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

TitleTranscriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.
Publication TypeJournal Article
Year of Publication2018
AuthorsKaletsky, R, Yao, V, Williams, A, Runnels, AM, Tadych, A, Zhou, S, Troyanskaya, OG, Murphy, CT
JournalPLoS Genet
Volume14
Issue8
Paginatione1007559
Date Published2018 08
ISSN1553-7404
KeywordsAlternative Splicing, Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Forkhead Transcription Factors, Gene Expression Profiling, Gene Expression Regulation, Gene Library, Insulin, Insulin-Like Growth Factor I, Models, Molecular, Phenotype, Protein Isoforms, Sequence Analysis, RNA, Signal Transduction, Transforming Growth Factor beta
Abstract

<p>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.</p>

DOI10.1371/journal.pgen.1007559
Alternate JournalPLoS Genet.
PubMed ID30096138
PubMed Central IDPMC6105014
Grant ListR01 GM071966 / GM / NIGMS NIH HHS / United States
R01 AG034446 / NIA NIH HHS / National Institute on Aging / United States
T32 HG003284 / NHGRI NIH HHS / National Human Genome Research Institute / United States
T32 GM007388 / NIGMS NIH HHS / National Institute of General Medical Sciences / United States