Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remained uncharacterised in the template region. Here we show that this is mainly due to high variability in telomere sequence. We predicted the telomere sequences using Tandem Repeats Finder and then we identified corresponding putative template regions in TR candidates. Remarkably long telomere units and the corresponding putative TRs were found in Tetrapisispora species. Notably, variable lengths of the annealing sequence of the template region (1-10 nt) were found. Consequently, species with the same telomere sequence may not harbour identical TR templates. Thus, TR sequence alone can be used to predict a template region and telomere sequence, but not to determine these exactly. A conserved feature of telomere sequences, tracts of adjacent Gs, led us to test the propensity of individual telomere sequences to form G4. The results show highly diverse values of G4-propensity, indicating the lack of ubiquitous conservation of this feature across Saccharomycetaceae.

Department of Experimental Biology Faculty of Science Masaryk University Brno 62500 Czech Republic

Institut Botànic de Barcelona Passeig del Migdia s n 08038 Barcelona Catalonia Spain

Institute of Biophysics Academy of Sciences of the Czech Republic Brno 61265 Czech Republic

Mendel Centre for Plant Genomics and Proteomics CEITEC Masaryk University Brno 62500 Czech Republic

Zobrazit více v PubMed

Lim CJ, Cech TR. Shaping human telomeres: From shelterin and CST complexes to telomeric chromatin organization. Nat. Rev. Mol. Cell Biol. 2021 doi: 10.1038/s41580-021-00328-y. PubMed DOI PMC

Lu W, Zhang Y, Liu D, Songyang Z, Wan M. Telomeres-structure, function, and regulation. Exp. Cell Res. 2013;319:133–141. doi: 10.1016/j.yexcr.2012.09.005. PubMed DOI PMC

Shay JW. Telomeres and aging. Curr. Opin. Cell Biol. 2018;52:1–7. doi: 10.1016/j.ceb.2017.12.001. PubMed DOI

Victorelli S, Passos JF. Telomeres and cell senescence—Size matters not. EBioMedicine. 2017;21:14–20. doi: 10.1016/j.ebiom.2017.03.027. PubMed DOI PMC

Blackburn EH. Telomere states and cell fates. Nature. 2000;408:53–56. doi: 10.1038/35040500. PubMed DOI

Lingner J, Cooper JP, Cech TR. Telomerase and DNA end replication: No longer a lagging strand problem? Science. 1995;269:1533–1534. doi: 10.1126/science.7545310. PubMed DOI

Soudet J, Jolivet P, Teixeira MT. Elucidation of the DNA end-replication problem in Saccharomyces cerevisiae. Mol. Cell. 2014;53:954–964. doi: 10.1016/j.molcel.2014.02.030. PubMed DOI

Wellinger RJ. In the end, what's the problem? Mol. Cell. 2014;53:855–856. doi: 10.1016/j.molcel.2014.03.008. PubMed DOI

Greider CW, Blackburn EH. Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell. 1985;43:405–413. doi: 10.1016/0092-8674(85)90170-9. PubMed DOI

Shay JW. Role of telomeres and telomerase in aging and cancer. Cancer Discov. 2016;6:584–593. doi: 10.1158/2159-8290.CD-16-0062. PubMed DOI PMC

Blasco MA. Telomerase beyond telomeres. Nat. Rev. Cancer. 2002;2:627–633. doi: 10.1038/nrc862. PubMed DOI

Koonin EV. The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate? Biol. Direct. 2006;1:22. doi: 10.1186/1745-6150-1-22. PubMed DOI PMC

Nosek J, Kosa P, Tomaska L. On the origin of telomeres: A glimpse at the pre-telomerase world. BioEssays. 2006;28:182–190. doi: 10.1002/bies.20355. PubMed DOI

Schrumpfova PP, Fajkus J. Composition and function of telomerase-a polymerase associated with the origin of eukaryotes. Biomolecules. 2020;10:1425. doi: 10.3390/biom10101425. PubMed DOI PMC

Chan SRWL, Blackburn EH. Telomeres and telomerase. Philos. Trans. R. Soc. B. 2004;359:109–121. doi: 10.1098/rstb.2003.1370. PubMed DOI PMC

