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 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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Genome-wide exploration of auxin response factors (ARFs) and their expression dynamics in response to abiotic stresses and growth regulators in coconut (Cocos nucifera L.)

Plant Gene ◽

10.1016/j.plgene.2021.100344 ◽

2021 ◽

pp. 100344

Author(s):

C.K.V. Santhi ◽

M.K. Rajesh ◽

S.V. Ramesh ◽

K.S. Muralikrishna ◽

K.P. Gangaraj ◽

...

Keyword(s):

Growth Regulators ◽

Abiotic Stresses ◽

Cocos Nucifera ◽

Auxin Response ◽

Response Factors ◽

Auxin Response Factors ◽

Genome Wide ◽

Cocos Nucifera L

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Two Auxin Response Elements Fine-Tune PINOID Expression During Gynoecium Development in Arabidopsis thaliana

Biomolecules ◽

10.3390/biom9100526 ◽

2019 ◽

Vol 9 (10) ◽

pp. 526

Author(s):

André Kuhn ◽

Bethany Runciman ◽

William Tasker-Brown ◽

Lars Østergaard

Keyword(s):

Dna Binding ◽

Binding Sites ◽

Target Genes ◽

Regulatory Elements ◽

Auxin Response ◽

Response Factors ◽

Regulatory Regions ◽

Dna Binding Sites ◽

Gene Regulatory ◽

Gynoecium Development

The plant hormone auxin controls almost all aspects of plant development through the gene regulatory properties of auxin response factors (ARFs) which bind so-called auxin responsive elements (AuxREs) in regulatory regions of their target genes. It has been proposed that ARFs interact and cooperate with other transcription factors (TFs) to bind to complex DNA-binding sites harboring cis-elements for several TFs. Complex DNA-binding sites have not been studied systematically for ARF target genes. ETTIN (ETT; ARF3) is a key regulator of gynoecium development. Cooperatively with its interacting partner INDEHISCENT (IND), ETT regulates PINOID (PID), a gene involved in the regulation gynoecium apical development (style development). Here, we mutated two ETT-bound AuxREs within the PID promoter and observed increased style length in gynoecia of plants carrying mutated promoter variants. Furthermore, mutating the AuxREs led to ectopic repression of PID in one developmental context while leading to ectopically upregulated PID expression in another stage. Our data also show that IND associates with the PID promoter in an auxin-sensitive manner. In summary, we demonstrate that targeted mutations of cis-regulatory elements can be used to dissect the importance of single cis-regulatory elements within complex regulatory regions supporting the importance of the ETT-IND interaction for PID regulation. At the same time, our work also highlights the challenges of such studies, as gene regulation is highly robust, and mutations within gene regulatory regions may only display subtle phenotypes.

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Auxin Response Factors — output control in auxin biology

10.1101/129122 ◽

2017 ◽

Cited By ~ 1

Author(s):

Mark Roosjen ◽

Sébastien Paque ◽

Dolf Weijers

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Structural Biology ◽

Auxin Signaling ◽

Auxin Response ◽

Response Factors ◽

Output Control ◽

Auxin Response Factors ◽

Almost All ◽

Near Future

AbstractThe phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal to the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family likely contributes to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics and structural biology have helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.

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Genome-wide identification of auxin response factors (ARFs) in three different species of Arachis

Plant Biotechnology Reports ◽

10.1007/s11816-021-00671-8 ◽

2021 ◽

Author(s):

Bikash Raul ◽

Oindrila Bhattacharjee ◽

Kunal Tembhare ◽

Tanyya Khanna ◽

Tarannum Shaheen ◽

...

Keyword(s):

Auxin Response ◽

Response Factors ◽

Auxin Response Factors ◽

Genome Wide

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Genome-wide identification and expression analysis of auxin response factors in peanut (Arachis hypogaea L.)

PeerJ ◽

10.7717/peerj.12319 ◽

2021 ◽

Vol 9 ◽

pp. e12319

Author(s):

Peipei Li ◽

Qian Ma ◽

Chengxin Qu ◽

Shuliang Zhu ◽

Kunkun Zhao ◽

...

Keyword(s):

Arachis Hypogaea ◽

Plant Growth And Development ◽

Auxin Response ◽

Response Factors ◽

Auxin Response Factors ◽

Genome Data ◽

Genome Wide ◽

Arachis Hypogaea L ◽

Pod Development ◽

Cultivated Species

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

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Genome-Wide Identification of the Auxin Response Factor (ARF) Gene Family and Their Expression Analysis during Flower Development of Osmanthus fragrans

Forests ◽

10.3390/f11020245 ◽

2020 ◽

Vol 11 (2) ◽

pp. 245 ◽

Cited By ~ 1

Author(s):

Gongwei Chen ◽

Yuanzheng Yue ◽

Ling Li ◽

Yuli Li ◽

Haiyan Li ◽

...

