scholarly journals Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fernanda Ferreira Salgado ◽  
Letícia Rios Vieira ◽  
Vivianny Nayse Belo Silva ◽  
André Pereira Leão ◽  
Priscila Grynberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Salinity Stress ◽  
Oil Palm ◽  
Functional Annotation ◽  
Target Genes ◽  
Early Response ◽  
Differentially Expressed ◽  
Putative Target

Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

Regulation of Erythro-Megakaryocytic Lineage Divergence By the Transcriptional Repressor Gfi1b and Its Rgs Targets

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2385-2385
Author(s):  
Ananya Sengupta ◽  
Ghanshyam Upadhyay ◽  
Sayani Sen ◽  
Shireen Saleque
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Genes ◽  
Transcriptional Repressor ◽  
Erythroid Differentiation ◽  
Mapk Signaling ◽  
Erythroid Cells ◽  
Hematopoietic Progenitors ◽  
Lineage Divergence

Abstract Introduction: Appropriate diversification of hematopoietic lineages from multi-potent progenitors is essential for normal development and health. The molecular programs that govern the divergence of erythroid and megakaryocytic lineages remain incompletely defined. Gene targeting experiments have shown the transcriptional repressor Gfi1b (Growth factor independence 1b) to be essential for erythro-megakaryocyte lineage development. Transcriptional repression of Gfi1b target genes is mediated by the cofactors LSD (lysine demethylase) 1 and Rcor (CoREST) 1. To understand the mechanism of Gfi1b action, its target genes were identified by chromatin immunoprecipitation (ChIP on Chip) screens. Three members of the Rgs (Regulator of G protein signaling) family were prominently represented in this target gene pool. In this study we present the role of Rgs18, a GTPase activating protein (GAP), in modulating erythro-megakaryocytic lineage divergence in hematopoietic progenitors. The results presented below demonstrate Rgs18 as a key arbitrator of this process in murine and human contexts. Approach: Following identification of Rgs18 as a potential Gfi1b and LSD1 target, its regulation by these factors was ascertained in erythro-megakaryocytic cells. Subsequently, to interrogate the role of Rgs18 in erythro-megakaryocyte differentiation, cDNA and shRNA mediated manipulations were performed in primary hematopoietic progenitors and cell lines, and the resulting phenotypes were analyzed. Finally, to trace the underlying mechanistic alterations responsible for these phenotypes the status of two branches of the MAPK (mitogen activated protein kinase) pathway and gene expression patterns of the mutually antagonistic transcription factors Fli1 (Friend leukemia integration [site] 1/Klf1 (Krupple like factor 1) were determined in Rgs18 manipulated cells. Result: Rgs18 expression was found to be low in immature megakaryoblasts in keeping with strong Gfi1b and LSD1 expression, but was reciprocally upregulated in mature megakaryocytes following declining Gfi1b and LSD1 levels in cells and on the rgs18 promoter. In contrast, expression of Gfi1b was strong in immature erythroid cells and increased further in mature cells, while Rgs18 expression which was modest in immature erythroid cells exhibited a reciprocal decline during maturation. Manipulation of Rgs18 expression in murine hematopoietic progenitors and a bipotential human cell line produced divergent outcomes, with expression augmenting megakaryocytic, and potently suppressing erythroid differentiation and vice versa. These phenotypes resulted from differential impact of Rgs18 expression on the P38 and ERK branches of MAPK signaling in the erythroid and megakaryocytic lineages. Repercussions of these signaling changes impacted relative expression of the mutually antagonistic transcription factors Fli1 and Klf1 and were compensated by ectopic Fli1 expression demonstrating activity of this transcription factor downstream of Rgs18. Conclusion: These results identify Rgs18 as a critical downstream effector of Gfi1b and an upstream regulator of MAPK signaling and Klf1/Fli1 gene expression. Sustained Gfi1b expression during erythroid differentiation represses Rgs18 and limits megakaryocytic gene expression. However during progression of megakaryocytic differentiation, declining Gfi1b levels results in robust expression of Rgs18 and lineage progression. Overall, this study provides new perspectives on lineage determination by highlighting multi-tier interactions between transcriptional and signaling networks in orchestrating hematopoietic lineage divergence. These insights could exemplify generic mechanisms exhibited by this large family of signal modulators in mediating lineage diversification in various contexts. Disclosures No relevant conflicts of interest to declare.

