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Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots

Plant iron deficiency ( Fe) activates a complex regulatory network which coordinates root Fe uptake and distribution to sink tissues. In Arabidopsis (Arabidopsis thaliana), FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT), a basic helix-loop-helix (bHLH) transcription factor (TF), regulates root Fe acquisition genes. Many other Fe-induced genes are FIT-independent, and instead regulated by other bHLH TFs and by yet unknown TFs. The cis-regulatory code, i.e. the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and co-expression clustering, we identified over 100 putative CREs (pCREs) that predicted -Fe-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 Fe 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 non-grass species. Our pCREs matched amongst others in vitro binding sites of B3, NAC, bZIP, and TCP TFs, which might be regulators of Fe responses. Altogether, our findings provide a comprehensive source of cis-regulatory information for -Fe-responsive genes, that advances our mechanistic understanding and informs future efforts in engineering plants with more efficient Fe uptake or transport systems.

Schwarz, B.; Azodi, C. B.; Shiu, S. H.; & Bauer, P;Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots, Plant Physiology 2020