Next Article in Journal
Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat
Next Article in Special Issue
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Previous Article in Journal / Special Issue
Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
BioInformatics Group, Fakultät CB Hochschule Mittweida, Technikumplatz 17, D-09648 Mittweida, Germany
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário–Asa Norte, Brasília, DF CEP: 70910-900, Brazil
Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Universität Leipzig, D-04107 Leipzig, Germany
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2018, 9(8), 372;
Received: 15 May 2018 / Revised: 17 July 2018 / Accepted: 18 July 2018 / Published: 26 July 2018
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA. View Full-Text
Keywords: non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast
Show Figures

Figure 1

MDPI and ACS Style

Waldl, M.; Thiel, B.C.; Ochsenreiter, R.; Holzenleiter, A.; De Araujo Oliveira, J.V.; Walter, M.E.M.T.; Wolfinger, M.T.; Stadler, P.F. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes 2018, 9, 372.

AMA Style

Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, De Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes. 2018; 9(8):372.

Chicago/Turabian Style

Waldl, Maria, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor De Araujo Oliveira, Maria Emília M. T. Walter, Michael T. Wolfinger, and Peter F. Stadler. 2018. "TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes" Genes 9, no. 8: 372.

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

Back to TopTop