Gene Expression Variation and Regulatory Evolution

Variation in gene expression underpins phenotypic diversity and fuels evolutionary change. Differences in transcript abundance among individuals, populations or species arise from mutations in regulatory DNA, modifications of regulatory proteins and changes in chromatin state. These alterations may occur in cis-regulatory elements adjacent to genes or through trans-acting factors that influence many targets. Natural selection acts on both constitutive expression differences and environmentally induced plastic responses, shaping traits from stress tolerance to developmental timing. Regulatory evolution is central to processes such as adaptation to new climates, domestication of crops and the emergence of novel cell types. By integrating comparative transcriptomics, functional assays and population genetics, researchers are uncovering how stabilising and directional selection interact with pleiotropy and network architecture to constrain or promote expression divergence. Insights into the mechanisms of regulatory change are illuminating the genetic basis of adaptive traits and offering routes to engineer gene networks for agriculture and medicine.

Research from Nature Portfolio

Recent studies of chemosensory tissues across multiple fruit-fly species have combined bulk and single-cell transcriptomics to reveal pervasive yet tissue-specific stabilising selection alongside episodes of rapid expression innovation. Thousands of genes show gains or losses of expression patterns in particular cell types, and sex-biased expression evolves independently in sensory and muscle lineages, illustrating the modularity of regulatory change.

Investigations of cis and trans regulatory divergence in domesticated cotton have uncovered extensive compensatory evolution following polyploid formation. Both homeologous subgenomes exhibit unique patterns of cis-element modification and trans-factor regulation, with co-expression network analyses highlighting modules associated with fibre traits. This work demonstrates how genome duplication can fuel regulatory novelty during crop domestication.

Gene Expression Variation and Regulatory Evolution publication trend

The graph below shows the total number of articles in gene expression variation and regulatory evolution across all publications each year (not limited to Nature Index journals).

Technical terms

cis-regulatory element: A non-coding DNA sequence near a gene that binds transcription factors to control that gene’s expression.

trans-regulatory factor: A diffusible molecule, often a transcription factor or RNA, that influences expression of target genes throughout the genome.

gene expression plasticity: The capacity of a genotype to alter its transcriptional output in response to environmental changes.

eQTL: A genomic locus where genetic variation correlates with quantitative differences in gene expression.

genotype-by-environment interaction: A phenomenon where the effect of a genetic variant on phenotype depends on the environmental context.

References

1. Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids. Nature Communications (2024).
2. Unraveling cis and trans regulatory evolution during cotton domestication. Nature Communications (2019).
3. Transcriptomic response to nitrogen availability reveals signatures of adaptive plasticity during tetraploid wheat domestication. The Plant Cell (2024).
4. Environmentally robust cis-regulatory changes underlie rapid climatic adaptation. Proceedings of the National Academy of Sciences of the United States of America (2023).
5. Rewards and dangers of regulatory innovation. Trends in Genetics (2024).