IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-31208-4.html
   My bibliography  Save this article

The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

Author

Listed:
  • Gaotian Zhang

    (Northwestern University)

  • Nicole M. Roberto

    (Northwestern University)

  • Daehan Lee

    (Northwestern University)

  • Steffen R. Hahnel

    (Northwestern University)

  • Erik C. Andersen

    (Northwestern University)

Abstract

Phenotypic variation in organism-level traits has been studied in Caenorhabditis elegans wild strains, but the impacts of differences in gene expression and the underlying regulatory mechanisms are largely unknown. Here, we use natural variation in gene expression to connect genetic variants to differences in organismal-level traits, including drug and toxicant responses. We perform transcriptomic analyses on 207 genetically distinct C. elegans wild strains to study natural regulatory variation of gene expression. Using this massive dataset, we perform genome-wide association mappings to investigate the genetic basis underlying gene expression variation and reveal complex genetic architectures. We find a large collection of hotspots enriched for expression quantitative trait loci across the genome. We further use mediation analysis to understand how gene expression variation could underlie organism-level phenotypic variation for a variety of complex traits. These results reveal the natural diversity in gene expression and possible regulatory mechanisms in this keystone model organism, highlighting the promise of using gene expression variation to understand how phenotypic diversity is generated.

Suggested Citation

  • Gaotian Zhang & Nicole M. Roberto & Daehan Lee & Steffen R. Hahnel & Erik C. Andersen, 2022. "The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31208-4
    DOI: 10.1038/s41467-022-31208-4
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-31208-4
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-31208-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Carlos L. Araya & Trupti Kawli & Anshul Kundaje & Lixia Jiang & Beijing Wu & Dionne Vafeados & Robert Terrell & Peter Weissdepp & Louis Gevirtzman & Daniel Mace & Wei Niu & Alan P. Boyle & Dan Xie & L, 2014. "Regulatory analysis of the C. elegans genome with spatiotemporal resolution," Nature, Nature, vol. 512(7515), pages 400-405, August.
    2. Bates, Douglas & Mächler, Martin & Bolker, Ben & Walker, Steve, 2015. "Fitting Linear Mixed-Effects Models Using lme4," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 67(i01).
    3. Scott A. Rifkin & David Houle & Junhyong Kim & Kevin P. White, 2005. "A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression," Nature, Nature, vol. 438(7065), pages 220-223, November.
    4. Tingley, Dustin & Yamamoto, Teppei & Hirose, Kentaro & Keele, Luke & Imai, Kosuke, 2014. "mediation: R Package for Causal Mediation Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 59(i05).
    5. Joshua S. Bloom & Ian M. Ehrenreich & Wesley T. Loo & Thúy-Lan Võ Lite & Leonid Kruglyak, 2013. "Finding the sources of missing heritability in a yeast cross," Nature, Nature, vol. 494(7436), pages 234-237, February.
    6. Giovanny Covarrubias-Pazaran, 2016. "Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-15, June.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Vonneilich, Nico & Lüdecke, Daniel & von dem Knesebeck, Olaf, 2020. "Educational inequalities in self-rated health and social relationships – analyses based on the European Social Survey 2002-2016," Social Science & Medicine, Elsevier, vol. 267(C).
    2. Lara Lopez & Fernando L. Vázquez & Ángela J. Torres & Patricia Otero & Vanessa Blanco & Olga Díaz & Mario Páramo, 2020. "Long-Term Effects of a Cognitive Behavioral Conference Call Intervention on Depression in Non-Professional Caregivers," IJERPH, MDPI, vol. 17(22), pages 1-24, November.
    3. Martina Hančová & Andrej Gajdoš & Jozef Hanč & Gabriela Vozáriková, 2021. "Estimating variances in time series kriging using convex optimization and empirical BLUPs," Statistical Papers, Springer, vol. 62(4), pages 1899-1938, August.
    4. repec:cup:judgdm:v:14:y:2019:i:3:p:349-363 is not listed on IDEAS
    5. Lisa Auweiler & Jessica Lang & Maria Thissen & Roman Pauli, 2023. "Workplace Bullying Experience Predicts Same-Day Affective Rumination but Not Next Morning Mood: Results from a Moderated Mediation Analysis Based on a One-Week Daily Diary Study," Sustainability, MDPI, vol. 15(21), pages 1-16, October.