scholarly journals KLF3 Represses the Inflammatory Response in Macrophages

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 36-36
Author(s):  
Jessica M Salmon ◽  
Casie Leigh Reed ◽  
Maddyson Bender ◽  
Helen Lorraine Mitchell ◽  
Vanessa Fox ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Time Course ◽  
Target Genes ◽  
Wild Type ◽  
Cell Counts ◽  
Inflammatory Macrophages

Krüppel-like factors (KLFs) are a family of transcription factors that play essential roles in the development and differentiation of the hematopoietic system. These transcription factors possess highly conserved C-terminal zinc-finger motifs, which enable their binding to GC-rich, or CACC-box, motifs in promoter and enhancer regions of target genes. The N-terminal domains of these proteins are more varied and mediate the recruitment of various co-factors, which can form a complex with either activator or repressor function. Acting primarily as a gene repressor through its recruitment of CtBPs and histone deacetylases (HDACs) [1], we have recently shown that KLF3 competes with KLF1 bound sites in the genome to repress gene expression during erythropoiesis [2]. However, the function of Klf3 in other lineages has been less well studied. This widely expressed transcription factor has reported roles in the differentiation of marginal zone B cells, eosinophil function and inflammation [3]. We utilised the Klf3-null mouse model [4] to more closely examine the role of Klf3 in innate inflammatory cells. These mice exhibit elevated white cell counts, including monocytes (Figure 1A), and inflammation of the skin. Conditional knockout of Klf4 in myeloid cells leads to a deficiency of inflammatory macrophages [5]. To test our hypothesis KLF3 normally represses inflammation, perhaps by antagonising the action of KLF4, bone-marrow derived macrophages (BMDM) were generated from wild-type or Klf3-null mice and stimulated with the bacterial toxin lipopolysaccharide (LPS). In wild type BMDM, LPS induces Klf3 gene expression and activation then delayed repression of target genes such as Lgals3 (galectin-3) over a 21 hour time course (Figure 1B). Quantitative real-time PCR and mRNA-seq of WT v Klf3-null macrophages identified ~100 differentially expressed genes involved in proliferation, macrophage activation and inflammation. We transduced the monocyte cell line, RAW264.7 (that expresses Klf4, Klf3 and Klf2), with a retroviral vector expressing a tamoxifen-inducible KLF3-ER fusion construct. KLF3 induced cell cycle arrest and macrophage differentiation. We will report on KLF3-induced gene expression changes (repression and activation), and ChIP-seq for KLF3, in RAW cells. The results shed light on the mechanism by which KLF3 normally represses monocyte/macrophage responses to infection. This study highlights the importance of key transcriptional regulators that tightly control gene expression during inflammation. Loss of Klf3 leads to alterations in this process, resulting in hyper-activation of inflammatory macrophages, increased white cell counts and inflammation of the skin. A greater knowledge of the inflammatory process and how it is regulated is important for our understanding of acute infection and inflammatory disease. Further studies are planned to investigate the role of the KLF3 transcription factor in response to inflammation in vivo. References: 1. Pearson, R., et al., Kruppel-like transcription factors: A functional family. Int J Biochem Cell Biol, 2007. W2. Ilsley, M.D., et al., Kruppel-like factors compete for promoters and enhancers to fine-tune transcription. Nucleic Acids Res, 2017. 45(11): p. 6572-6588. W3. Knights, A.J., et al., Kruppel-like factor 3 (KLF3) suppresses NF-kappaB-driven inflammation in mice. J Biol Chem, 2020. 295(18): p. 6080-6091. W4. Sue, N., et al., Targeted disruption of the basic Kruppel-like factor gene (Klf3) reveals a role in adipogenesis. Mol Cell Biol, 2008. 28(12): p. 3967-78. W5. Alder, J.K., et al., Kruppel-like factor 4 is essential for inflammatory monocyte differentiation in vivo. J Immunol, 2008. 180(8): p. 5645-52. Figure 1: Elevated WCC (A) and inflammatory markers (B) in BMDM after LPS stimulation. 1. Total WCC in adult mice (3-6 months old) of the indicated genotypes. There is a statistically significant increase in the WCC in Klf3-/- v wild type mice (P<0.001 by student's t test). B. Time course (hours) after LPS stimulation of confluent BMDM. Klf3 is induced 3-fold by LPS and KLF3-target genes such as Lgals3 are not fully repressed by 21 hours in knockout mice. Figure 1 Disclosures Perkins: Novartis Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees.

