TY - JOUR
T1 - Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
AU - Kaletsky, Rachel
AU - Yao, Victoria
AU - Williams, April
AU - Runnels, Alexi M.
AU - Tadych, Alicja
AU - Zhou, Shiyi
AU - Troyanskaya, Olga G.
AU - Murphy, Coleen T.
N1 - Funding Information:
CTM is the Director of the Glenn Center for Aging Research at Princeton and an HHMI-Simons Faculty Scholar. OGT is a senior fellow of the Genetic Networks program of the Canadian Institute for Advanced Research (CIFAR). This work was supported by the NIH (DP1 Pioneer Award (GM119167) and Cognitive Aging R01 (AG034446) to CTM, and R01 GM071966 to OGT), as well as by the Glenn Medical Foundation. VY and AMR were supported in part by NIH T32 HG003284 and T32GM007388 grants. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the Murphy lab for valuable discussion, SB King for assistance, the Center for C. elegans Genetics (CGC) for strains. We thank Christina DeCoste and the Molecular Biology Flow Cytometry Resource Facility. An early version of a portion of this work appeared in the doctoral thesis of A. Williams.
Publisher Copyright:
© 2018 Kaletsky et al. http://creativecommons.org/licenses/by/4.0/.
PY - 2018/8
Y1 - 2018/8
N2 - 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.
AB - 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.
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U2 - 10.1371/journal.pgen.1007559
DO - 10.1371/journal.pgen.1007559
M3 - Article
C2 - 30096138
AN - SCOPUS:85053074565
SN - 1553-7390
VL - 14
JO - PLoS genetics
JF - PLoS genetics
IS - 8
M1 - e1007559
ER -