ArticleNucleic acids research2016
Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT).
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Single-tissue proteomics inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- CaV1 and CaV2 calcium channels mediate the release of distinct pools of synaptic vesicles.eLife · 2023Article
- Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans.Genetics · 2023Article
- Hand Dissection of Caenorhabditis elegans Intestines.Journal of visualized experiments : JoVE · 2022Article
- Identification of healthspan-promoting genes in Caenorhabditis elegans based on a human GWAS study.Biogerontology · 2022Article
- Review
- Tissue-specific DamID protocol using nanopore sequencing.Journal of biological methods · 2021Article
- Article
- Tissue-specific isoforms of the single C. elegans Ryanodine receptor gene unc-68 control specific functions.PLoS genetics · 2020Article
- Gene expression hallmarks of cellular ageing.Biogerontology · 2018Review
- Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.PLoS genetics · 2018Article
- Transcriptional Signatures of Aging.Journal of molecular biology · 2017Review
- Spatiotemporal expression profiling of long intervening noncoding RNAs in Caenorhabditis elegans.Scientific reports · 2017Article
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7 authors.
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Abstract
Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. We have developed an easy and robust method for tissue-specific RNA-seq by taking advantage of the endogenous trans-splicing process. In this method, transgenic worms are generated in which a spliced leader (SL) RNA gene is fused with a sequence tag and driven by a tissue-specific promoter. Only in the tissue of interest, the tagged SL RNA gene is transcribed and then trans-spliced onto mRNAs. The tag allows enrichment and sequencing of mRNAs from that tissue only. As a proof of principle, we profiled the muscle transcriptome, which showed high coverage and efficient enrichment of muscle specific genes, with low background noise. To demonstrate the robustness of our method, we profiled muscle gene expression in dauer larvae and aging worms, revealing gene expression changes consistent with the physiology of these stages. The resulting muscle transcriptome also revealed 461 novel RNA transcripts, likely muscle-expressed long non-coding RNAs. In summary, the splicing-based RNA tagging (SRT) method provides a convenient and robust tool to profile trans-spliced genes and identify novel transcripts in a tissue-specific manner, with a low false positive rate.
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