scholarly journals Characterisation of the R2R3 Myb subgroup 9 family of transcription factors in tomato

2021 ◽  
Author(s):  
Gwen. V. Davis ◽  
Beverley. J. Glover
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Epidermal Cell ◽  
Expression Patterns ◽  
Single Species ◽  
Ectopic Activity ◽  
Rt Pcr ◽  
Cell Outgrowth ◽  
Endogenous Expression ◽  
R2r3 Myb

AbstractTomato (Solanum lycopersicum) has many epidermal cell outgrowths including conical cells and multiple types of trichomes. These include the anther-specific trichome mesh which holds the anthers connate. The R2R3 Myb Subgroup 9 family of transcription factors is involved in development of epidermal cell outgrowths throughout the angiosperms. No previous study has examined all members of this transcription factor family in a single species. All 7 R2R3 Myb Subgroup 9 genes were isolated from tomato. They were ectopically expressed in tobacco to assess their ability to induce epidermal cell outgrowth. Endogenous expression patterns were examined by semi-quantitative RT-PCR at different stages of floral development relative to the development of anther trichomes. We report variation in the degree of epidermal cell outgrowth produced in transgenic tobacco for each ectopically expressed gene. Based on expression profile and ectopic activity, SlMIXTA-2 is likely involved in the production of leaf trichomes while SlMYB17-2 is the best candidate for the regulation of the anther trichome mesh. Analysis of the phenotypes of transgenic plants ectopically expressing all 7 genes has revealed the different extent to which members of the same transcription factor subfamily can induce cellular outgrowth.HighlightCharacterisation of all members of an important family of transcription factors within tomato showing that all are able to induce epidermal cell outgrowths to varying degrees.

scholarly journals The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Annekarin Meyer ◽  
Stefanie Herkt ◽  
Heike Kunze-Schumacher ◽  
Nicole Kohrs ◽  
Julia Ringleb ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Malignant Disease ◽  
Expression Patterns ◽  
Gene Activation ◽  
Erythroid Differentiation ◽  
Mature Micrornas ◽  
Gene Regulatory ◽  
Regulatory Loop ◽  
Transcriptional Complex

AbstractA network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.

scholarly journals Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming

Blood ◽  
2009 ◽  
Vol 114 (11) ◽  
pp. 2299-2306 ◽  
Author(s):  
Orapan Sripichai ◽  
Christine M. Kiefer ◽  
Natarajan V. Bhanu ◽  
Toshihiko Tanno ◽  
Seung-Jae Noh ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Expression ◽  
Histone Modification ◽  
Globin Gene ◽  
Expression Patterns ◽  
Fetal Hemoglobin ◽  
Transcriptome Profiling ◽  
Globin Genes

Abstract Therapeutic regulation of globin genes is a primary goal of translational research aimed toward hemoglobinopathies. Signal transduction was used to identify chromatin modifications and transcription factor expression patterns that are associated with globin gene regulation. Histone modification and transcriptome profiling were performed using adult primary CD34+ cells cultured with cytokine combinations that produced low versus high levels of gamma-globin mRNA and fetal hemoglobin (HbF). Embryonic, fetal, and adult globin transcript and protein expression patterns were determined for comparison. Chromatin immunoprecipitation assays revealed RNA polymerase II occupancy and histone tail modifications consistent with transcriptional activation only in the high-HbF culture condition. Transcriptome profiling studies demonstrated reproducible changes in expression of nuclear transcription factors associated with high HbF. Among the 13 genes that demonstrated differential transcript levels, 8 demonstrated nuclear protein expression levels that were significantly changed by cytokine signal transduction. Five of the 8 genes are recognized regulators of erythropoiesis or globin genes (MAFF, ID2, HHEX, SOX6, and EGR1). Thus, cytokine-mediated signal transduction in adult erythroid cells causes significant changes in the pattern of globin gene and protein expression that are associated with distinct histone modifications as well as nuclear reprogramming of erythroid transcription factors.

scholarly journals Transcriptome profilings reveal the candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass.

