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Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant

Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated b...

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Autores principales: Wu, Jianfei, Gao, Fan, Li, Tongtong, Guo, Haixia, Zhang, Li, Fan, Yijie, Chen, Aiyun, Wang, Jianjun, Shi, Fengjuan, Shan, Guangyao, Guo, Huihui, Zeng, Fanchang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775021/
https://www.ncbi.nlm.nih.gov/pubmed/35052364
http://dx.doi.org/10.3390/genes13010024
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author Wu, Jianfei
Gao, Fan
Li, Tongtong
Guo, Haixia
Zhang, Li
Fan, Yijie
Chen, Aiyun
Wang, Jianjun
Shi, Fengjuan
Shan, Guangyao
Guo, Huihui
Zeng, Fanchang
author_facet Wu, Jianfei
Gao, Fan
Li, Tongtong
Guo, Haixia
Zhang, Li
Fan, Yijie
Chen, Aiyun
Wang, Jianjun
Shi, Fengjuan
Shan, Guangyao
Guo, Huihui
Zeng, Fanchang
author_sort Wu, Jianfei
collection PubMed
description Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.
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spelling pubmed-87750212022-01-21 Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant Wu, Jianfei Gao, Fan Li, Tongtong Guo, Haixia Zhang, Li Fan, Yijie Chen, Aiyun Wang, Jianjun Shi, Fengjuan Shan, Guangyao Guo, Huihui Zeng, Fanchang Genes (Basel) Communication Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information. MDPI 2021-12-23 /pmc/articles/PMC8775021/ /pubmed/35052364 http://dx.doi.org/10.3390/genes13010024 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Wu, Jianfei
Gao, Fan
Li, Tongtong
Guo, Haixia
Zhang, Li
Fan, Yijie
Chen, Aiyun
Wang, Jianjun
Shi, Fengjuan
Shan, Guangyao
Guo, Huihui
Zeng, Fanchang
Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title_full Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title_fullStr Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title_full_unstemmed Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title_short Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant
title_sort genome-wide cis-regulatory element based discovery of auxin-responsive genes in higher plant
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8775021/
https://www.ncbi.nlm.nih.gov/pubmed/35052364
http://dx.doi.org/10.3390/genes13010024
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