA (TER). The domain architecture of p65 consists of an N-terminal domain, a La-RRM motif, and a C-terminal domain (CTD). Using single-molecule Förster resonance energy transfer (smFRET), we demonstrate the p65(CTD) is necessary for the RNA remodeling activity of the protein and is sufficient to induce a substantial conformational change in stem IV of TER. Moreover, nuclease protection assays directly map the site of p65(CTD) interaction to stem IV and reveal that, in addition to bending stem IV, p65 binding reorganizes nucleotides that comprise the low-affinity TERT binding site within stem-loop IV.
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Affiliation(s)
| | - John Loper
- Department of Chemistry and Biochemistry
| | | | - Michael D. Stone
- Department of Chemistry and Biochemistry
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
- Corresponding author.E-mail .
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Gregson CL, Steel SA, O'Rourke KP, Allan K, Ayuk J, Bhalla A, Clunie G, Crabtree N, Fogelman I, Goodby A, Langman CM, Linton S, Marriott E, McCloskey E, Moss KE, Palferman T, Panthakalam S, Poole KES, Stone MD, Turton J, Wallis D, Warburton S, Wass J, Duncan EL, Brown MA, Davey-Smith G, Tobias JH. 'Sink or swim': an evaluation of the clinical characteristics of individuals with high bone mass. Osteoporos Int 2012; 23:643-54. [PMID: 21455762 PMCID: PMC3261396 DOI: 10.1007/s00198-011-1603-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/31/2011] [Indexed: 01/31/2023]
Abstract
SUMMARY High bone mineral density on routine dual energy X-ray absorptiometry (DXA) may indicate an underlying skeletal dysplasia. Two hundred fifty-eight individuals with unexplained high bone mass (HBM), 236 relatives (41% with HBM) and 58 spouses were studied. Cases could not float, had mandible enlargement, extra bone, broad frames, larger shoe sizes and increased body mass index (BMI). HBM cases may harbour an underlying genetic disorder. INTRODUCTION High bone mineral density is a sporadic incidental finding on routine DXA scanning of apparently asymptomatic individuals. Such individuals may have an underlying skeletal dysplasia, as seen in LRP5 mutations. We aimed to characterize unexplained HBM and determine the potential for an underlying skeletal dysplasia. METHODS Two hundred fifty-eight individuals with unexplained HBM (defined as L1 Z-score ≥ +3.2 plus total hip Z-score ≥ +1.2, or total hip Z-score ≥ +3.2) were recruited from 15 UK centres, by screening 335,115 DXA scans. Unexplained HBM affected 0.181% of DXA scans. Next 236 relatives were recruited of whom 94 (41%) had HBM (defined as L1 Z-score + total hip Z-score ≥ +3.2). Fifty-eight spouses were also recruited together with the unaffected relatives as controls. Phenotypes of cases and controls, obtained from clinical assessment, were compared using random-effects linear and logistic regression models, clustered by family, adjusted for confounders, including age and sex. RESULTS Individuals with unexplained HBM had an excess of sinking when swimming (7.11 [3.65, 13.84], p < 0.001; adjusted odds ratio with 95% confidence interval shown), mandible enlargement (4.16 [2.34, 7.39], p < 0.001), extra bone at tendon/ligament insertions (2.07 [1.13, 3.78], p = 0.018) and broad frame (3.55 [2.12, 5.95], p < 0.001). HBM cases also had a larger shoe size (mean difference 0.4 [0.1, 0.7] UK sizes, p = 0.009) and increased BMI (mean difference 2.2 [1.3, 3.1] kg/m(2), p < 0.001). CONCLUSION Individuals with unexplained HBM have an excess of clinical characteristics associated with skeletal dysplasia and their relatives are commonly affected, suggesting many may harbour an underlying genetic disorder affecting bone mass.
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Affiliation(s)
- C L Gregson
- Musculoskeletal Research Unit, University of Bristol, Bristol, UK.
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Wu JY, Mihalusova M, Stone MD, Zhuang X. Single-Molecule Analysis of the Functional Structure of Telomerase RNP. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Hengesbach M, Stone MD. Single Molecule Analysis of Human Telomerase RNA Pseudoknot Folding and Dynamics. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Berman AJ, Akiyama BM, Stone MD, Cech TR. The RNA accordion model for template positioning by telomerase RNA during telomeric DNA synthesis. Nat Struct Mol Biol 2011; 18:1371-5. [PMID: 22101935 PMCID: PMC3230705 DOI: 10.1038/nsmb.2174] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/07/2011] [Indexed: 12/27/2022]
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that maintains the ends of linear eukaryotic chromosomes and whose activation is a hallmark of 90% of all cancers. This RNP minimally contains a reverse transcriptase protein subunit (TERT) that catalyzes telomeric DNA synthesis and an RNA subunit (TER) that has templating, architectural and protein-scaffolding roles. Telomerase is unique among polymerases in that it synthesizes multiple copies of the template on the 3′ end of a primer following a single binding event, a process known as repeat addition processivity (RAP). Using biochemical assays and single-molecule Förster resonance energy transfer (smFRET) experiments on Tetrahymena thermophila telomerase, we now directly demonstrate that TER contributes to template positioning within the active site and to the template translocation required for RAP. We propose that the single-stranded RNA elements flanking the template act as a molecular accordion, undergoing reciprocal extension and compaction during telomerase translocation.