Rubin GM. Isolation of a telomeric DNA sequence from Drosophila melanogaster. Cold Spring Harb. Symp. Quant. Biol. 1978;42(Pt 2):1041–1046. doi: 10.1101/sqb.1978.042.01.104. PubMed DOI

Traverse KL, Pardue ML. A spontaneously opened ring chromosome of Drosophila melanogaster has acquired He-T DNA sequences at both new telomeres. Proc. Natl. Acad. Sci. U. S. A. 1988;85:8116–8120. doi: 10.1073/pnas.85.21.8116. PubMed DOI PMC

Fajkus P, Peska V, Fajkus J, Sykorova E. Origin and fates of TERT gene copies in polyploid plants. Int. J. Mol. Sci. 2021;22:1783. doi: 10.3390/ijms22041783. PubMed DOI PMC

Peska V, Garcia S. Origin, diversity, and evolution of telomere sequences in plants. Front. Plant Sci. 2020;11:117. doi: 10.3389/fpls.2020.00117. PubMed DOI PMC

Schrumpfova PP, Fojtova M, Fajkus J. Telomeres in plants and humans: Not so different, not so similar. Cells-Basel. 2019;8:58. doi: 10.3390/cells8010058. PubMed DOI PMC

Shampay J, Szostak JW, Blackburn EH. DNA sequences of telomeres maintained in yeast. Nature. 1984;310:154–157. doi: 10.1038/310154a0. PubMed DOI

Walmsley RW, Chan CS, Tye BK, Petes TD. Unusual DNA sequences associated with the ends of yeast chromosomes. Nature. 1984;310:157–160. doi: 10.1038/310157a0. PubMed DOI

Cervenak F, Sepsiova R, Nosek J, Tomaska L. Step-by-step evolution of telomeres: Lessons from yeasts. Genome Biol. Evol. 2020 doi: 10.1093/gbe/evaa268. PubMed DOI PMC

Cutova M, et al. Divergent distributions of inverted repeats and G-quadruplex forming sequences in Saccharomyces cerevisiae. Genomics. 2020;112:1897–1901. doi: 10.1016/j.ygeno.2019.11.002. PubMed DOI

Moye AL, et al. Telomeric G-quadruplexes are a substrate and site of localization for human telomerase. Nat. Commun. 2015;6:7643. doi: 10.1038/ncomms8643. PubMed DOI PMC

Ares M, Jr, Chakrabarti K. Stuttering against marginotomy. Nat. Struct. Mol. Biol. 2008;15:18–19. doi: 10.1038/nsmb0108-18. PubMed DOI PMC

Fajkus P, et al. Telomerase RNAs in land plants. Nucleic Acids Res. 2019;47:9842–9856. doi: 10.1093/nar/gkz695. PubMed DOI PMC

Peska V, et al. Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences. J. Exp. Bot. 2020;71:5786–5793. doi: 10.1093/jxb/eraa293. PubMed DOI

Kachouri-Lafond R, et al. Large telomerase RNA, telomere length heterogeneity and escape from senescence in Candida glabrata. FEBS Lett. 2009;583:3605–3610. doi: 10.1016/j.febslet.2009.10.034. PubMed DOI

McCormick-Graham M, Romero DP. A single telomerase RNA is sufficient for the synthesis of variable telomeric DNA repeats in ciliates of the genus Paramecium. Mol. Cell Biol. 1996;16:1871–1879. doi: 10.1128/mcb.16.4.1871. PubMed DOI PMC

Feng J, et al. The RNA component of human telomerase. Science. 1995;269:1236–1241. doi: 10.1126/science.7544491. PubMed DOI

Singer MS, Gottschling DE. TLC1: Template RNA component of Saccharomyces cerevisiae telomerase. Science. 1994;266:404–409. doi: 10.1126/science.7545955. PubMed DOI

Dandjinou AT, et al. A phylogenetically based secondary structure for the yeast telomerase RNA. Curr. Biol. 2004;14:1148–1158. doi: 10.1016/j.cub.2004.05.054. PubMed DOI

Gunisova S, et al. Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements. RNA. 2009;15:546–559. doi: 10.1261/rna.1194009. PubMed DOI PMC

Tzfati Y, Fulton TB, Roy J, Blackburn EH. Template boundary in a yeast telomerase specified by RNA structure. Science. 2000;288:863–867. doi: 10.1126/science.288.5467.863. PubMed DOI

