Kruse, Elisabeth ; Göringer, H. Ulrich (2023)
Nanopore-based direct RNA sequencing of the Trypanosoma brucei transcriptome identifies novel lncRNAs.
In: Genes, 14 (3)
doi: 10.3390/genes14030610
Artikel, Bibliographie
Kurzbeschreibung (Abstract)
Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized to date. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known, because of the inherent cDNA-recoding and DNA-amplification limitations of short-read RNA sequencing. Here, we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 32 of which are stage-specifically expressed. We also present insights into the complexity of the transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms, to provide a bias-free understanding of the intricate RNA landscape in .
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2023 |
| Autor(en): | Kruse, Elisabeth ; Göringer, H. Ulrich |
| Art des Eintrags: | Bibliographie |
| Titel: | Nanopore-based direct RNA sequencing of the Trypanosoma brucei transcriptome identifies novel lncRNAs |
| Sprache: | Englisch |
| Publikationsjahr: | 28 Februar 2023 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Genes |
| Jahrgang/Volume einer Zeitschrift: | 14 |
| (Heft-)Nummer: | 3 |
| DOI: | 10.3390/genes14030610 |
| Kurzbeschreibung (Abstract): | Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized to date. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known, because of the inherent cDNA-recoding and DNA-amplification limitations of short-read RNA sequencing. Here, we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 32 of which are stage-specifically expressed. We also present insights into the complexity of the transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms, to provide a bias-free understanding of the intricate RNA landscape in . |
| ID-Nummer: | pmid:36980882 |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Molecular Genetics 10 Fachbereich Biologie > Genregulation und RNA-Therapeutika |
| Hinterlegungsdatum: | 04 Apr 2023 07:05 |
| Letzte Änderung: | 04 Apr 2023 08:13 |
| PPN: | 506558894 |
| Export: | |
| Suche nach Titel in: | TUfind oder in Google |
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