scholarly journals Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in Gerbera hybrida

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3382 ◽  
Author(s):  
Gan Huang ◽  
Meixiang Han ◽  
Wei Yao ◽  
Yaqin Wang
Keyword(s):  
Transcriptome Analysis ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Early Stage ◽  
Signal Pathways ◽  
Transcriptional Level ◽  
Commercial Development ◽  
Gerbera Hybrida ◽  
Petal Growth

Gerbera hybrida is a cut-flower crop of global importance, and an understanding of the mechanisms underlying petal development is vital for the continued commercial development of this plant species. Brassinosteroids (BRs), a class of phytohormones, are known to play a major role in cell expansion, but their effect on petal growth in G. hybrida is largely unexplored. In this study, we found that the brassinolide (BL), the most active BR, promotes petal growth by lengthening cells in the middle and basal regions of petals, and that this effect on petal growth was greater than that of gibberellin (GA). The RNA-seq (high-throughput cDNA sequencing) technique was employed to investigate the regulatory mechanisms by which BRs control petal growth. A global transcriptome analysis of the response to BRs in petals was conducted and target genes regulated by BR were identified. These differentially expressed genes (DEGs) include various transcription factors (TFs) that were activated during the early stage (0.5 h) of BL treatment, as well as cell wall proteins whose expression was regulated at a late stage (10 h). BR-responsive DEGs are involved in multiple plant hormone signal pathways, hormone biosynthesis and biotic and abiotic stress responses, showing that the regulation of petal growth by BRs is a complex network of processes. Thus, our study provides new insights at the transcriptional level into the molecular mechanisms of BR regulation of petal growth in G. hybrida.

Drugs used to treat bipolar disorder act via microRNAs to regulate expression of genes involved in neurite outgrowth

2020 ◽  
Vol 34 (3) ◽  
pp. 370-379 ◽  
Author(s):  
Srisaiyini Kidnapillai ◽  
Ben Wade ◽  
Chiara C Bortolasci ◽  
Bruna Panizzutti ◽  
Briana Spolding ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Neurite Outgrowth ◽  
Neural Plasticity ◽  
Drug Combination ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Drug Effects ◽  
Differentially Expressed ◽  
Transcriptional Level ◽  
Expression Of Genes

Background: The drugs commonly used to treat bipolar disorder have limited efficacy and drug discovery is hampered by the paucity of knowledge of the pathophysiology of this disease. This study aims to explore the role of microRNAs in bipolar disorder and understand the molecular mechanisms of action of commonly used bipolar disorder drugs. Methods: The transcriptional effects of bipolar disorder drug combination (lithium, valproate, lamotrigine and quetiapine) in cultured human neuronal cells were studied using next generation sequencing. Differential expression of genes ( n=20) and microRNAs ( n=6) was assessed and the differentially expressed microRNAs were confirmed with TaqMan MicroRNA Assays. The expression of the differentially expressed microRNAs were inhibited to determine bipolar disorder drug effects on their target genes ( n=8). Independent samples t-test was used for normally distributed data and Kruskal-Wallis/Mann-Whitney U test was used for data not distributed normally. Significance levels were set at p<0.05. Results: We found that bipolar disorder drugs tended to increase the expression of miR-128 and miR-378 ( p<0.05). Putative target genes of these microRNAs targeted pathways including those identified as “neuron projection development” and “axonogenesis”. Many of the target genes are inhibitors of neurite outgrowth and neurogenesis and were downregulated following bipolar disorder drug combination treatment (all p<0.05). The bipolar disorder drug combination tended to decrease the expression of the target genes ( NOVA1, GRIN3A, and VIM), however this effect could be reversed by the application of microRNA inhibitors. Conclusions: We conclude that at a transcriptional level, bipolar disorder drugs affect several genes in concert that would increase neurite outgrowth and neurogenesis and hence neural plasticity, and that this effect is mediated (at least in part) by modulation of the expression of these two key microRNAs.

scholarly journals Interaction between Signal Pathways upon Formation of Plant Defense in Response to Environmental Stress Factors

2021 ◽  
Vol 68 (6) ◽  
pp. 989-1002
Author(s):  
A. R. Lubyanova ◽  
M. V. Bezrukova ◽  
F. M. Shakirova
Keyword(s):  
Salicylic Acid ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Molecular Techniques ◽  
Environmental Stressors ◽  
Stress Factors ◽  
Signal Pathways ◽  
Regulatory Signal ◽  
Derivatives Of

