Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

Abstract

Plant iron deficiency (2Fe) activates a complex regulatory network that coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loophelix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other 2Fe-induced genes are FIT independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant 2Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression clustering, we identified over 100 putative CREs (pCREs) that predicted 2Fe-induced gene expression in computational models. To assess pCRE properties and possible functions, we used large-scale in vitro TF binding data, positional bias, and evolutionary conservation. As one example, our approach uncovered pCREs resembling IDE1 (iron deficiency-responsive element 1), a known grass 2Fe response CRE. Arabidopsis IDE1-likes were associated with FIT-dependent gene expression, more specifically with biosynthesis of Fe-chelating compounds. Thus, IDE1 seems to be conserved in grass and nongrass species. Our pCREs matched among others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of 2Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for 2Fe-responsive genes that advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems.

Interconnection of iron and osmotic stress signalling in plants: is FIT a regulatory hub to cross‐connect abscisic acid responses?

“…Moreover, bZIP transcription factors are predicted trans‐acting factors that regulate Fe deficiency responses, based on a computational approach for enrichment of putative cis‐regulatory elements in the promoters of Fe deficiency response genes (Schwarz et al . 2020). Because of these strong associations of FIT with CIPK11 and ABI5, we consider it reasonable to postulate that FIT is linked with ABI5.…”

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming

“…Separate studies showed that systematic analysis of transcriptome datasets is powerful in the identification of the cistrome behind a complex reaction [7,8,19]. The basic assumption in these studies, as well as in the metaRE algorithm, is that only robust and significant cis-element association with transcriptional response will be detected across multiple, diverse transcriptomic datasets that test similar experimental variables.…”

“…They revealed enrichment of transcription factors binding sites in the DEGs and their association with external factors that cause similar changes in the organism. An interesting approach has been applied to study the cistrome for iron deficiency response in Arabidopsis (Arabidopsis thaliana) roots [8]. Authors searched for the enrichment of k-mers in upstream regulatory regions of Fe-responsive genes taken from several experiments.…”

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

“…Machine learning approaches have provided new and powerful ways for understanding and predicting gene expression in plants (Azodi et al, 2020b; Wang et al, 2020b; Washburn et al, 2019). These approaches have been used to predict expression levels (Washburn et al, 2019; Sartor et al, 2019), regulatory architecture (Mejía-Guerra and Buckler, 2019), as well as gene expression responses to abiotic stress (Zou et al, 2011; Uygun et al, 2017, 2019; Azodi et al, 2020a; Schwarz et al, 2020). These studies highlight the potential to develop predictive models that use putative cis-regulatory motifs to predict gene expression responses to stress.…”