Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses

Phytohormones regulate many aspects of plant life by activating transcription factors (TFs) that bind sequence-specific response elements (REs) in regulatory regions of target genes. Despite their short length, REs are degenerate, with a core of just 3 to 4 bp. This degeneracy is paradoxical, as it...

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Veröffentlicht in:The Plant cell 2019-11, Vol.31 (11), p.2559-2572
Hauptverfasser: Lieberman-Lazarovich, Michal, Yahav, Chen, Israeli, Alon, Efroni, Idan
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container_end_page 2572
container_issue 11
container_start_page 2559
container_title The Plant cell
container_volume 31
creator Lieberman-Lazarovich, Michal
Yahav, Chen
Israeli, Alon
Efroni, Idan
description Phytohormones regulate many aspects of plant life by activating transcription factors (TFs) that bind sequence-specific response elements (REs) in regulatory regions of target genes. Despite their short length, REs are degenerate, with a core of just 3 to 4 bp. This degeneracy is paradoxical, as it reduces specificity and REs are extremely common in the genome. To study whether RE degeneracy might serve a biological function, we developed an algorithm for the detection of regulatory sequence conservation and applied it to phytohormone REs in 45 angiosperms. Surprisingly, we found that specific RE variants are highly conserved in core hormone response genes. Experimental evidence showed that specific variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum). Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a distinct transcriptional response profile. Our approach has implications for precise genome editing and for rational promoter design.
doi_str_mv 10.1105/tpc.19.00129
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subjects Abscisic Acid - metabolism
Algorithms
Arabidopsis - genetics
Arabidopsis - metabolism
Base Sequence
Conserved Sequence - genetics
Cytokinins - metabolism
DNA, Plant - analysis
Gene Expression Regulation, Plant
Genes, Plant - genetics
Genome, Plant
Large-Scale Biology
LARGE-SCALE BIOLOGY ARTICLE
Magnoliopsida - genetics
Plant Growth Regulators - metabolism
Plant Proteins - genetics
Plant Proteins - metabolism
Promoter Regions, Genetic
Regulatory Sequences, Nucleic Acid - genetics
Regulatory Sequences, Nucleic Acid - physiology
Response Elements - genetics
Sequence Analysis, DNA
Solanum lycopersicum - genetics
Solanum lycopersicum - metabolism
title Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses
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