Keyword(s):

Flower Development ◽

Developmental Stages ◽

Expression Profiles ◽

Auxin Response ◽

Comprehensive Overview ◽

Response Factors ◽

Systematic Analysis ◽

Osmanthus Fragrans ◽

Genome Wide ◽

A Genome

Auxins have long been implicated in many aspects of plant growth and development. Auxin response factors (ARFs) are important proteins in auxin-mediated pathways and they play key roles in plant physiological and biochemical processes, including flower development. Endogenous indoleacetic acid (IAA) levels were measured and ARFs were studied in the flowers during the developmental stages in order to further elucidate the role of auxin in flower development of Osmanthus fragrans. A systematic analysis of OfARFs was conducted by carrying out a genome-wide search of ARFs. A total of 50 ARF genes (OfARFs) were detected and validated from the Osmanthus fragrans genome. Furthermore, a comprehensive overview of the OfARFs was undertaken, including phylogenetic relationship, gene structures, conserved domains, motifs, promoters, chromosome locations, gene duplications, and subcellular locations of the gene product. Finally, expression profiling, while using transcriptome sequencing from a previous study and quantitative real-time PCR (qRT-PCR), revealed that many OfARF genes have different expression levels in various tissues and flower developmental stages. By comparing the expression profiles among the flower developmental stages, and the relationship between ARFs and endogenous IAA levels, it can be supposed that OfARFs function in flower development of O. fragrans in an auxin-mediated pathway.

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Genome-wide analysis of the auxin response factors (ARF) gene family in barley (Hordeum vulgare L.)

Journal of Plant Biochemistry and Biotechnology ◽

10.1007/s13562-018-0458-6 ◽

2018 ◽

Vol 28 (1) ◽

pp. 14-24 ◽

Cited By ~ 8

Author(s):

Huseyin Tombuloglu

Keyword(s):

Hordeum Vulgare ◽

Gene Family ◽

Auxin Response ◽

Hordeum Vulgare L ◽

Response Factors ◽

Auxin Response Factors ◽

Genome Wide Analysis ◽

Genome Wide

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Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis

Blood ◽

10.1182/blood-2011-09-380634 ◽

2012 ◽

Vol 119 (16) ◽

pp. 3724-3733 ◽

Cited By ~ 70

Author(s):

Louis C. Doré ◽

Timothy M. Chlon ◽

Christopher D. Brown ◽

Kevin P. White ◽

John D. Crispino

Keyword(s):

Gene Expression ◽

Transcriptional Activation ◽

Target Genes ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Regulatory Elements ◽

Gata Factor ◽

Related Factors ◽

Genome Wide ◽

A Genome

Abstract There are many examples of transcription factor families whose members control gene expression profiles of diverse cell types. However, the mechanism by which closely related factors occupy distinct regulatory elements and impart lineage specificity is largely undefined. Here we demonstrate on a genome wide scale that the hematopoietic GATA factors GATA-1 and GATA-2 bind overlapping sets of genes, often at distinct sites, as a means to differentially regulate target gene expression and to regulate the balance between proliferation and differentiation. We also reveal that the GATA switch, which entails a chromatin occupancy exchange between GATA2 and GATA1 in the course of differentiation, operates on more than one-third of GATA1 bound genes. The switch is equally likely to lead to transcriptional activation or repression; and in general, GATA1 and GATA2 act oppositely on switch target genes. In addition, we show that genomic regions co-occupied by GATA2 and the ETS factor ETS1 are strongly enriched for regions marked by H3K4me3 and occupied by Pol II. Finally, by comparing GATA1 occupancy in erythroid cells and megakaryocytes, we find that the presence of ETS factor motifs is a major discriminator of megakaryocyte versus red cell specification.

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Chromatin accessibility dynamics of myogenesis at single cell resolution

10.1101/155473 ◽

2017 ◽

Cited By ~ 11

Author(s):

Hannah A. Pliner ◽

Jonathan Packer ◽

José L. McFaline-Figueroa ◽

Darren A. Cusanovich ◽

Riza Daza ◽

...

Keyword(s):

Single Cell ◽

Chromatin Remodeling ◽

Target Genes ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

New Approach ◽

Genome Wide ◽

A Genome ◽

Histone Modifying Enzymes ◽

Dna Regulatory Elements

AbstractOver a million DNA regulatory elements have been cataloged in the human genome, but linking these elements to the genes that they regulate remains challenging. We introduce Cicero, a statistical method that connects regulatory elements to target genes using single cell chromatin accessibility data. We apply Cicero to investigate how thousands of dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of co-accessible regulatory elements linked by Cicero meet criteria of “chromatin hubs”, in that they are physically proximal, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of gene expression. Pseudotemporal analysis revealed a subset of elements bound by MYOD in myoblasts that exhibit early opening, potentially serving as the initial sites of recruitment of chromatin remodeling and histone-modifying enzymes. The methodological framework described here constitutes a powerful new approach for elucidating the architecture, grammar and mechanisms of cis-regulation on a genome-wide basis.

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