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

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.

Non-Canonical Activation of CREB Mediates Neuroprotection in aC. elegansModel of Excitotoxic Necrosis

“…GluRs mediate both basic signaling and synaptic plasticity (Rose et al 2003(Rose et al , 2005Rose and Rankin 2006;Emtage et al 2009;Stetak et al 2009). CREB (worm homolog name: CRH-1) and the components of its canonical activation cascade are also well conserved in the worm, and regulate learning and memory and synaptic plasticity Bates et al 2006;Suo et al 2006;Kauffman et al 2010;Nishida et al 2011;Timbers and Rankin 2011;Yu et al 2014;Lakhina et al 2015;Chen et al 2016;Moss et al 2016;Freytag et al 2017;Nishijima and Maruyama 2017;Arey et al 2018;Kaletsky et al 2018). CREB/CRH-1 can be activated by phosphorylation (on a site homologous to Ser133) by the nematode's combined CaMK I/IV homolog CMK-1, whose basal activity is greatly stimulated by CaMKK/CKK-1 Yu et al 2014) (while the other CREB phosphorylation sites seen in mammals do not seem to be conserved in the nematode).…”

Organism-wide single-cell transcriptomics of long-livedC. elegans daf-2-/-mutants reveals tissue-specific reprogramming of gene expression networks

“…Dozens of genes are highly expressed in the lateral seam cells of daf-2 -/animals, including several hormone-induced transcription factors (nhr-gene family), groundhog-like genes (grd-gene family), and a large network of genes involved in endosomal packaging and distribution of neuromodulators (Table S8). These result suggest that seam cells facilitate non-cell autonomous signaling via endosomal diffusion of neuromodulators (Kaletsky, Yao et al 2018), possibly through a sterol-induced mechanism of extracellular matrix remodeling which facilitates increased vesicle trafficking.…”

“…The biomarker lists generated by the software were analyzed using the WormBase SimpleMine database, which provides high-throughput descriptions of gene function and tissue-specific expression. Several genes were identified which provide anatomical, biochemical, and genetic information about the cell type clusters supported by the literature (Tomaselli, Reichardt et al 1986, Way and Chalfie 1989, Way, Wang et al 1991, Gendreau, Moskowitz et al 1994, Wang and Way 1996, Tavernarakis, Shreffler et al 1997, Duggan, Ma et al 1998, Koh and Rothman 2001, Jia, Chen et al 2004, Fukushige, Brodigan et al 2006, Smit, Schnabel et al 2008, Barrios, Ghosh et al 2012, Frooninckx, Van Rompay et al 2012, Goodwin, Sasaki et al 2012, Komuniecki, Harris et al 2012, Sasidharan, Sumakovic et al 2012, Jedrusik-Bode 2013, Towlson, Vertes et al 2013, Ackley 2014, Ortiz, Noble et al 2014, Peymen, Watteyne et al 2014, Burdick, Walton et al 2016, Kaletsky, Yao et al 2018.…”

“…To achieve a comprehensive and unbiased view of the adult C. elegans transcriptome, we employed whole-worm single-cell 10x Genomics ® ChromiumV1 TM 3'-mRNA-sequencing combined with unsupervised machine learning-based characterization of cell-specific gene expression patterns (Zheng, Terry et al 2017, Butler, Hoffman et al 2018). Suspensions of live dissociated C. elegans cells were prepared from age-synchronized populations of whole day-one adult wild-type and daf-2 -/worms as described, using a 5-micron filter (Kaletsky, Lakhina et al 2016, Kaletsky, Yao et al 2018. Live cells were individually-partitioned into aqueous oilemulsion nanodroplets using 10x ChromiumV1 TM microfluidics technology.…”

WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data

“…In the present study, we used the same criteria as the 932 respective authors, except that we separated up and downregulated genes where 933 necessary. For example, in the Kaletsky et al tissue-specific data, the authors provided 934 data for all genes expressed in each tissue, enriched genes (expressed at FDR great 935 than 0.05, and log2 fold change greater than 2 relative to other tissues), or unique genes 936 (log2 RPKM greater than 5) significantly differentially expressed in comparison to the 937 expression of each of the three other tissues (FDR greater than 0.05, log2 fold change 938 greater than 2 for each comparison) (Kaletsky et al 2018). We found the best 939 resolution of WormCat categories between the tissues occurred with the enriched 940 datasets, rather than with all genes or unique gene sets.…”