Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3′-end-seq

Simon Haenni, Zhe Ji, Mainul Hoque, Nigel Rust, Helen Sharpe, Ralf Eberhard, Cathy Browne, Michael O. Hengartner, Jane Mellor, Bin Tian, André Furger

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)6304-6318
Number of pages15
JournalNucleic acids research
Volume40
Issue number13
DOIs
StatePublished - Jul 2012

All Science Journal Classification (ASJC) codes

  • Genetics

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