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 |
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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. |
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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. 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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.</description><subject>Abscisic Acid - metabolism</subject><subject>Algorithms</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - metabolism</subject><subject>Base Sequence</subject><subject>Conserved Sequence - genetics</subject><subject>Cytokinins - metabolism</subject><subject>DNA, Plant - analysis</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes, Plant - genetics</subject><subject>Genome, Plant</subject><subject>Large-Scale Biology</subject><subject>LARGE-SCALE BIOLOGY ARTICLE</subject><subject>Magnoliopsida - genetics</subject><subject>Plant Growth Regulators - metabolism</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Promoter Regions, Genetic</subject><subject>Regulatory Sequences, Nucleic Acid - genetics</subject><subject>Regulatory Sequences, Nucleic Acid - physiology</subject><subject>Response Elements - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Solanum lycopersicum - genetics</subject><subject>Solanum lycopersicum - metabolism</subject><issn>1040-4651</issn><issn>1532-298X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkc1LwzAYxoMoTqc3r0qPHuzMm7RNehFkTidMFFHxFtI0nR1tU5N24H9v5ubQU17y_HjejwehE8AjABxfdq0aQTrCGEi6gw4gpiQkKX_f9TWOcBglMQzQoXML7BkG6T4aUIgSRiJ-gB5utG6DsWmctkvZlaYJTBGo0oWTSte66YI3aUvZdC541vO-8kgzD54q_xNMja1NIyuvuHbl4I7QXiErp4837xC93k5extNw9nh3P76ehSrCSReyHGecMZapjEeFTBXjRKo8woSmUGQKmIacZHnOcUYpiykoTguicc5ZkkpNh-hq7dv2Wa1z5ee0shKtLWtpv4SRpfivNOWHmJulSDgHoNgbnG8MrPnstetEXTqlK7-XNr0ThHAK4C-UePRijSprnLO62LYBLFYJCJ-AgFT8JODxs7-jbeHfk3vgdA0sXGfsVicJTyCOGP0GLkeNDA</recordid><startdate>20191101</startdate><enddate>20191101</enddate><creator>Lieberman-Lazarovich, Michal</creator><creator>Yahav, Chen</creator><creator>Israeli, Alon</creator><creator>Efroni, Idan</creator><general>American Society of Plant Biologists (ASPB)</general><general>American Society of Plant Biologists</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-1776-8257</orcidid><orcidid>https://orcid.org/0000-0003-1750-9842</orcidid><orcidid>https://orcid.org/0000-0002-3339-2042</orcidid><orcidid>https://orcid.org/0000-0002-0219-8685</orcidid></search><sort><creationdate>20191101</creationdate><title>Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses</title><author>Lieberman-Lazarovich, Michal ; 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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. 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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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