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Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol

Truong, Lisa and Chen, Yen-Wei and Barrere-Cain, Rio and Shuck, Karissa and Xiao, Wen and Levenson, Max T. and da Veiga Beltrame, Eduardo and Panter, Blake and Reich, Ella and Sternberg, Paul W. and Yang, Xia and Allard, Patrick (2022) Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol. . (Unpublished)

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Single-cell RNA transcriptomic platforms have significantly contributed to our understanding of tissue heterogeneity as well as of developmental and cellular differentiation trajectories. They also provide an opportunity to map an organism’s response to environmental cues with high resolution and unbiasedly identify the cell types that are the most transcriptionally sensitive to exposures. Here, we applied single nucleus RNA-seq experimental and computational approaches to C. elegans to establish the transcriptome of the adult nematode and comprehensively characterize the transcriptional impact of ethanol as a model environmental exposure on the entire organism at cell type-resolution over several generations. Clustering, tissue and phenotype enrichment, and gene ontology analyses identified 31 clusters representing a diverse number of adult cell types, including those from syncytial and multi-nucleated tissues which are difficult to assess by single cell RNA-seq, such as the mitotic and meiotic germline, hypodermal cells, and the intestine. We applied this method to identify the impact of inter- and trans-generational exposure to two human-relevant doses of alcohol. Cell type proportions were not significantly altered by ethanol. However, Euclidean distance analysis identified several germline, striated muscle, and neuronal clusters as being major transcriptional targets of ethanol at both the F1 and F3 generations although the relative order of clusters changed between generations. The impact on germline clusters was further confirmed by phenotypic enrichment analysis as well as functional validation, namely a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq of the adult C. elegans represents a powerful approach for the detailed examination of an adult organism’s response to environmental cues.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Information ItemData - Broad Single Cell Portal: ItemRaw data at Gene Expression Omnibus (GEO)
Barrere-Cain, Rio0000-0002-0522-253X
Xiao, Wen0000-0001-6559-3036
Levenson, Max T.0000-0002-1470-3968
da Veiga Beltrame, Eduardo0000-0002-1529-9207
Sternberg, Paul W.0000-0002-7699-0173
Allard, Patrick0000-0001-7765-1547
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The authors would like to thank Doug Arneson for input on single-nucleus sequencing parameters; Ingrid Cely, In Sook Ahn, and Graciel Diamante for discussions and trouble-shooting advice; Eyal Ben David for advice on single-cell/nuclei dissociation methods; Jessica Scholes, Jeffrey Calim, Felicia Codrea, and Salem Haile for guidance with single-nucleus cytometry; Michael Mashock and Marco De Simone for their library preparation and sequencing expertise. Matteo Pellegrini for advice and input on data analysis. We thank Judith Kimble, Tina Lynch, and Sarah Crittenden for advice on smFISH and providing the sygl-1 probe. The Caenorhabditis Genetics Center (CGC) provided the strains used in this study. We thank Yuji Kohara for permission to use NEXTDB in situ data. LT is supported by the NIH Training Grant in Genomic Analysis and Interpretation T32 HG002536; YWC is supported by the UCLA Eureka fellowship and Burroughs Wellcome Fund Inter-school Training Program in Chronic Diseases; PA is supported by NIEHS R01 ES027487, NIAAA R21 AA024889, the John Templeton Foundation, and the Burroughs Wellcome Innovation in Regulatory Science Award. EDVB and PWS are supported by U24HG002223. Author Contributions. LT, RBC, KS, WX, MTL, BP, and EL performed biological experiments and corresponding analyses, YWC performed bioinformatic analyses, PA and XY supervised experiments, PA and XY supervised analyses, EB devised a visualization approach that assisted cell type assignment and cluster identification which PS supervised, LT, RBC, YWC, XY, and PA wrote the manuscript. DATA AVAILABILITY. All raw data is accessible on NCBI's Gene Expression Omnibus (GEO), at: The data is also available through the Broad Single Cell Portal: The authors have declared no competing interest.
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32 HG002536
Burroughs Wellcome FundUNSPECIFIED
NIHR01 ES027487
NIHR21 AA024889
John Templeton FoundationUNSPECIFIED
Subject Keywords:C. elegans, snRNA-seq, ethanol, alcohol
Record Number:CaltechAUTHORS:20220725-414617000
Persistent URL:
Official Citation:Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol Lisa Truong, Yen-Wei Chen, Rio Barrere-Cain, Karissa Shuck, Wen Xiao, Max T. Levenson, Eduardo da Veiga Beltrame, Blake Panter, Ella Reich, Paul W. Sternberg, Xia Yang, Patrick Allard bioRxiv 2022.07.21.500524; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:115810
Deposited By: George Porter
Deposited On:27 Jul 2022 15:48
Last Modified:27 Jul 2022 15:48

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