Abstract In the course of evolution, plants have developed numerous specific regulatory signal pathways, which are hormonal for the most part. Phytohormones comprise not only such generally recognized endogenous growth regulators as abscisic acid, auxins, cytokinins, gibberellins, brassinosteroids (BS), ethylene, salicylic acid (SA), and jasmonates but also recently described derivatives of apocarotenoids—strigolactones (SL). Signal pathways interact at the level of biosynthesis of messengers and their translocation as well as upon activation of target genes. Since abiotic and biotic environmental stressors negatively influence plant productivity, understanding of molecular mechanisms of regulation induced by stress agents may help researchers to produce stress-resistant and high-yielding plants using molecular techniques. This paper is a review of present-day literature dealing with the interaction and interference of nonhormonal and hormonal signals regulating growth and development of plants under ever-changing environmental conditions.

scholarly journals Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Huini Tang ◽  
...  
Keyword(s):  
Circadian Rhythm ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Genetic Constitution ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Extracellular Region

Abstract Background: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. Results: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. Conclusions: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

scholarly journals Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate target genes to improve treatment outcomes

2019 ◽  
Author(s):  
Saket Choudhary ◽  
Suzanne C. Burns ◽  
Hoda Mirsafian ◽  
Wenzheng Li ◽  
Dat T. Vo ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
Early Response ◽  
Radiation Sensitivity ◽  
Integrated Analysis ◽  
High Dose ◽  
Transcriptional Level ◽  
Altered Expression ◽  
Improve Treatment ◽  
Main Component

AbstractBackgroundHigh-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response.MethodsWe conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation.ResultsChanges at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy.ConclusionsOur integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.

scholarly journals Global Transcriptome and Weighted Gene Co-expression Network Analyses of Growth-Stage-Specific Drought Stress Responses in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Songtao Liu ◽  
Tinashe Zenda ◽  
Anyi Dong ◽  
Yatong Yang ◽  
Nan Wang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Transcriptome Analysis ◽  
Stress Responses ◽  
Growth Stage ◽  
Molecular Mechanisms ◽  
Grain Filling ◽  
Growth Stages ◽  
Specific Response ◽  
Network Analyses

Drought is the major abiotic stress threatening maize (Zea mays L.) production globally. Despite recent scientific headway in deciphering maize drought stress responses, the overall picture of key genes, pathways, and co-expression networks regulating maize drought tolerance is still fragmented. Therefore, deciphering the molecular basis of maize drought tolerance remains pertinent. Here, through a comprehensive comparative leaf transcriptome analysis of drought-tolerant hybrid ND476 plants subjected to water-sufficient and water-deficit treatment conditions at flared (V12), tasseling (VT), the prophase of grain filling (R2), and the anaphase of grain filling (R4) crop growth stages, we report growth-stage-specific molecular mechanisms regulating maize drought stress responses. Based on the transcriptome analysis, a total of 3,451 differentially expressed genes (DEGs) were identified from the four experimental comparisons, with 2,403, 650, 397, and 313 DEGs observed at the V12, VT, R1, and R4 stages, respectively. Subsequently, 3,451 DEGs were divided into 12 modules by weighted gene co-expression network analysis (WGCNA), comprising 277 hub genes. Interestingly, the co-expressed genes that clustered into similar modules exhibited diverse expression tendencies and got annotated to different GO terms at different stages. MapMan analysis revealed that DEGs related to stress signal transduction, detoxification, transcription factor regulation, hormone signaling, and secondary metabolites biosynthesis were universal across the four growth stages. However, DEGs associated with photosynthesis and amino acid metabolism; protein degradation; transport; and RNA transcriptional regulation were uniquely enriched at the V12, VT, R2, and R4 stages, respectively. Our results affirmed that maize drought stress adaptation is a growth-stage-specific response process, and aid in clarifying the fundamental growth-stage-specific mechanisms regulating drought stress responses in maize. Moreover, genes and metabolic pathways identified here can serve as valuable genetic resources or selection targets for further functional validation experiments.

scholarly journals The Dual Role of STAT1 in Ovarian Cancer: Insight Into Molecular Mechanisms and Application Potentials

2021 ◽  
Vol 9 ◽  
Author(s):  
Xin Li ◽  
Fanchen Wang ◽  
Xiaolin Xu ◽  
Jinguo Zhang ◽  
Guoxiong Xu
Keyword(s):  
Ovarian Cancer ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Early Stage ◽  
Transforming Growth Factor Β ◽  
Janus Kinase ◽  
Atypical Symptoms ◽  
Stat1 Signaling