2020 ◽  
Author(s):  
Yinruizhi Li ◽  
Mengdi Wang ◽  
Ke Teng ◽  
Di Dong ◽  
Zhuocheng Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Perennial Ryegrass ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Nitrogen Utilization ◽  
Utilization Rate ◽  
Nitrogen Stress ◽  
Molecular Response ◽  
Stress Effect

Abstract Background：Lolium perenne L. is a kind of high quality forage grass, which can provide a good nutritional basis for herbivorous livestock. However, how to improve the nitrogen utilization rate of ryegrass and avoid the nitrate toxicity caused by excessive nitrogen has been troubling people for a long time. Up to now, the molecular response mechanism of ryegrass to nitrogen is not clear, especially under the condition of excessive nitrogen. Based on this, we tried to obtain a new insight into molecular response of ryegrass in nitrogen utilization and excessive nitrogen stress, providing the molecular theoretical basis for solving this problem.Results: In this study, the transcription of perennial ryegrass at different nitrogen levels was identified by high-throughput next-generation DNA sequencing. Phenotypic characterizations investigated that ryegrass in treatment N0.5 has a better growth state than the other three groups. The treatment N1 and N10 contained excessive nitrogen, which had a stress effect on plant growth. Analysis of differentially expressed genes indicated that 345, 105 genes are considered to involve in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. GO enrichment analysis revealed that plant response to nitrogen mainly enrich in two categories, including “biological process” and “molecular function”. KEGG enrichment analysis suggested that “Photosynthesis-antenna proteins” may respond positively to nitrogen under appropriate nitrogen conditions, whereas “steroid biosynthesis”, “carotenoid biosynthesis” and “C5-branched dibasic acid metabolism” had been identified as top significant enrichment pathways response to excessive nitrogen. Transcription factors analysis showed that 21 TFs related to nitrogen utilization were classified into 10 transcription factor families, especially AP2-EREBP and MYB TF families. 4 TFs related to excessive nitrogen stress were identified, which belonged to 4 transcription factor families including LOB, NAC, AP2-EREBP and HB. The expression patterns of these selected genes above were also analyzed. Conclusions: These results made a contribution to comprehend the molecular mechanism of perennial ryegrass response to nitrogen. It provides new ideas for guiding the production practice and variety improvement of forage and even food crops from the perspective of molecular biology.

scholarly journals CmMYB#7, an R3 MYB transcription factor, acts as a negative regulator of anthocyanin biosynthesis in chrysanthemum

2019 ◽  
Vol 70 (12) ◽  
pp. 3111-3123 ◽  
Author(s):  
Lili Xiang ◽  
Xiaofen Liu ◽  
Heng Li ◽  
Xueren Yin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Transient Expression ◽  
Regulatory Mechanism ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Negative Regulator ◽  
Myb Transcription Factor ◽  
Anthocyanin Content

Abstract ‘Jimba’, a well-known white flowered chrysanthemum cultivar, occasionally and spontaneously produces red colored petals under natural cultivation, but there is little information about the molecular regulatory mechanism underlying this process. We analysed the expression patterns of 91 MYB transcription factors in ‘Jimba’ and ‘Turning red Jimba’ and identified an R3 MYB, CmMYB#7, whose expression was significantly decreased in ‘Turning red Jimba’ compared with ‘Jimba’, and confirmed it is a passive repressor of anthocyanin biosynthesis. CmMYB#7 competed with CmMYB6, which together with CmbHLH2 is an essential component of the anthocyanin activation complex, for interaction with CmbHLH2 through the bHLH binding site in the R3 MYB domain. This reduced binding of the CmMYB6–CmbHLH2 complex and inhibited its ability to activate CmDFR and CmUFGT promoters. Moreover, using transient expression assays we demonstrated that changes in the expression of CmMYB#7 accounted for alterations in anthocyanin content. Taken together, our findings illustrate that CmMYB#7 is a negative regulator of anthocyanin biosynthesis in chrysanthemum.

scholarly journals Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome

2020 ◽  
Vol 21 (2) ◽  
pp. 138-154
Author(s):  
Vinay Singh ◽  
Neeraj Kumar ◽  
Anuj K. Dwivedi ◽  
Rita Sharma ◽  
Manoj K. Sharma
Keyword(s):  
Transcription Factors ◽  
Large Scale ◽  
Agronomic Traits ◽  
Expression Patterns ◽  
Biomass Composition ◽  
Phylogenomic Analysis ◽  
Myb Transcription Factors ◽  
Myb Genes ◽  
R2r3 Myb ◽  
R2r3 Myb Transcription Factors

Background : Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods: We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used inhouse generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results: We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum. Conclusion: The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.

scholarly journals Information-dependent Enrichment Analysis Reveals Time-dependent Transcriptional Regulation of the Estrogen Pathway of Toxicity

2016 ◽  
Author(s):  
Salil N. Pendse ◽  
Alexandra Maertens ◽  
Michael Rosenberg ◽  
Dipanwita Roy ◽  
Rick A. Fasani ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Fold Change ◽  
Gene Set Enrichment Analysis ◽  
High Dose ◽  
Functional Responses ◽  
Pathways Of Toxicity

