Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq
Summary: Quantifying tRNAs is crucial for understanding how they regulate mRNA translation but is hampered by their extensive sequence similarity and premature termination of reverse transcription at multiple modified nucleotides. Here, we describe the use of modification-induced misincorporation tR...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722004592 |
| _version_ | 1818471938070151168 |
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| author | Andrew Behrens Danny D. Nedialkova |
| author_facet | Andrew Behrens Danny D. Nedialkova |
| author_sort | Andrew Behrens |
| collection | DOAJ |
| description | Summary: Quantifying tRNAs is crucial for understanding how they regulate mRNA translation but is hampered by their extensive sequence similarity and premature termination of reverse transcription at multiple modified nucleotides. Here, we describe the use of modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which overcomes these limitations with optimized library construction and a comprehensive toolkit for data analysis and visualization. We outline algorithm improvements that enhance the efficiency and accuracy of read alignment and provide details on data analysis outputs using example datasets.For complete details on the use and execution of this protocol, please refer to Behrens et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-14T03:58:37Z |
| format | Article |
| id | doaj.art-e267662317224828a2a167f79fcb8e90 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-14T03:58:37Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-e267662317224828a2a167f79fcb8e902022-12-22T02:13:41ZengElsevierSTAR Protocols2666-16672022-09-0133101579Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseqAndrew Behrens0Danny D. Nedialkova1Mechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, 82152 Martinsried, GermanyMechanisms of Protein Biogenesis, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Chemistry, Technical University of Munich, 85748 Garching, Germany; Corresponding authorSummary: Quantifying tRNAs is crucial for understanding how they regulate mRNA translation but is hampered by their extensive sequence similarity and premature termination of reverse transcription at multiple modified nucleotides. Here, we describe the use of modification-induced misincorporation tRNA sequencing (mim-tRNAseq), which overcomes these limitations with optimized library construction and a comprehensive toolkit for data analysis and visualization. We outline algorithm improvements that enhance the efficiency and accuracy of read alignment and provide details on data analysis outputs using example datasets.For complete details on the use and execution of this protocol, please refer to Behrens et al. (2021). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722004592BioinformaticsSequencingRNAseqMolecular BiologyGene ExpressionSystems biology |
| spellingShingle | Andrew Behrens Danny D. Nedialkova Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq STAR Protocols Bioinformatics Sequencing RNAseq Molecular Biology Gene Expression Systems biology |
| title | Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq |
| title_full | Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq |
| title_fullStr | Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq |
| title_full_unstemmed | Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq |
| title_short | Experimental and computational workflow for the analysis of tRNA pools from eukaryotic cells by mim-tRNAseq |
| title_sort | experimental and computational workflow for the analysis of trna pools from eukaryotic cells by mim trnaseq |
| topic | Bioinformatics Sequencing RNAseq Molecular Biology Gene Expression Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722004592 |
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