    6. Luciano Rogério Braatz de Andrade & Massaine Bandeira e Sousa & Eder Jorge Oliveira & Marcos Deon Vilela de Resende & Camila Ferreira Azevedo, 2019. "Cassava yield traits predicted by genomic selection methods," PLOS ONE, Public Library of Science, vol. 14(11), pages 1-22, November.
    7. Shephard, Daniel D. & Kaneza, Yves V. & Moclair, Paul, 2017. "What curriculum? Which methods? A cluster randomized controlled trial of social and financial education in Rwanda," Children and Youth Services Review, Elsevier, vol. 82(C), pages 310-320.
    8. Andrews, Mary E. & Mattan, Bradley D. & Richards, Keana & Moore-Berg, Samantha L. & Falk, Emily B., 2022. "Using first-person narratives about healthcare workers and people who are incarcerated to motivate helping behaviors during the COVID-19 pandemic," Social Science & Medicine, Elsevier, vol. 299(C).
    9. Guo, Liang & Decoster, Stijn & Babalola, Mayowa T. & De Schutter, Leander & Garba, Omale A. & Riisla, Katrin, 2018. "Authoritarian leadership and employee creativity: The moderating role of psychological capital and the mediating role of fear and defensive silence," Journal of Business Research, Elsevier, vol. 92(C), pages 219-230.
    10. Tian Fan & Jun Zheng & Xiao Hu & Ningxin Su & Yue Yin & Chunliang Yang & Liang Luo, 2021. "The contribution of metamemory beliefs to the font size effect on judgments of learning: Is word frequency a moderating factor?," PLOS ONE, Public Library of Science, vol. 16(9), pages 1-22, September.
    11. Auzepy, Alix & Bannier, Christina E. & Gärtner, Florian, 2024. "Looking beyond ESG preferences: The role of sustainable finance literacy in sustainable investing," CFS Working Paper Series 719, Center for Financial Studies (CFS).
    12. Sandra Jaworeck & Peter Kriwy, 2021. "It’s Sunny, Be Healthy? An International Comparison of the Influence of Sun Exposure and Latitude Lines on Self-Rated Health," IJERPH, MDPI, vol. 18(8), pages 1-19, April.
    13. Jay Vornhagen & Emily K. Roberts & Lavinia Unverdorben & Sophia Mason & Alieysa Patel & Ryan Crawford & Caitlyn L. Holmes & Yuang Sun & Alexandra Teodorescu & Evan S. Snitkin & Lili Zhao & Patricia J., 2022. "Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    14. Thomas Schultze & Andreas Mojzisch & Stefan Schulz-Hardt, 2019. "Why dyads heed advice less than individuals do," Judgment and Decision Making, Society for Judgment and Decision Making, vol. 14(3), pages 349-363, May.
    15. Takeshi Matsui & Martin N. Mullis & Kevin R. Roy & Joseph J. Hale & Rachel Schell & Sasha F. Levy & Ian M. Ehrenreich, 2022. "The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    16. Louis Albert & Jevita Potheegadoo & Bruno Herbelin & Fosco Bernasconi & Olaf Blanke, 2024. "Numerosity estimation of virtual humans as a digital-robotic marker for hallucinations in Parkinson’s disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    17. Mitchell J. Feldmann & Dominique D. A. Pincot & Glenn S. Cole & Steven J. Knapp, 2024. "Genetic gains underpinning a little-known strawberry Green Revolution," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    18. JANSSENS, Jochen & DE CORTE, Annelies & SÖRENSEN, Kenneth, 2016. "Water distribution network design optimisation with respect to reliability," Working Papers 2016007, University of Antwerp, Faculty of Business and Economics.
    19. Raymond Hernandez & Elizabeth A. Pyatak & Cheryl L. P. Vigen & Haomiao Jin & Stefan Schneider & Donna Spruijt-Metz & Shawn C. Roll, 2021. "Understanding Worker Well-Being Relative to High-Workload and Recovery Activities across a Whole Day: Pilot Testing an Ecological Momentary Assessment Technique," IJERPH, MDPI, vol. 18(19), pages 1-17, October.
    20. Christopher Hassall & Michael Nisbet & Evan Norcliffe & He Wang, 2024. "The Potential Health Benefits of Urban Tree Planting Suggested through Immersive Environments," Land, MDPI, vol. 13(3), pages 1-12, February.
    21. Jie Zhao & Ji Chen & Damien Beillouin & Hans Lambers & Yadong Yang & Pete Smith & Zhaohai Zeng & Jørgen E. Olesen & Huadong Zang, 2022. "Global systematic review with meta-analysis reveals yield advantage of legume-based rotations and its drivers," Nature Communications, Nature, vol. 13(1), pages 1-9, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31208-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.