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Article

Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum

1
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany
2
Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at Leipzig University and University Hospital Leipzig, Philipp-Rosenthal-Str. 27, D-04103 Leipzig, Germany
3
Institute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, Germany
4
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, Leipzig University, D-04103 Leipzig, Germany
5
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
6
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
7
Facultad de Ciencias, Universidad Nacional de Colombia, 111321 Bogotá, D.C., Colombia
8
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
*
Author to whom correspondence should be addressed.
Co-first author, these authors contributed equally to this work.
Academic Editors: Clément Carré and Damien Brégeon
Non-Coding RNA 2021, 7(2), 32; https://doi.org/10.3390/ncrna7020032
Received: 23 April 2021 / Revised: 18 May 2021 / Accepted: 26 May 2021 / Published: 28 May 2021
(This article belongs to the Special Issue Research on RNA Modification)
Dictyostelium discoideum is a social amoeba, which on starvation develops from a single-cell state to a multicellular fruiting body. This developmental process is accompanied by massive changes in gene expression, which also affect non-coding RNAs. Here, we investigate how tRNAs as key regulators of the translation process are affected by this transition. To this end, we used LOTTE-seq to sequence the tRNA pool of D. discoideum at different developmental time points and analyzed both tRNA composition and tRNA modification patterns. We developed a workflow for the specific detection of modifications from reverse transcriptase signatures in chemically untreated RNA-seq data at single-nucleotide resolution. It avoids the comparison of treated and untreated RNA-seq data using reverse transcription arrest patterns at nucleotides in the neighborhood of a putative modification site as internal control. We find that nucleotide modification sites in D. discoideum tRNAs largely conform to the modification patterns observed throughout the eukaroytes. However, there are also previously undescribed modification sites. We observe substantial dynamic changes of both expression levels and modification patterns of certain tRNA types during fruiting body development. Beyond the specific application to D. discoideum our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq. View Full-Text
Keywords: Dictyostelium discoideum; transfer RNAs; fruiting body development; chemical modifications; tRNA sequencing; LOTTE-seq; immature reverse transcriptase arrest Dictyostelium discoideum; transfer RNAs; fruiting body development; chemical modifications; tRNA sequencing; LOTTE-seq; immature reverse transcriptase arrest
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MDPI and ACS Style

Hoffmann, A.; Erber, L.; Betat, H.; Stadler, P.F.; Mörl, M.; Fallmann, J. Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum. Non-Coding RNA 2021, 7, 32. https://doi.org/10.3390/ncrna7020032

AMA Style

Hoffmann A, Erber L, Betat H, Stadler PF, Mörl M, Fallmann J. Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum. Non-Coding RNA. 2021; 7(2):32. https://doi.org/10.3390/ncrna7020032

Chicago/Turabian Style

Hoffmann, Anne, Lieselotte Erber, Heike Betat, Peter F. Stadler, Mario Mörl, and Jörg Fallmann. 2021. "Changes of the tRNA Modification Pattern during the Development of Dictyostelium discoideum" Non-Coding RNA 7, no. 2: 32. https://doi.org/10.3390/ncrna7020032

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