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

AI Article Synopsis

  • - The study introduces a new method for analyzing tissue-specific gene expression in C. elegans, using fluorescence-activated nuclei sorting (FANS) and deep sequencing to focus on the intestine post-embryonically.
  • - Researchers compiled the intestinal transcriptome, confirming that genes highly expressed in the intestine have GATA-elements in their promoters and are related to intestinal functions.
  • - They identified over 3000 previously unknown pre-mRNA cleavage and polyadenylation sites, revealing that many intestinal genes utilize alternative polyA sites, which are influenced by specific upstream elements that regulate their expression.

Article 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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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401467PMC
http://dx.doi.org/10.1093/nar/gks282DOI Listing

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