tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation
tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.518949/full |
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| author | Anahi Molla-Herman Margarita T. Angelova Maud Ginestet Clément Carré Christophe Antoniewski Jean-René Huynh |
| author_facet | Anahi Molla-Herman Margarita T. Angelova Maud Ginestet Clément Carré Christophe Antoniewski Jean-René Huynh |
| author_sort | Anahi Molla-Herman |
| collection | DOAJ |
| description | tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline (tRFs-Galaxy) to study tRFs populations and shed light onto tRNA fragments biogenesis in Drosophila melanogaster. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant ovaries affecting two different highly conserved steps of tRNA biogenesis: 5′pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2′-O-methylation (dTrm7_34 and dTrm7_32). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology. |
| first_indexed | 2024-12-12T15:45:57Z |
| format | Article |
| id | doaj.art-27f5756565cf404dbd4ae5bb7d139873 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T15:45:57Z |
| publishDate | 2020-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-27f5756565cf404dbd4ae5bb7d1398732022-12-22T00:19:44ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-10-011110.3389/fgene.2020.518949518949tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA MethylationAnahi Molla-Herman0Margarita T. Angelova1Maud Ginestet2Clément Carré3Christophe Antoniewski4Jean-René Huynh5Collège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, FranceTransgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, FranceCollège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, FranceTransgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, FranceARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, FranceCollège de France, CIRB, CNRS Inserm UMR 7241, PSL Research University, Paris, FrancetRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline (tRFs-Galaxy) to study tRFs populations and shed light onto tRNA fragments biogenesis in Drosophila melanogaster. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant ovaries affecting two different highly conserved steps of tRNA biogenesis: 5′pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2′-O-methylation (dTrm7_34 and dTrm7_32). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.https://www.frontiersin.org/article/10.3389/fgene.2020.518949/fullDrosophilaNm methylationRNase PtRNAtRFsoogenesis |
| spellingShingle | Anahi Molla-Herman Margarita T. Angelova Maud Ginestet Clément Carré Christophe Antoniewski Jean-René Huynh tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation Frontiers in Genetics Drosophila Nm methylation RNase P tRNA tRFs oogenesis |
| title | tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation |
| title_full | tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation |
| title_fullStr | tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation |
| title_full_unstemmed | tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation |
| title_short | tRNA Fragments Populations Analysis in Mutants Affecting tRNAs Processing and tRNA Methylation |
| title_sort | trna fragments populations analysis in mutants affecting trnas processing and trna methylation |
| topic | Drosophila Nm methylation RNase P tRNA tRFs oogenesis |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.518949/full |
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