Regulatory networks articles from across Nature Portfolio

Plants have uniquely adapted to manage endoplasmic reticulum stress triggered by protein misfolding. The authors review the dynamics of gene expression regulation underlying the unfolded protein response in plants, highlighting recent insights provided by systems-level approaches and omics data.

Transkingdom Network Analysis (TkNA) is a unique analytical framework for inferring causal factors underlying host–microbiota and other multi-omic interactions, by integrating data from multiple cohorts and diverse omics types.

Single-cell expression data from bacteria are used to classify gene regulatory architectures in relation to gene expression dynamics and the cell cycle, revealing distinct categories of gene regulatory mechanisms.

We present SCORPION, a computational tool to model gene regulatory networks based on single-cell transcriptomic data and prior knowledge of gene regulation. SCORPION networks can be modeled for specific cell types in individual samples, and are therefore suitable for conducting comparisons between experimental groups.

Kate Galloway highlights a paper by Kueh et al., who showed that the cell cycle indirectly influences concentrations of the transcription factor PU.1 to stabilize cell-fate trajectories in mice.

We outline protein interaction networks for 13 ion channels isolated from mouse hearts and show that several protein components are shared between ion channel networks. Multi-omic data integration couples these findings to features of the human heart electrocardiogram and we evaluate the functional effect of ten network proteins on cardiac electrophysiology.

Sleep disruption is a common but poorly understood feature of neurodevelopmental disorders including autism spectrum disorder. A study by Bian et al. reveals that sleep disruption in adolescent mice leads to long-lasting changes in social novelty preferences. Importantly, these perturbations can be restored through balanced actions in midbrain dopamine systems.

Elizabeth Mason recalls a seminal study by Raj et al., who used single-molecule approaches to expose principles governing how genes in a network cooperate to buffer perturbation while maintaining essential cellular functions.

Chemical and pathogenic hazards in aquaculture supply chains threaten the provision of safe aquatic food. The Seafood Risk Tool is an integrated, semi-quantitative system that develops bespoke supply chain and risk management strategies.