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Affiliation(s)
- Andrea J Berman
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, USA
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Hengesbach M, Akiyama BM, Stone MD. Single-molecule analysis of telomerase structure and function. Curr Opin Chem Biol 2011; 15:845-52. [PMID: 22057212 DOI: 10.1016/j.cbpa.2011.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/05/2011] [Accepted: 10/17/2011] [Indexed: 02/06/2023]
Abstract
The telomerase ribonucleoprotein is a specialized reverse transcriptase required to maintain protective chromosome end-capping structures called telomeres. In most cells, telomerase is not active and the natural shortening of telomeres with each round of DNA replication ultimately triggers cell growth arrest. In contrast, the presence of telomerase confers a high level of renewal capacity upon rapidly dividing cells. Telomerase is aberrantly activated in 90% of human cancers and thus represents an important target for anticancer therapeutics. However, the naturally low abundance of telomerase has hampered efforts to obtain high-resolution models for telomerase structure and function. To circumvent these challenges, single-molecule techniques have recently been employed to investigate telomerase assembly, structure, and catalysis.
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Affiliation(s)
- Martin Hengesbach
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA
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Duckers JM, Evans BAJ, Fraser WD, Stone MD, Bolton CE, Shale DJ. Low bone mineral density in men with chronic obstructive pulmonary disease. Respir Res 2011; 12:101. [PMID: 21812978 PMCID: PMC3161864 DOI: 10.1186/1465-9921-12-101] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 08/03/2011] [Indexed: 01/28/2023] Open
Abstract
Background Osteoporosis is common in patients with COPD but the likely multi-factorial causes contributing to this condition (e.g. sex, age, smoking, therapy) mask the potential contribution from elements related to COPD. In order to study osteoporosis and bone mineral density (BMD) related to COPD, we studied a well-defined group of patients and controls. Methods BMD, forced expiratory volume in one second (FEV1), circulating bone biomarkers and biochemistry were determined in 30 clinically stable male ex-smokers with confirmed COPD and 15 age matched "ex-smoker" male controls. None of the patients were on inhaled corticosteroids or received more than one short course of steroids. Results Mean (SD) FEV1% predicted of patients was 64(6)%, the majority having Global Initiative for Chronic Obstructive Lung Disease (GOLD) II airflow obstruction. There were 5/30 patients and 1/15 controls who were osteoporotic, while a further 17 patients and 5 controls were osteopenic. The BMD at the hip was lower in patients than controls, but not at the lumbar spine. Mean values of procollagen type 1 amino-terminal propeptide and osteocalcin, both markers of bone formation, and Type 1 collagen β C-telopeptide, a marker of bone resorption, were similar between patients and controls. However, all bone biomarkers were inversely related to hip BMD in patients (r = -0.51, r = -0.67, r = -0.57, p < 0.05) but did not relate to lumbar spine BMD. 25-OH Vitamin D was lower in patients. Conclusions Men with COPD had a greater prevalence of osteoporosis and osteopenia than age matched male controls, with a marked difference in BMD at the hip. Bone biomarkers suggest increased bone turnover.
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Affiliation(s)
- James M Duckers
- Section of Respiratory Medicine, Wales Heart Research Institute, School of Medicine, Cardiff University, University Hospital of Wales, Heath Park, Cardiff, CF14 4XN, UK.
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Abstract
The activity of the telomerase ribonucleoprotein enzyme is essential for the maintenance of genome stability and normal cell development. Despite the biomedical importance of telomerase activity, detailed structural models for the enzyme remain to be established. Here we report a single-molecule assay for direct structural analysis of catalytically active telomerase enzymes. In this assay, oligonucleotide hybridization was used to probe the primer-extension activity of individual telomerase enzymes with single nucleotide sensitivity, allowing precise discrimination between inactive, active and processive enzyme binding events. FRET signals from enzyme molecules during the active and processive binding events were then used to determine the global organization of telomerase RNA within catalytically active holoenzymes. Using this assay, we have identified an active conformation of telomerase among a heterogeneous population of enzymes with distinct structures.
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Affiliation(s)
- John Y Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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Méndez JE, Evans M, Stone MD. Promoters and barriers to mammography screening in multiethnic inner city patients. Am J Surg 2009; 198:526-8. [DOI: 10.1016/j.amjsurg.2009.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/27/2009] [Accepted: 07/06/2009] [Indexed: 11/29/2022]
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