scholarly journals Genome-Wide Identification of the ARF Gene Family and ARF3 Target Genes Regulating Ovary Initiation in Hazel via ChIP Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Heng Wei ◽  
Yunqing Cheng ◽  
Ying Sun ◽  
Xingzheng Zhang ◽  
Hongli He ◽  
...  
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Developmental Stages ◽  
Immunohistochemical Analysis ◽  
Ovary Development ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Chip Sequencing ◽  
Molecular Weights ◽  
Phenylpropanoid Biosynthesis

Hazel (Corylus spp.) is an economically important nut species with a unique biological characteristic of ovary differentiation and development initiating from the ovary primordium after pollination. Auxin participates in ovary initiation and has an essential impact on hazel fruit yield and quality. The regulation of auxin in ovary development is thought to be related to auxin response factors (ARFs); however, its detailed regulatory mechanism remains unclear. The spatiotemporal expression pattern of C. heterophylla ARF3 (ChARF3) was accessed via ARF gene family member identification and expression abundance analysis as well as immunohistochemistry. ChARF3 target genes were identified via chromatin immunoprecipitation followed by next-generation sequencing (ChIP-Seq). In total, 14 ChARF members containing at least B3 and Auxin_resp domains were found to be distributed on 9 of 11 chromosomes, and the protein molecular weights were predicted to range from 70.93–139.22 kD. Among eight differentially expressed ChARFs, ChARF3 showed the most significant differences over four ovary developmental stages. Immunohistochemical analysis revealed that ChARF3 was expressed in the ovary primordium and funiculus, integument, endosperm, radicle, and cotyledon indicating its potential regulatory roles in ovary differentiation and development. In total, 3,167 ChARF3 target genes were identified through ChIP-Seq in four ovary developmental stages and were significantly enriched in the biosynthesis of secondary metabolites (ko01110), phenylpropanoid biosynthesis (ko00940), and phytohormone signal transduction (ko04075). ChARF3 was hypothesized to be involved in the regulation of auxin-induced genes and the transcription factors MADS, AP2/ERF, TCP, FT, and LFY. These results suggest that ChARF3 may regulate ovary initiation and ovule development by mediating genes related to auxin biosynthesis and transport, cell division and proliferation, and flower and fruit development. This study provides new insights into the molecular mechanism of hazel yield formation.

scholarly journals Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species

2021 ◽  
Vol 11 ◽  
Author(s):  
Qiaoying Pei ◽  
Nan Li ◽  
Qihang Yang ◽  
Tong Wu ◽  
Shuyan Feng ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Families ◽  
Plant Growth And Development ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Functional Analyses ◽  
Significant Positive Selection

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our analysis revealed that ARF genes of the three Apiaceae species in 34 branches of the phylogenetic tree underwent significant positive selection. Additionally, our findings indicated that whole-genome duplication played an important role in ARF gene family expansion. Coriander contained a greater number of ARF genes than celery and carrot because of more gene duplications and less gene losses. We also analyzed the expression of ARF genes in three tissues by RNA-seq and verified the results by quantitative real-time PCR. Furthermore, we found that several paralogous genes exhibited divergent expression patterns. Overall, this study provides a valuable resource for exploring how ARF family genes regulate plant growth and development in other plants. Since this is the first report of the ARF gene family in Apiaceae, our results will serve as a guide for comparative and functional analyses of ARF and other gene families in Apiaceae.

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

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 24
Author(s):  
Jianfei Wu ◽  
Fan Gao ◽  
Tongtong Li ◽  
Haixia Guo ◽  
Li Zhang ◽  
...  
Keyword(s):  
Target Genes ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Auxin Response ◽  
Higher Plant ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Wide ◽  
A Genome ◽  
Almost All

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.

scholarly journals Computational study of environmental stress-related transcription factor binding sites in the promoter regions of maize auxin response factor (ARF) gene family

2020 ◽  
Vol 12 (3) ◽  
pp. 646-657
Author(s):  
Abbas SAIDI ◽  
Zohreh HAJIBARAT
Keyword(s):  
Gene Family ◽  
Computational Study ◽  
Expression Profiles ◽  
Regulation Of Gene Expression ◽  
Gene Clusters ◽  
Auxin Response ◽  
Promoter Regions ◽  
Response Factors ◽  
Biotic Stresses ◽  
Auxin Response Factors

Auxin response factors (ARF) gene family plays key roles in plant development and act as transcription factors (TFs) in the regulation of gene expression. An extensive bioinformatics analysis including analysis of conserved motifs, chromosomal map, phylogenetic relationships, and expression profiles were performed for the maize ARF gene family. In this study, a set of publicly available 38 ARF maize (Zea mays) nucleotide sequences were downloaded. Using microarray data, a bioinformatics search for identification of TFBs in ARF genes using plant promoter analysis (PlantPAN) was carried out. The 38 maize ARF genes were categorized into three groups (Class I, II, and III).  ARF genes have been studied by molecular methods in several different plant species however to better understand the mechanisms of these genes more studies are needed. Gene cluster analysis showed that the same set of genes on the chromosomes were positively correlated with the same number of gene clusters.  Several TFBs including AP2/ERF, ERF, WRKY, bZIP, bHLH, GATA, and NAC were identified in the promoter regions. These TFBs are responsible for modulation of several biotic stress-responsive genes.  The main aims of the present study were to obtain genomic information for the ZmARF gene family and their expression under abiotic and biotic stresses.