The twenty-first century vision for toxicology involves a transition away from high-dose animal studies and into in vitro and computational models. This movement requires mapping pathways of toxicity through an understanding of how in vitro systems respond to chemical perturbation. Uncovering transcription factors responsible for gene expression patterns is essential for defining pathways of toxicity, and ultimately, for determining chemical mode of action, through which a toxicant acts. Traditionally this is achieved via chromatin immunoprecipitation studies and summarized by calculating, which transcription factors are statistically associated with the up- and down-regulated genes. These lists are commonly determined via statistical or fold-change cutoffs, a procedure that is sensitive to statistical power and may not be relevant to determining transcription factor associations. To move away from an arbitrary statistical or fold-change based cutoffs, we have developed in the context of the Mapping the Human Toxome project, a novel enrichment paradigm called Information Dependent Enrichment Analysis (IDEA) to guide identification of the transcription factor network. We used the test case of endocrine disruption of MCF-7 cells activated by 17β estradiol (E2). Using this new approach, we were able to establish a time course for transcriptional and functional responses to E2. ERα and ERβ are associated with short-term transcriptional changes in response to E2. Sustained exposure leads to the recruitment of an additional ensemble of transcription factors and alteration of cell-cycle machinery. TFAP2C and SOX2 were the transcription factors most highly correlated with dose. E2F7, E2F1 and Foxm1, which are involved in cell proliferation, were enriched only at 24h. IDEA is, therefore, a novel tool to identify candidate pathways of toxicity, clearly outperforming Gene-set Enrichment Analysis but with similar results as Weighted Gene Correlation Network Analysis, which helps to identify genes not annotated to pathways.

scholarly journals Functional analysis of enhancer elements regulating the expression of the Drosophila homeodomain transcription factor DRx by gene targeting

Hereditas ◽  
2021 ◽  
Vol 158 (1) ◽  
Author(s):  
Christine Klöppel ◽  
Kirsten Hildebrandt ◽  
Dieter Kolb ◽  
Nora Fürst ◽  
Isabelle Bley ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brain Development ◽  
Gene Targeting ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Adult Brain ◽  
Central Complex ◽  
Larval Brain ◽  
Endogenous Expression ◽  
The Brain

Abstract Background The Drosophila brain is an ideal model system to study stem cells, here called neuroblasts, and the generation of neural lineages. Many transcriptional activators are involved in formation of the brain during the development of Drosophila melanogaster. The transcription factor Drosophila Retinal homeobox (DRx), a member of the 57B homeobox gene cluster, is also one of these factors for brain development. Results In this study a detailed expression analysis of DRx in different developmental stages was conducted. We show that DRx is expressed in the embryonic brain in the protocerebrum, in the larval brain in the DM and DL lineages, the medulla and the lobula complex and in the central complex of the adult brain. We generated a DRx enhancer trap strain by gene targeting and reintegration of Gal4, which mimics the endogenous expression of DRx. With the help of eight existing enhancer-Gal4 strains and one made by our group, we mapped various enhancers necessary for the expression of DRx during all stages of brain development from the embryo to the adult. We made an analysis of some larger enhancer regions by gene targeting. Deletion of three of these enhancers showing the most prominent expression patterns in the brain resulted in specific temporal and spatial loss of DRx expression in defined brain structures. Conclusion Our data show that DRx is expressed in specific neuroblasts and defined neural lineages and suggest that DRx is another important factor for Drosophila brain development.

scholarly journals miRNA858b Inhibits Proanthocyanidin Accumulation by Repression of DkMYB19 and DkMYB20 in Persimmon

2019 ◽  
Author(s):  
Sichao Yang ◽  
Meng Zhang ◽  
Liqing Xu ◽  
Zhengrong Luo ◽  
Qinglin Zhang
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Transient Transformation ◽  
Activity Detection ◽  
Wild Type ◽  
Transcript Accumulation ◽  
Rna Ligase ◽  
R2r3 Myb