Waldl M, et al. TERribly difficult: Searching for telomerase RNAs in Saccharomycetes. Genes (Basel) 2018;9:372. doi: 10.3390/genes9080372. PubMed DOI PMC

Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933–2935. doi: 10.1093/bioinformatics/btt509. PubMed DOI PMC

Chen JL, Blasco MA, Greider CW. Secondary structure of vertebrate telomerase RNA. Cell. 2000;100:503–514. doi: 10.1016/s0092-8674(00)80687-x. PubMed DOI

Qi X, et al. The common ancestral core of vertebrate and fungal telomerase RNAs. Nucleic Acids Res. 2013;41:450–462. doi: 10.1093/nar/gks980. PubMed DOI PMC

Xie M, et al. Structure and function of the smallest vertebrate telomerase RNA from teleost fish. J. Biol. Chem. 2008;283:2049–2059. doi: 10.1074/jbc.M708032200. PubMed DOI

Logeswaran D, Li Y, Podlevsky JD, Chen JJ. Monophyletic origin and divergent evolution of animal telomerase RNA. Mol. Biol. Evol. 2020 doi: 10.1093/molbev/msaa203. PubMed DOI PMC

Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. doi: 10.1093/nar/27.2.573. PubMed DOI PMC

Cohn M, McEachern MJ, Blackburn EH. Telomeric sequence diversity within the genus Saccharomyces. Curr. Genet. 1998;33:83–91. doi: 10.1007/s002940050312. PubMed DOI

Dietrich FS, et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004;304:304–307. doi: 10.1126/science.1095781. PubMed DOI

McEachern MJ, Blackburn EH. Runaway telomere elongation caused by telomerase RNA gene mutations. Nature. 1995;376:403–409. doi: 10.1038/376403a0. PubMed DOI

Ortiz-Merino RA, et al. Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. PLoS Biol. 2017;15:e2002128. doi: 10.1371/journal.pbio.2002128. PubMed DOI PMC

Seto AG, Livengood AJ, Tzfati Y, Blackburn EH, Cech TR. A bulged stem tethers Est1p to telomerase RNA in budding yeast. Genes Dev. 2002;16:2800–2812. doi: 10.1101/gad.1029302. PubMed DOI PMC

Uchida W, Matsunaga S, Sugiyama R, Kawano S. Interstitial telomere-like repeats in the Arabidopsis thaliana genome. Genes Genet. Syst. 2002;77:63–67. doi: 10.1266/ggs.77.63. PubMed DOI

Tremousaygue D, et al. Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant J. 2003;33:957–966. doi: 10.1046/j.1365-313x.2003.01682.x. PubMed DOI

Farmery JHR, Smith ML, Diseases NB-R, Lynch AG. Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci. Rep. 2018;8:1300. doi: 10.1038/s41598-017-14403-y. PubMed DOI PMC

Bedrat A, Lacroix L, Mergny JL. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res. 2016;44:1746–1759. doi: 10.1093/nar/gkw006. PubMed DOI PMC

Bosoy D, Peng Y, Mian IS, Lue NF. Conserved N-terminal motifs of telomerase reverse transcriptase required for ribonucleoprotein assembly in vivo. J. Biol. Chem. 2003;278:3882–3890. doi: 10.1074/jbc.M210645200. PubMed DOI

Wang SS, Zakian VA. Sequencing of Saccharomyces telomeres cloned using T4 DNA polymerase reveals two domains. Mol. Cell Biol. 1990;10:4415–4419. doi: 10.1128/mcb.10.8.4415. PubMed DOI PMC

Forstemann K, Lingner J. Telomerase limits the extent of base pairing between template RNA and telomeric DNA. EMBO Rep. 2005;6:361–366. doi: 10.1038/sj.embor.7400374. PubMed DOI PMC

Fulneckova J, et al. A broad phylogenetic survey unveils the diversity and evolution of telomeres in eukaryotes. Genome Biol. Evol. 2013;5:468–483. doi: 10.1093/gbe/evt019. PubMed DOI PMC

Fajkus P, et al. Allium telomeres unmasked: The unusual telomeric sequence (CTCGGTTATGGG)n is synthesized by telomerase. Plant J. 2016;85:337–347. doi: 10.1111/tpj.13115. PubMed DOI