The signal transducer and activator of transcription 1 (STAT1) is a transducer protein and acts as a transcription factor but its role in ovarian cancer (OC) is not completely understood. Practically, there are two-faced effects of STAT1 on tumorigenesis in different kinds of cancers. Existing evidence reveals that STAT1 has both tumor-suppressing and tumor-promoting functions involved in angiogenesis, cell proliferation, migration, invasion, apoptosis, drug resistance, stemness, and immune responses mainly through interacting and regulating target genes at multiple levels. The canonical STAT1 signaling pathway shows that STAT1 is phosphorylated and activated by the receptor-activated kinases such as Janus kinase in response to interferon stimulation. The STAT1 signaling can also be crosstalk with other signaling such as transforming growth factor-β signaling involved in cancer cell behavior. OC is often diagnosed at an advanced stage due to symptomless or atypical symptoms and the lack of effective detection at an early stage. Furthermore, patients with OC often develop chemoresistance and recurrence. This review focuses on the multi-faced role of STAT1 and highlights the molecular mechanisms and biological functions of STAT1 in OC.

scholarly journals Exposure of Microglia to Interleukin-4 Represses NF-κB-Dependent Transcription of Toll-Like Receptor-Induced Cytokines

2021 ◽  
Vol 12 ◽  
Author(s):  
Ella A. Zuiderwijk-Sick ◽  
Céline van der Putten ◽  
Raissa Timmerman ◽  
Jennifer Veth ◽  
Erica M. Pasini ◽  
...  
Keyword(s):  
Immune Responses ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Surface Protein ◽  
Innate Immune ◽  
Interleukin 4 ◽  
Transcriptional Level ◽  
Innate Immune Responses ◽  
Toll Like Receptor ◽  
Nuclear Extracts

Interleukin (IL)-4 is a cytokine that affects both adaptive and innate immune responses. In the central nervous system, microglia express IL-4 receptors and it has been described that IL-4-exposed microglia acquire anti-inflammatory properties. We here demonstrate that IL-4 exposure induces changes in the cell surface protein expression profile of primary rhesus macaque microglia and enhances their potential to induce proliferation of T cells with a regulatory signature. Moreover, we show that Toll like receptor (TLR)-induced cytokine production is broadly impaired in IL-4-exposed microglia at the transcriptional level. IL-4 type 2 receptor-mediated signaling is shown to be crucial for the inhibition of microglial innate immune responses. TLR-induced nuclear translocalization of NF-κB appeared intact, and we found no evidence for epigenetic modulation of target genes. By contrast, nuclear extracts from IL-4-exposed microglia contained significantly less NF-κB capable of binding to its DNA consensus site. Further identification of the molecular mechanisms that underlie the inhibition of TLR-induced responses in IL-4-exposed microglia may aid the design of strategies that aim to modulate innate immune responses in the brain, for example in gliomas.

scholarly journals Therapeutic effect and mechanisms of intra-articular injections of microRNA-140-5p on early-stage osteoarthritis in rats

2020 ◽  
Author(s):  
Hai-bo Si ◽  
Ti-min Yang ◽  
Yang Chen ◽  
Rui-wen Mao ◽  
Li-ming Wu ◽  
...  
Keyword(s):  
Therapeutic Effect ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Early Stage ◽  
Cartilage Thickness ◽  
Control Group ◽  
Biological Processes ◽  
Strong Fluorescence ◽  
Bioinformatics Analyses ◽  
Surgically Induced

Abstract Background MicroRNAs (miRs) have received extensive attention in osteoarthritis (OA) pathogenesis in recent years, and our previous study have confirmed that single intra-articular injection (IAJ) of miR-140-5p alleviates early-stage OA (EOA) progression in rats. This study aims to further investigate the effects of single IAJ of miR-140-5p on different stage OA and multiple IAJs of miR-140-5p on EOA, as well as the potential mechanisms. Methods Firstly, OA model was surgically induced in rats, 9 rats were treated with IAJ of Cy5-miR-140-5p at 1 week after surgery, and fluorescence distribution was measured. Then, 72 rats were treated with single IAJ of miR-140-5p at different time after surgery or multiple IAJs of miR-140-5p at 1 week after surgery, and OA progression were evaluated macroscopically and histologically. Finally, bioinformatics analyses were performed and the potential targets and molecular mechanisms of miR-140-5p were predicted. Results Strong fluorescence was observed in the chondrocytes and joint where Cy5-miR-140-5p was injected. Behavioural scores, chondrocyte numbers and cartilage thickness in cartilage were higher, while pathological scores were lower in the miR-140-5p group than in the control group. Specifically, the earlier a single IAJ of miR-140-5p, the better the therapeutic effect, and multiple IAJs exhibited better therapeutic effect than single IAJ on EOA. Bioinformatics analyses predicted 84 potential target genes of rno-miR-140-5p and revealed that these genes enrich in various biological processes and pathways. Conclusions IAJs of miR-140-5p effectively alleviate EOA progression by modulating various biological processes and pathways, and may be a promising therapeutics for EOA.

