scholarly journals A network of transcriptional repressors mediates auxin response specificity

2018 ◽  
Author(s):  
Jekaterina Truskina ◽  
Jingyi Han ◽  
Carlos S. Galvan-Ampudia ◽  
Stéphanie Lainé ◽  
Géraldine Brunoud ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Open Chromatin ◽  
Transcriptional Repressors ◽  
In Planta ◽  
Auxin Response ◽  
Specific Expression ◽  
Developmental Patterns ◽  
Auxin Signalling ◽  
Response Specificity

INTRODUCTORY PARAGRAPHThe regulation of signalling capacity plays a pivotal role in setting developmental patterns in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2). A subset of these ARFs comprises transcriptional activators of target genes in response to auxin, and are essential for regulating auxin signalling throughout the plant lifecycle (3). While ARF activators show tissue-specific expression patterns, it is unknown how their expression patterns are established. Chromatin modifications and accessibility studies revealed the chromatin of loci encoding ARF activators is constitutively open for transcription. Using a high-throughput yeast one-hybrid (Y1H) approach, we discovered a network of transcriptional regulators of ARF activator genes from Arabidopsis thaliana. Expression analyses demonstrated that the majority of these regulators act as repressors of ARF transcription in planta. Our observations support a scenario where the default configuration of open chromatin enables a network of transcriptional repressors to shape the expression pattern of ARF activators and provide specificity in auxin signalling output throughout development.

scholarly journals Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. Results Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. Conclusions In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background: As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.Results: Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.Conclusions: In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Estrogen Receptor β: An Overview and Update

2008 ◽  
Vol 6 (1) ◽  
pp. nrs.06003 ◽  
Author(s):  
Chunyan Zhao ◽  
Karin Dahlman-Wright ◽  
Jan-Åke Gustafsson
Keyword(s):  
Estrogen Receptor ◽  
Target Genes ◽  
Expression Patterns ◽  
Estrogen Signaling ◽  
Receptor Subtypes ◽  
Specific Expression ◽  
Microarray Experiments ◽  
Downstream Target ◽  
Animal Disease Models ◽  
Selective Ligands

The discovery of a second estrogen receptor (ER), designated ERβ (NR3A2), has redefined our knowledge about the mechanisms underlying cellular signaling by estrogens and has broad implications for our understanding of regulation of estrogen-responsive tissues. Highly variable and even contrasting effects of estrogens in different tissues seem to be at least partially explained by different estrogen signaling pathways, involving ERα (NR3A1) and/or ERβ. To date, two key conclusions can be drawn from the significant body of work carried out on the specific roles of the two receptor subtypes in diverse estrogen target tissues. First, ERα and ERβ have different biological functions, as indicated by their specific expression patterns and the distinct phenotypes observed in ERα and ERβ knockout (αERKO and βERKO) mice. Second, ERα and ERβ appear to have overlapping but also unique sets of downstream target genes, as judged from a set of microarray experiments. Thus, ERα and ERβ have different transcriptional activities in certain ligand, cell-type, and promoter contexts, which may help to explain some of the major differences in their tissue-specific biological actions. The phenotypes observed for βERKO mice have suggested certain therapeutic areas to be further explored. The development of ERβ-selective ligands active in animal disease models indicates new avenues for clinical exploration. ERβ agonists are being explored and validated as drugs for a growing number of indications. Hopefully, some ERβ targeted drugs will prove to be efficient in enhancing human health.

scholarly journals Quantitative Amplification of Cleaved Ends (qACE) to assay miRNA-directed target cleavage

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 240 ◽  
Author(s):  
Suresh Damodaran ◽  
Sajag Adhikari ◽  
Marie Turner ◽  
Senthil Subramanian
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Mirna Regulation ◽  
Temporal Expression ◽  
Specific Expression ◽  
Rna Molecules ◽  
Specific Target Gene ◽  
Pcr Method ◽  
Spatio Temporal ◽  
Fusion Primer

