ArticleNucleic acids research2012
Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- An AI-guided framework reveals conserved features governing microRNA strand selection.Nucleic acids research · 2026Article
- LIN-39 is a neuron-specific developmental determinant of longevity in Caenorhabditis elegans with reduced insulin signaling.Nature communications · 2025Article
- A dataset of expression profile of certain microRNAs in Caenorhabditis elegans.Scientific data · 2025Article
- Fluorescence-activated nuclear sorting (FANS) of nuclei from in vitro-generated syncytiotrophoblast.Placenta · 2025Article
- Multiomic profiling of transcription factor binding and function in human brain.Nature neuroscience · 2024Article
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- An updated C. elegans nuclear body muscle transcriptome for studies in muscle formation and function.Skeletal muscle · 2023Article
- Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in Caenorhabditis elegans.Genetics · 2023Article
- Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity.Journal of assisted reproduction and genetics · 2022Article
- Laser Microdissection for Species-Agnostic Single-Tissue Applications.Journal of visualized experiments : JoVE · 2022Article
- INTACT vs. FANS for Cell-Type-Specific Nuclei Sorting: A Comprehensive Qualitative and Quantitative Comparison.International journal of molecular sciences · 2021Article
- Tissue-specific DamID protocol using nanopore sequencing.Journal of biological methods · 2021Article
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- Innate Immunity in the C. elegans Intestine Is Programmed by a Neuronal Regulator of AWC Olfactory Neuron Development.Cell reports · 2020Article
- TheGenome research · 2019Article
- Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression.BMC genomics · 2019Article
- The transcription factor SKN-1 and detoxification gene ugt-22 alter albendazole efficacy in Caenorhabditis elegans.International journal for parasitology. Drugs and drug resistance · 2018Article
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Authors and funding
11 authors.
Funding
Abstract
Despite the many advantages of Caenorhabditis elegans, biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by fluorescence-activated nuclei sorting (FANS), followed by deep sequencing of linearly amplified 3'-end regions of transcripts (3'-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyadenylation. In agreement with intestinal-specific gene expression, highly expressed genes have enriched GATA-elements in their promoter regions and their functional properties are associated with processes that are characteristic for the intestine. We systematically mapped pre-mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have previously not been identified. The detailed analysis of the 3'-ends of the nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes. Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or A-rich upstream auxiliary elements that may contribute to the regulation of 3'-end formation in the intestine.
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