scholarly journals Identification of MLL-Fusion/Myc⊣miR-26a/Mir-29a⊣Tet1 Signaling Circuit in MLL-Rearranged Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1011-1011
Author(s):  
Hao Huang ◽  
Xi Jiang ◽  
Jinhua Wang ◽  
Yuanyuan Li ◽  
Ping Chen ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Transcriptional Repression ◽  
Fusion Proteins ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Conflicts Of Interest ◽  
Present Report ◽  
Transcriptional Level ◽  
Acute Leukemias

Abstract Approximately 10% of human acute leukemias are involved in chromosomal translocations between the mixed lineage leukemia (MLL) gene and over 50 partner genes. MLL-rearranged leukemias occur preferentially in infant and young children and are often associated with poor outcome. MicroRNAs (miRNAs) are an abundant class of small noncoding RNAs which repress gene expression and mRNA stability by base pairing with target mRNAs usually at the 3’-untranslated regions (UTRs). The ten-eleven translocation 1 (TET1), the founding member of the TET family of enzymes (TET1/2/3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), was first identified in MLL-rearranged leukemia. But its definitive role in leukemia was unclear until our recent report published in PNAS (Huang H. et al. 2013). In contrast to the frequent repression and tumor-suppressor roles of the three TET genes observed in various cancers, we showed that TET1 is a direct target of MLL-fusion proteins and significantly up-regulated in MLL-rearranged leukemia, leading to a global increase of 5hmC level. Furthermore, Tet1 plays an indispensable oncogenic role in MLL-rearranged leukemia, through coordination with MLL-fusion proteins in regulating their critical co-targets including Hoxa/Meis1/Pbx3 genes. However, whether TET1 is also post-transcriptionally regulated by miRNAs in hematopoietic cells remains unknown. In the present report, through genome-wide miRNA expression profiling assays, we found that miR-26a and miR-29a were expressed at a significantly lower level in MLL-rearranged AML than in normal controls. The down-regulation of miR-26a and miR-29a is, at least in part, attributed to the transcriptional repression mediated by MLL-fusion proteins and MYC. Interestingly, both miR-26a and miR-29a target TET1 directly at the post-transcriptional level. More importantly, we showed that miR-26a or miR-29a significantly inhibited MLL-fusion-mediated cell transformation in vitro and leukemogenesis in vivo down regulating expression of Tet1 and its downstream target genes. Thus, our data suggest that the transcriptional repression of miR-26a and miR-29a is required for the aberrant overexpression and potent oncogenic role of TET1 in MLL-rearranged leukemia, and that miR-26a and miR-29a play important tumor-suppressor role in leukemogenesis. Taken together, our data reveals a previously unappreciated signaling pathway involving the MLL-fusion/Myc⊣miR-26a/miR-29a⊣Tet1 circuit in MLL-rearranged leukemia. Our data not only provides novel insight into our understanding of the complex molecular mechanisms underlying the pathogenesis of MLL-rearranged leukemia, but also may lead to the development of novel, more effective therapeutic strategies to treat this type of dismal disease. Disclosures No relevant conflicts of interest to declare.

scholarly journals 14-3-3 Proteins Are Involved in BR-Induced Ray Petal Elongation in Gerbera hybrida

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaohui Lin ◽  
Shina Huang ◽  
Gan Huang ◽  
Yanbo Chen ◽  
Xiaojing Wang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Growth And Development ◽  
Protein Transport ◽  
Expression Patterns ◽  
Primary Metabolism ◽  
Response Patterns ◽  
Gerbera Hybrida ◽  
Petal Length ◽  
Positive Regulators ◽  
Petal Growth

14-3-3 proteins play a major role in the regulation of primary metabolism, protein transport, ion channel activity, signal transduction and biotic/abiotic stress responses. However, their involvement in petal growth and development is largely unknown. Here, we identified and characterized the expression patterns of seven genes of the 14-3-3 family in gerbera. While none of the genes showed any tissue or developmental specificity of spatiotemporal expression, all seven predicted proteins have the nine α-helices typical of 14-3-3 proteins. Following treatment with brassinolide, an endogenous brassinosteroid, the Gh14-3-3 genes displayed various response patterns; for example, Gh14-3-3b and Gh14-3-3f reached their highest expression level at early (2 h) and late (24 h) timepoints, respectively. Further study revealed that overexpression of Gh14-3-3b or Gh14-3-3f promoted cell elongation, leading to an increase in ray petal length. By contrast, silencing of Gh14-3-3b or Gh14-3-3f inhibited petal elongation, which was eliminated partly by brassinolide. Correspondingly, the expression of petal elongation-related and brassinosteroid signaling-related genes was modified in transgenic petals. Taken together, our research suggests that Gh14-3-3b and Gh14-3-3f are positive regulators of brassinosteroid-induced ray petal elongation and thus provides novel insights into the molecular mechanism of petal growth and development.

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