microRNA (miRNA) regulation is crucial to achieve precise spatio-temporal expression patterns of their target genes. This makes it crucial to determine the levels of cleavage of a particular target mRNA in different tissues and under different conditions. We developed a quantitative PCR method “quantitative Amplification of Cleaved Ends (qACE)” to assay levels of specific cleavage products in order to determine the extent of miRNA regulation for a specific target gene. qACE uses cDNA generated from adapter-ligated RNA molecules and relies on a carefully designed fusion primer that spans the adapter-cleaved RNA junction in qPCR to specifically amplify and quantify cleaved products. The levels of full-length transcripts can also be assayed in the same cDNA preparation using primers that span across the miRNA cleavage site. We used qACE to demonstrate that soybean roots over-expressing miR164 had increased levels of target cleavage and that miRNA deficient Arabidopsis thaliana hen1-1 mutants had reduced levels of target cleavage. We used qACE to discover that differential cleavage by miR164 in nodule vs. adjacent root tissue contributed to nodule-specific expression of NAC1 transcription factors in soybean. These experiments show that qACE can be used to discover and demonstrate differential cleavage by miRNAs to achieve specific spatio-temporal expression of target genes in plants.

scholarly journals Transcriptomes Analysis Reveals the Regulatory Roles of Noncoding RNA in Tanshinones Synthesis Pathway of Salvia Miltiorrhiza

2021 ◽  
Author(s):  
Caicai Lin ◽  
Changhao Zhou ◽  
Zhongqian Liu ◽  
Xingfeng Li ◽  
Zhenqiao Song
Keyword(s):  
Noncoding Rna ◽  
Target Genes ◽  
Salvia Miltiorrhiza ◽  
Expression Patterns ◽  
Noncoding Rnas ◽  
Synthesis Process ◽  
Circular Rnas ◽  
Regulation Mechanism ◽  
Pentatricopeptide Repeat ◽  
Specific Expression

Abstract Background: Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play fundamental roles in plant development. However, the information of these noncoding RNAs (ncRNAs) in Salvia miltiorrhiza remains largely unexplored. In this study, the expression pattern of ncRNAs in six tissues from the same strain of S. miltiorrhiza was analyzed to study the biological function of ncRNAs on active ingredients synthesis.Methods: Analysis of tanshinone content differences of two root simples was carried out on high-performance liquid chromatography (HPLC). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the targets of diferentially expressed ncRNAs in different organs.Results: A total of 6,929 lncRNAs, 6,239 circRNAs, and 360 miRNAs were identified. Forty-eight lncRNAs, 70 miRNAs, and 26 circRNAs expressed differentially between red and white root tissues with significantly different tanshinone content. GO and KEGG pathway analysis of target genes of differently expressed ncRNAs indicated that some target genes are involved in the synthesis pathway of terpene, including diterpene and sesquiterpene. We also found many target genes related to secondary metabolites, including 2-C-Methyl-d-erythritol 2,4-cyclodiphosphate Synthase (SmMCS) and several CYP450s. Furthermore, most target genes may be related to the resistance of pathogens, such as receptor kinases, disease-resistant proteins, and pentatricopeptide repeat-containing proteins. Conclusions: The present study exhibited the tissue-specific expression patterns of ncRNAs preliminarily in S. miltiorrhiza, which may reflect that the formation of white root or red root is related to regulation by ncRNAs. It would provide a basis for further research about the regulation mechanism in the tanshinone synthesis process.

scholarly journals Characterization and abiotic stress-responsive expression analysis of SGT1 genes in Brassica oleracea

Genome ◽  
2016 ◽  
Vol 59 (4) ◽  
pp. 243-251 ◽  
Author(s):  
Ashokraj Shanmugam ◽  
Senthil Kumar Thamilarasan ◽  
Jong-In Park ◽  
Mi Young Jung ◽  
Ill-Sup Nou
Keyword(s):  
Brassica Oleracea ◽  
Expression Analysis ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Expression Patterns ◽  
Strong Association ◽  
Stress Conditions ◽  
Plant Responses ◽  
Functional Domain ◽  
Specific Expression

SGT1 genes are involved in enhancing plant responses to various biotic and abiotic stresses. Brassica oleracea is known to contain two types of SGT1 genes, namely suppressor of G2 allele of SKP1 and suppressor of GCR2. In this study, through systematic analysis, four putative SGT1 genes were identified and characterized in B. oleracea. In phylogenetic analysis, the genes clearly formed separate groups, namely BolSGT1a, BolSGT1b (both suppressor of G2 allele of SKP1 types), and BolSGT1 (suppressor of GCR2). Functional domain analysis and organ-specific expression patterns suggested possible roles for BolSGT1 genes during stress conditions. BolSGT1 genes showed significant changes in expression in response to heat, cold, drought, salt, or ABA treatment. Interaction network analysis supported the expression analysis, and showed that the BolSGT1a and BolSGT1b genes are strongly associated with co-regulators during stress conditions. However, the BolSGT1 gene did not show any strong association. Hence, BolSGT1 might be a stress resistance-related gene that functions without a co-regulator. Our results show that BolSGT1 genes are potential target genes to improve B. oleracea resistance to abiotic stresses such as heat, cold, and salt.