Peska V, et al. Characterisation of an unusual telomere motif (TTTTTTAGGG)n in the plant Cestrum elegans (Solanaceae), a species with a large genome. Plant J. 2015;82:644–654. doi: 10.1111/tpj.12839. PubMed DOI

Teixeira MT, Gilson E. Telomere maintenance, function and evolution: The yeast paradigm. Chromosome Res. 2005;13:535–548. doi: 10.1007/s10577-005-0999-0. PubMed DOI

Matsumoto S, Sugimoto N. New insights into the functions of nucleic acids controlled by cellular microenvironments. Top. Curr. Chem. (Cham) 2021;379:17. doi: 10.1007/s41061-021-00329-7. PubMed DOI

Wallgren M, et al. G-rich telomeric and ribosomal DNA sequences from the fission yeast genome form stable G-quadruplex DNA structures in vitro and are unwound by the Pfh1 DNA helicase. Nucleic Acids Res. 2016;44:6213–6231. doi: 10.1093/nar/gkw349. PubMed DOI PMC

Jurikova K, et al. Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae. J. Biol. Chem. 2020;295:8958–8971. doi: 10.1074/jbc.RA120.012914. PubMed DOI PMC

Tran PL, Mergny JL, Alberti P. Stability of telomeric G-quadruplexes. Nucleic Acids Res. 2011;39:3282–3294. doi: 10.1093/nar/gkq1292. PubMed DOI PMC

Smith JS, et al. Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 2011;18:478–485. doi: 10.1038/nsmb.2033. PubMed DOI PMC

Cohn M, Blackburn EH. Telomerase in yeast. Science. 1995;269:396–400. doi: 10.1126/science.7618104. PubMed DOI

Tran TD, et al. Centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea. Plant J. 2015;84:1087–1099. doi: 10.1111/tpj.13058. PubMed DOI

Sykorova E, et al. Telomere variability in the monocotyledonous plant order Asparagales. Proc. Biol. Sci. 2003;270:1893–1904. doi: 10.1098/rspb.2003.2446. PubMed DOI PMC

McCormick-Graham M, Haynes WJ, Romero DP. Variable telomeric repeat synthesis in Paramecium tetraurelia is consistent with misincorporation by telomerase. EMBO J. 1997;16:3233–3242. doi: 10.1093/emboj/16.11.3233. PubMed DOI PMC

Peska V, Sitova Z, Fajkus P, Fajkus J. BAL31-NGS approach for identification of telomeres de novo in large genomes. Methods. 2017;114:16–27. doi: 10.1016/j.ymeth.2016.08.017. PubMed DOI

Brazda V, et al. G4Hunter web application: A web server for G-quadruplex prediction. Bioinformatics. 2019;35:3493–3495. doi: 10.1093/bioinformatics/btz087. PubMed DOI PMC

Kikin O, D'Antonio L, Bagga PS. QGRS Mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 2006;34:W676–682. doi: 10.1093/nar/gkl253. PubMed DOI PMC

Vorlickova M, et al. Circular dichroism and guanine quadruplexes. Methods. 2012;57:64–75. doi: 10.1016/j.ymeth.2012.03.011. PubMed DOI

Renaud de la Faverie A, Guedin A, Bedrat A, Yatsunyk LA, Mergny JL. Thioflavin T as a fluorescence light-up probe for G4 formation. Nucleic Acids Res. 2014;42:e65. doi: 10.1093/nar/gku111. PubMed DOI PMC

Shen XX, et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell. 2018;175:1533–1545. doi: 10.1016/j.cell.2018.10.023. PubMed DOI PMC

Cervenak F, et al. Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins. Sci. Rep. 2019;9:13365. doi: 10.1038/s41598-019-49628-6. PubMed DOI PMC

Characterisation of the Arabidopsis thaliana telomerase TERT-TR complex

TeloBase: a community-curated database of telomere sequences across the tree of life

Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences

Identification of the Sequence and the Length of Telomere DNA

Telomerase RNA in Hymenoptera (Insecta) switched to plant/ciliate-like biogenesis

Telomeres and Their Neighbors

Editorial: Telomere Flexibility and Versatility: A Role of Telomeres in Adaptive Potential