Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots (Plant Physiol.)

Iron (Fe) is an important micronutrient needed by plants for survival. Plants have evolved a range of morphological, physiological and molecular responses to Fe availability, including the transcriptional regulation of over one thousand genes in response to Fe deficiency (-Fe) in Arabidopsis. However, the cis-regulatory elements (CREs) and their combinations that regulate the adaptive response to -Fe remain largely unknown. Schwarz and colleagues used computational models to identify putative CREs during -Fe. Arabidopsis root transcriptomics and co-expression data were used to identify more than one hundred potential CREs that are indicative of -Fe induced gene expression.  Multiple gene expression data sets were used to define iron deficiency co-expression clusters, and a model for their regulation was developed using a machine learning technique. Common CREs across co-expression clusters were identified and compared to known transcription factor binding motifs. Interestingly, the authors found evidence supporting a role in Arabidopsis for the IDE1 element known to have a role in grasses, which use a different strategy for iron uptake.  Taken together, Schwarz et al. provided a comprehensive source of cis-regulatory information predictive of iron deficiency responsive genes in Arabidopsis roots.  (Summary by Adenike Oyekunle) Plant Physiol. 10.1104/pp.19.00760