Abstract 222: The Estrogen-related Receptor (ERR) Drives Cardiac Myocyte Maturation in Cooperation With GATA4

2020 ◽  
Vol 127 (Suppl_1) ◽  
Author(s):  
Tomoya Sakamoto ◽  
Shibiao Wan ◽  
Kirill Batmanov ◽  
Daniel P Kelly
Keyword(s):  
Target Genes ◽  
Cardiac Myocyte ◽  
Developmental Stages ◽  
Induced Pluripotent Stem Cell ◽  
Cardiac Differentiation ◽  
Peroxisome Proliferator ◽  
Structural Genes ◽  
Peroxisome Proliferator Activated Receptor ◽  
Chip Sequencing ◽  
Super Enhancer

During transition from fetal to adult developmental stages, the heart undergoes robust mitochondrial biogenesis in parallel with growth and structural maturation. Recently we identified a role for ERRα/γ in this broad program of postnatal cardiac maturation. We sought to delineate the mechanisms whereby ERRs coordinate transcriptional regulation of both metabolic and structural genes in the maturation of human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs). CRISPR-based gene deletion studies demonstrated that ERRα/γ is necessary for activation of genes involved in mitochondrial and structural maturation during hiPSC-CM differentiation including mitochondrial function, ion transport, Ca 2+ handling, and the adult sarcomere. Whole-genome RNA-sequencing and ChIP-sequencing (ChIP-seq) studies indicated that ERRγ directly regulates both metabolic and structural genes by remodeling H3K27ac depositions in related enhancer regions. Integration of the ERRγ ChIP-seq data with published hiPSC-CM datasets demonstrated that approximately 50% of super-enhancer regions overlapped ERRγ peaks, suggesting ERR is involved in the maintenance and function of cardiac super-enhancer regions. Corresponding motif analyses and intersection analyses with published GATA4 ChIP-seq datasets suggested that ERRγ cooperates with GATA4 on many structural, but not metabolic targets. Specifically, binding sites for both factors are often co-localized around cardiac contractile, ion channel, and Ca 2+ handling genes, including TNNI3, MYBPC3, MYH7, TTN, KCNQ1, and RYR2 . In contrast, ERRγ sites on target genes involved in mitochondrial maturation such as ATP5B, COX4I1, CPT1B , and FABP3 lacked GATA4 sites. Experiments using luciferase reporters demonstrated functional cooperation between ERRγ and GATA4 that depends on the known ERR coactivator, peroxisome proliferator-activated receptor gamma co-activator 1alpha (PGC-1α). We conclude that the ERR cooperates with GATA4 to drive cardiac structural gene transcription during cardiac differentiation, whereas ERR regulates genes involved in energy metabolism independent of GATA4. Activation of ERR signaling could prove to be an effective tool to drive hiPSC-CM maturation.

Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa)

Gene ◽  
2007 ◽  
Vol 394 (1-2) ◽  
pp. 13-24 ◽  
Author(s):  
Dekai Wang ◽  
Kemei Pei ◽  
Yaping Fu ◽  
Zongxiu Sun ◽  
Sujuan Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Auxin Response ◽  
Response Factors ◽  
Auxin Response Factors ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions have not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

scholarly journals Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samina Shabbir ◽  
Prerona Boruah ◽  
Lingli Xie ◽  
Muhammad Fakhar-e-Alam Kulyar ◽  
Mohsin Nawaz ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Ovarian Follicle ◽  
Follicular Development ◽  
Differentially Expressed ◽  
Ovary Development ◽  
Estrogen Metabolism ◽  
Genome Wide ◽  
Micro Rnas ◽  
Hu Sheep

AbstractOvary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells

2016 ◽  
Vol 9 (2) ◽  
pp. 126-144 ◽  
Author(s):  
Yaping Sun ◽  
Matthew Iyer ◽  
Richard McEachin ◽  
Meng Zhao ◽  
Yi-Mi Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dendritic Cells ◽  
Histone Deacetylase ◽  
Antigen Processing ◽  
Target Genes ◽  
Hdac Inhibition ◽  
Histone Deacetylase Inhibition ◽  
Immune Effector ◽  
Chip Sequencing ◽  
Genome Wide

STAT3 is a master transcriptional regulator that plays an important role in the induction of both immune activation and immune tolerance in dendritic cells (DCs). The transcriptional targets of STAT3 in promoting DC activation are becoming increasingly understood; however, the mechanisms underpinning its role in causing DC suppression remain largely unknown. To determine the functional gene targets of STAT3, we compared the genome-wide binding of STAT3 using ChIP sequencing coupled with gene expression microarrays to determine STAT3-dependent gene regulation in DCs after histone deacetylase (HDAC) inhibition. HDAC inhibition boosted the ability of STAT3 to bind to distinct DNA targets and regulate gene expression. Among the top 500 STAT3 binding sites, the frequency of canonical motifs was significantly higher than that of noncanonical motifs. Functional analysis revealed that after treatment with an HDAC inhibitor, the upregulated STAT3 target genes were those that were primarily the negative regulators of proinflammatory cytokines and those in the IL-10 signaling pathway. The downregulated STAT3-dependent targets were those involved in immune effector processes and antigen processing/presentation. The expression and functional relevance of these genes were validated. Specifically, functional studies confirmed that the upregulation of IL-10Ra by STAT3 contributed to the suppressive function of DCs following HDAC inhibition.

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