Universität zu Köln

Schwarz, Birte ORCID: 0000-0003-2801-9638, Azodi, Christina B., Shiu, Shin-Han ORCID: 0000-0001-6470-235X and Bauer, Petra (2020). Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots(1)([OPEN]). Plant Physiol., 182 (3). S. 1420 - 1440. ROCKVILLE: AMER SOC PLANT BIOLOGISTS. ISSN 1532-2548

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Abstract

Plant iron deficiency (-Fe) 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-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, that is, the cis-regulatory elements (CREs) and their combinations that regulate plant -Fe-responses, remains largely elusive. Using Arabidopsis root transcriptome data and coexpression 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 nongrass species. Our pCREs matched among 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 advance our mechanistic understanding and inform future efforts in engineering plants with more efficient Fe uptake or transport systems. More than 100 putative cis-regulatory elements robustly predict Arabidopsis root iron deficiency responses in computational models and shed light on the mechanisms of transcriptional regulation.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Schwarz, Birte UNSPECIFIED orcid.org/0000-0003-2801-9638 UNSPECIFIED Azodi, Christina B. UNSPECIFIED UNSPECIFIED UNSPECIFIED Shiu, Shin-Han UNSPECIFIED orcid.org/0000-0001-6470-235X UNSPECIFIED Bauer, Petra UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-342810
DOI:	10.1104/pp.19.00760
Journal or Publication Title:	Plant Physiol.
Volume:	182
Number:	3
Page Range:	S. 1420 - 1440
Date:	2020
Publisher:	AMER SOC PLANT BIOLOGISTS
Place of Publication:	ROCKVILLE
ISSN:	1532-2548
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language TRANSCRIPTION FACTOR-BINDING; MODEL DATA-ANALYSIS; GENE-EXPRESSION; SEED-GERMINATION; CIRCADIAN CLOCK; ABSCISIC-ACID; FERULOYL-COA; FACTOR FIT; DATA SET; ACQUISITION Multiple languages Plant Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/34281