Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i>
<i>Dictyostelium discoideum</i> 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 a...
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| Format: | Article |
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MDPI AG
2021-05-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/7/2/32 |
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| author | Anne Hoffmann Lieselotte Erber Heike Betat Peter F. Stadler Mario Mörl Jörg Fallmann |
| author_facet | Anne Hoffmann Lieselotte Erber Heike Betat Peter F. Stadler Mario Mörl Jörg Fallmann |
| author_sort | Anne Hoffmann |
| collection | DOAJ |
| description | <i>Dictyostelium discoideum</i> 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 <i>D. discoideum</i> 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 <i>D. discoideum</i> 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 <i>D. discoideum</i> our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq. |
| first_indexed | 2024-03-10T10:57:04Z |
| format | Article |
| id | doaj.art-ee9bf2e41cba4a8f9638d8d003ffe143 |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T10:57:04Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-ee9bf2e41cba4a8f9638d8d003ffe1432023-11-21T21:50:17ZengMDPI AGNon-Coding RNA2311-553X2021-05-01723210.3390/ncrna7020032Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i>Anne Hoffmann0Lieselotte Erber1Heike Betat2Peter F. Stadler3Mario Mörl4Jörg Fallmann5Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, GermanyInstitute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, GermanyInstitute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, GermanyBioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, GermanyInstitute for Biochemistry, Leipzig University, Brüderstraße 34, D-04103 Leipzig, GermanyBioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, D-04107 Leipzig, Germany<i>Dictyostelium discoideum</i> 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 <i>D. discoideum</i> 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 <i>D. discoideum</i> 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 <i>D. discoideum</i> our results demonstrate that the developmental variability of tRNA expression and modification can be traced efficiently with LOTTE-seq.https://www.mdpi.com/2311-553X/7/2/32<i>Dictyostelium discoideum</i>transfer RNAsfruiting body developmentchemical modificationstRNA sequencingLOTTE-seq |
| spellingShingle | Anne Hoffmann Lieselotte Erber Heike Betat Peter F. Stadler Mario Mörl Jörg Fallmann Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> Non-Coding RNA <i>Dictyostelium discoideum</i> transfer RNAs fruiting body development chemical modifications tRNA sequencing LOTTE-seq |
| title | Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> |
| title_full | Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> |
| title_fullStr | Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> |
| title_full_unstemmed | Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> |
| title_short | Changes of the tRNA Modification Pattern during the Development of <i>Dictyostelium discoideum</i> |
| title_sort | changes of the trna modification pattern during the development of i dictyostelium discoideum i |
| topic | <i>Dictyostelium discoideum</i> transfer RNAs fruiting body development chemical modifications tRNA sequencing LOTTE-seq |
| url | https://www.mdpi.com/2311-553X/7/2/32 |
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