Systems-level transcriptional regulation of Caenorhabditis elegans metabolism

Shivani Nanda, Marc Antoine Jacques, Wen Wang, Chad L. Myers, L. Safak Yilmaz, Albertha J.M. Walhout

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

Metabolism is controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and transcriptional regulation of metabolic enzymes and transporters. So far, metabolism regulation has mostly been described for individual genes and pathways, and the extent of transcriptional regulation of the entire metabolic network remains largely unknown. Here, we find that three-quarters of all metabolic genes are transcriptionally regulated in the nematode Caenorhabditis elegans. We find that many annotated metabolic pathways are coexpressed, and we use gene expression data and the iCEL1314 metabolic network model to define coregulated subpathways in an unbiased manner. Using a large gene expression compendium, we determine the conditions where subpathways exhibit strong coexpression. Finally, we develop “WormClust,” a web application that enables a gene-by-gene query of genes to view their association with metabolic (sub)-pathways. Overall, this study sheds light on the ubiquity of transcriptional regulation of metabolism and provides a blueprint for similar studies in other organisms, including humans.

Original languageEnglish (US)
Article numbere11443
JournalMolecular Systems Biology
Volume19
Issue number5
DOIs
StatePublished - May 9 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2023 The Authors. Published under the terms of the CC BY 4.0 license.

Keywords

  • gene regulation
  • metabolic network model
  • metabolism
  • systems biology
  • transcription

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural

Fingerprint

Dive into the research topics of 'Systems-level transcriptional regulation of Caenorhabditis elegans metabolism'. Together they form a unique fingerprint.

Cite this