AbstractPersimmon proanthocyanidin (PA) biosynthetic had been reported to be regulated by several transcription factors, but the miRNAs function involved in this process was poorly understood. We identified a miRNA858b that putatively targeted two R2R3-MYB transcription factors, DkMYB19/DkMYB20. Transcript accumulation of DkMYB19/DkMYB20 and miRNA858b showed contrasting divergent expression patterns during fruit development. DkMYB19/DkMYB20 were confirmed to be localized in the nucleus. The interaction between miRNA858b and DkMYB19/DkMYB20 were experimentally validated by 5’ RNA ligase-mediated RACE and LUC enzyme activity detection. Overexpression of miRNA858b led to the down-regulation of DkMYB19/DkMYB20 which reduced the accumulation of PA, whereas the reduced miRNA858b activity that up-regulated the DkMYB19/DkMYB20 resulted in high levels of PA in STTM858b transient expression in leaves in vivo. Similarly, the transient transformation of miRNA858b in fruit wafers in vitro also reduced the accumulation of PA by repressing the DkMYB19/DkMYB20, while the up-regulation of DkMYB19/DkMYB20 enhanced the accumulation of PA in STTM858b or DkMYB19/DkMYB20 transient transformation in fruit wafers. PA content decreased after overexpression of miRNA858b in Arabidopsis wild type and DkMYB19/DkMYB20 in persimmon leaf callus consisted with the above results. These findings suggested that miRNA858b repressed the expression of DkMYB19/DkMYB20 which contribute to PA accumulation in persimmon.

scholarly journals Expression of RONIN and NANOG-associated proteins in goat parthenogenetic embryos

2017 ◽  
Vol 11 (2) ◽  
pp. 145 ◽  
Author(s):  
Marcelo Tigre Moura ◽  
Pamela Ramos-Deus ◽  
José Carlos Ferreira-Silva ◽  
Priscila Germany Corrêa Silva ◽  
Ludymila Furtado Cantanhêde ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
Preimplantation Embryos ◽  
Rt Pcr ◽  
Cleavage Stage ◽  
Specific Expression ◽  
Early Embryos ◽  
Associated Proteins ◽  
Gene Transcripts

The expression of a subset of transcription factors is enriched in early preimplantation embryos, which contributes to their cellular plasticity. RONIN, NANOG and its associated proteins are PluripotencyAssociated Transcription Factors (PATF) that control relevant downstream pathways in pluripotent stem cells, but their activity in early embryos remained less understood. The work was aimed to determine the expression of RONIN and four NANOG-associated PATFs in goat preimplantation embryos. Goat embryos were produced in vitro by parthenogenetic activation. Gene transcripts of cleavage-stage embryos were investigated by reverse transcriptase-polymerase chain reaction (RT-PCR), while blastocysts were analyzed by both RTPCR and quantitative RT-PCR (RT-qPCR) assays. Gene transcripts of ZFP281, NAC1, and NR0B1 were detected in cleavage-stage embryos, while RONIN and OCT4 were not found expressed. Detection in blastocysts by RT-PCR confirmed the activity of NR0B1, RONIN, and OCT4. Moreover, all five PATF were detected in blastocysts by RT-qPCR (ZFP281, NAC1, RONIN, OCT4, and NR0B1). In conclusion, RONIN and NANOG-associated proteins are active during goat parthenogenetic preimplantation development and hold stage-specific expression patterns.

Sexually dimorphic gene expression patterns during gonadal differentiation in olive flounder, Paralichthys olivaceus

2015 ◽  
Vol 65 (3-4) ◽  
pp. 193-207 ◽  
Author(s):  
Aiyun Wen ◽  
Feng You ◽  
Peng Sun ◽  
Jun Li ◽  
Dongdong Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Synergistic Effects ◽  
Paralichthys Olivaceus ◽  
Expression Patterns ◽  
Olive Flounder ◽  
Gene Expression Patterns ◽  
Gonadal Differentiation ◽  
Rt Pcr ◽  
Related Transcription Factor

The present study aims to elucidate the different expression patterns and possible roles of Doublesex and Mab-3-related transcription factor 1 (dmrt1), dmrt4, SRY-related transcription factor 9 (sox9) and cytochrome P450 aromatase 19a (cyp19a) during gonadal differentiation in olive flounder, Paralichthys olivaceus. We first analyzed the gene expression patterns in tissues using RT-PCR, which indicated dmrt1, sox9 and cyp19a were sex-related genes with sexual dimorphic expression. The quantitative expression changes of these three genes together with dmrt4 during gonadal differentiation were further examined using real-time RT-PCR. The results showed that dmrt1 was scarcely expressed in the primitive gonad and during following periods of gonadal differentiation. Its expression increased rapidly in the differentiating testis. Dmrt4 was strongly expressed in primitive gonads and much less expressed during following periods of gonadal differentiation. Its expression became strong in differentiating testes. While sox9 was highly expressed in the primitive gonad, it was expressed with fluctuations during following periods of gonadal differentiation. Cyp19a started expressing in primitive gonads, and its expression quantity fluctuated during latter periods of gonadal differentiation, but was strongly expressed in the early stage of differentiating ovaries. Results of in situ hybridization showed that dmrt4 and sox9 transcripts were both mainly localized in spermatocytes and our results suggested these four sex-related genes might be involved in gonadal differentiation through their synergistic effects in flounder.

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