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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

57 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

Funding

EPA Cephalosporin Fund (to A.F. and S.H.), MRC (to H.S.), Swiss National Science Foundation (SNSF, to S.H.), the Ernst Hadorn Foundation (to R.E. and M.H.), and NIH (GM084089 and HG005129, to B.T., M.H., and Z.J.). Funding for open access charge: Department of Biochemistry, University of Oxford (to A.F.).

ASJC Scopus subject areas

  • Genetics

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