Predicting gene expression responses to environment in <i>Arabidopsis thaliana</i> using natural variation in DNA sequence.

ABSTRACT: The evolution of gene expression responses is a critical component of adaptation to variable environments. Predicting how DNA sequence influences expression is challenging because the genotype to phenotype map is not well resolved for cis regulatory elements, transcription factor binding, regulatory interactions, and epigenetic features, not to mention how these factors respond to environment. We tested if flexible machine learning models could learn some of the underlying cis-regulatory genotype to phenotype map. We tested this approach using cold-responsive transcriptome profiles in 5 diverse Arabidopsis thaliana accessions. We first tested for evidence that cis regulation plays a role in environmental response, finding 14 and 15 motifs that were significantly

SUBMITTER: Takou M 

PROVIDER: S-EPMC11071634 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature