Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

Rachel Kaletsky, Victoria Yao, April Williams, Alexi M. Runnels, Alicja Tadych, Shiyi Zhou, Olga G. Troyanskaya, Coleen T. Murphy

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are critical for understanding molecular mechanisms that control their phenotypes. We used adult cell-specific isolation to identify the transcriptomes of C. elegans’ four major tissues (or “tissue-ome”), identifying ubiquitously expressed and tissue-specific “enriched” genes. These data newly reveal the hypodermis’ metabolic character, suggest potential worm-human tissue orthologies, and identify tissue-specific changes in the Insulin/IGF-1 signaling pathway. Tissue-specific alternative splicing analysis identified a large set of collagen isoforms. Finally, we developed a machine learning-based prediction tool for 76 sub-tissue cell types, which we used to predict cellular expression differences in IIS/FOXO signaling, stage-specific TGF-β activity, and basal vs. memory-induced CREB transcription. Together, these data provide a rich resource for understanding the biology governing multicellular adult animals.

Original languageEnglish (US)
Article numbere1007559
JournalPLoS genetics
Volume14
Issue number8
DOIs
StatePublished - Aug 2018

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

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