RT Journal Article SR Electronic T1 Putative cis-regulatory elements predict iron deficiency responses in Arabidopsis roots JF bioRxiv FD Cold Spring Harbor Laboratory SP 603290 DO 10.1101/603290 A1 Birte Schwarz A1 Christina B. Azodi A1 Shin-Han Shiu A1 Petra Bauer YR 2019 UL http://biorxiv.org/content/early/2019/04/11/603290.abstract AB Iron (Fe) is a key cofactor in many cellular redox processes, including respiration and photosynthesis. Plant Fe deficiency (-Fe) activates a complex regulatory network which coordinates root Fe uptake and distribution to sink tissues, while avoiding over-accumulation of Fe and other metals to toxic levels. In Arabidopsis (Arabidopsis thaliana), FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR), a bHLH transcription factor (TF), is required for up-regulation of root Fe acquisition genes. However, other root and shoot -Fe-induced genes involved in Fe allocation and signaling are FIT-independent. The cis-regulatory code, i.e. the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis genome and transcriptome data, we identified over 100 putative CREs (pCREs) that were predictive of -Fe-induced up-regulation of genes in root tissue. We used large-scale in vitro TF binding data, association with FIT-dependent or FIT-independent co-expression clusters, positional bias, and evolutionary conservation to assess pCRE properties and possible functions. In addition to bHLH and MYB TFs, also B3, NAC, bZIP, and TCP TFs might be important regulators for -Fe responses. Our approach uncovered IDE1 (Iron Deficiency-responsive Element 1), a -Fe response CRE in grass species, to be conserved in regulating genes for biosynthesis of Fe-chelating compounds also in Arabidopsis. 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.One sentence summary >100 putative cis-regulatory elements robustly predict Arabidopsis root Fe deficiency-responses in computational models, and shed light on the mechanisms of transcriptional regulation.CIS-BPCatalog of inferred sequence binding preferencesCNSConserved non-coding sequenceDAP-seqDNA affinity purification sequencingFe/-FeIron/Iron deficiencyFeSIron-SulfurFETFisher’s exact testFITFE DEFICIENCY-INDUCED TRANSCRIPTION FACTORfreq-pCREFrequent pCREGO(Biological process) Gene ontologyGSGold standardIDEIron Deficiency-responsive Elementlog2FClog2 fold-changeMAMugineic acidmin-pCREMinimum set pCREPCCPearson’s correlation coefficientpCREPutative cis-regulatory elementPWMPosition weight matrixRFRandom ForestTFTranscription factorTFBMTranscription factor binding motifTSSTranscription start siteTTSTranscription termination siteZnZinc