scholarly journals Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Deng ◽  
Yajuan Qin ◽  
Pan Yang ◽  
Jianjun Du ◽  
Zheng Kuang ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Computational Prediction ◽  
Regulatory Relationship ◽  
Specific Expression ◽  
Economic Significance ◽  
Specific Expression Pattern

MicroRNA (miRNA) is an important endogenous post-transcriptional regulator, while lettuce (Lactuca sativa) is a leafy vegetable of global economic significance. However, there are few studies on miRNAs in lettuce, and research on miRNA regulatory network in lettuce is absent. In this study, through deep sequencing of small RNAs in different tissues, together with a reference genome, 157 high-confidence miRNA loci in lettuce were comprehensively identified, and their expression patterns were determined. Using a combination of computational prediction and high-throughput experimental verification, a set of reliable lettuce miRNA targets were obtained. Furthermore, through RNA-Seq, the expression profiles of these targets and a comprehensive view of the negative regulatory relationship between miRNAs and their targets was acquired based on a correlation analysis. To further understand miRNA functions, a miRNA regulatory network was constructed, with miRNAs at the core and combining transcription factors and miRNA target genes. This regulatory network, mainly composed of feed forward loop motifs, greatly increases understanding of the potential functions of miRNAs, and many unknown potential regulatory links were discovered. Finally, considering its specific expression pattern, Lsa-MIR408 as a hub gene was employed to illustrate the function of the regulatory network, and genetic experiments revealed its ability to increase the fresh weight and achene size of lettuce. In short, this work lays a solid foundation for the study of miRNA functions and regulatory networks in lettuce.

scholarly journals Genome-wide identification and expression analysis of the NF-Y family of transcription factors in tea plant

2019 ◽  
Author(s):  
Yi Yue ◽  
Di Zhang ◽  
Huimin Dou ◽  
Xinyi Liu ◽  
Lewen Gao ◽  
...  
Keyword(s):  
Target Genes ◽  
Interaction Analysis ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Tea Plant ◽  
Plant Genome ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Extensive Evaluation ◽  
Y Family

Abstract Background Nuclear factor-Y(NF-Y) is a heterotrimeric transcription factor commonly found in higher eukaryotes. It usually consists of three subunits: NF-YA, NF-YB and NF-YC, which binds to CCAAT sequences to regulate the expression of target genes. Although NF-Y proteins have been reported in many plants like Arabidopsis and wheat, a comprehensive and systematic analysis of NF-Y genes in tea plant has not yet been reported. Results In this study, a total of 35 CsNF-Y genes, including 10 CsNF-YA, 16 CsNF-YB, and 9 CsNF-YC genes, were identified in the sequenced genomes of tea plant. The conserved domains analysis and multiple alignments suggested that domains were conserved within subgroups but differed between subgroups in the CsNF-Y family. Functional prediction and protein interaction analysis were performed by phylogenetic analyses with orthologous genes. Further, expression pattern analysis in various tissues of tea plant by transcriptome data indicated that these genes play different roles in tea plant development and many exhibit tissue-specific expression patterns. Conclusions In this study, we characterized 35 CsNF-Ys based on their distributions on tea plant genome, gene structures, phylogenetic relationship with Orthologous NF-Y genes, and their expression patterns. This study provides extensive evaluation of the tea plant NF-Y family and may contribute to the future studies about the CsNF-Y gene family.

scholarly journals Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7510 ◽  
Author(s):  
Yanan Shi ◽  
Huanlong Liu ◽  
Yameng Gao ◽  
Yujiao Wang ◽  
Min Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Moso Bamboo ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Hormone Regulation ◽  
In Planta ◽  
Phyllostachys Edulis ◽  
Specific Expression

Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.

scholarly journals Design principles of a minimal auxin response system

2019 ◽  
Author(s):  
Hirotaka Kato ◽  
Sumanth K. Mutte ◽  
Hidemasa Suzuki ◽  
Isidro Crespo ◽  
Shubhajit Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression System ◽  
Expression Patterns ◽  
Land Plants ◽  
Marchantia Polymorpha ◽  
Gene Duplications ◽  
Auxin Response ◽  
Response System ◽  
Genes Expression

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1–3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development2–4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.

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