Preprint Article Version 1 This version is not peer-reviewed

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

Version 1 : Received: 15 May 2018 / Approved: 16 May 2018 / Online: 16 May 2018 (11:58:28 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

Journal reference: Genes 2018, 9, 372
DOI: 10.3390/genes9080372

Abstract

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 still remain without annotated telomerase RNA.

Subject Areas

non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast

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