120. OXYGEN REGULATED GENE EXPRESSION IN MOUSE CUMULUS CELLS

2009 ◽  
Vol 21 (9) ◽  
pp. 39
Author(s):  
K. Tam ◽  
K. Banwell ◽  
D. Froiland ◽  
D. Russell ◽  
K. Kind ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Oxygen Concentration ◽  
In Vitro Maturation ◽  
Target Genes ◽  
Cumulus Cells ◽  
Differentially Expressed ◽  
Oxygen Levels ◽  
Regulated Gene Expression

Hypoxia inducible factors (HIFs) are heterodimeric transcription factors that mediate the expression of a range of genes in response to low oxygen. Previously we showed that subsequent developmental outcomes were influenced by oxygen levels during in vitro maturation. The aim of the current study was to examine the effects of varying oxygen concentration during in vitro maturation of mouse COCs on expression of HIF target genes in the cumulus cells. I mmature COCs were collected from the ovaries of eCG-stimulated CBAB6F1 females (21 d) and cultured for 17-18 h under 2, 5 or 20% O2. Hyaluronidase-treated and recovered cumulus cells were collected and mRNA extracted for analysis. A microarray approach (Affymetrix 430_2) was used to identify genes in cumulus cells that were differentially expressed under varying oxygen concentrations (2, 5, 10 and 20%). This revealed 218 differentially expressed probes, of which 34 were up-regulated with decreasing oxygen levels. The great majority of these were classified as HIF-regulated genes. Specific analysis from real time RT-PCR of HIF regulated target genes Slc2a1, Ldha, Pgk1, Eno1, Ndrg1, Bnip3 were all significantly up-regulated (by at least 5–fold) when cells were cultured at 2% or 5% oxygen, when compared to 20% oxygen. Hif-1a mRNA decreased when cumulus cells were cultured in 2%, compared to 20% oxygen. This study demonstrates that cumulus cell gene expression is influenced by oxygen concentration, and suggests that these effects are mediated by the HIF transcription factors.

DNA methylation events in transcription factors and gene expression changes in colon cancer

Epigenomics ◽  
2020 ◽  
Vol 12 (18) ◽  
pp. 1593-1610
Author(s):  
Anna Díez-Villanueva ◽  
Rebeca Sanz-Pamplona ◽  
Robert Carreras-Torres ◽  
Ferran Moratalla-Navarro ◽  
M Henar Alonso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Colon Cancer ◽  
Transcription Factors ◽  
Target Genes ◽  
Linear Models ◽  
Cpg Islands ◽  
Promoter Regions ◽  
Differential Gene

Aim: Gain insight about the role of DNA methylation in the malignant growth of colon cancer. Patients & methods: Methylation and gene expression from 90 adjacent-tumor paired tissues and 48 healthy tissues were analyzed. Tumor genes whose change in expression was explained by changes in methylation were identified using linear models adjusted for tumor stromal content. Results: No differences in methylation were found between adjacent and healthy tissues, but clear differences were found between adjacent and tumor samples. We identified hypermethylated CpG islands located in promoter regions that drive differential gene expression of transcription factors and their target genes. Conclusion: Changes in methylation of a few genes provoke important changes in gene expression, by expanding the signal through transcription activation/repression.

scholarly journals The Role of microRNAs in the Pathogenesis of Erdheim-Chester Disease and Their Potential Use As Biomarkers for Diagnosis and Prognosis of the Disease

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2397-2397
Author(s):  
Ran Weissman ◽  
Nir Pilar ◽  
Benjamin H Durham ◽  
Michelle Ki ◽  
Roei D Mazor ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Mirna Expression ◽  
Target Genes ◽  
Differentially Expressed ◽  
Mirna Expression Pattern ◽  
Differentially Expressed Mirnas ◽  
Potential Use ◽  
Novel Therapeutic

Abstract Background: Erdheim-Chester disease (ECD) is a rare hematological malignancy, belonging to the L-group histiocytoses. ECD is characterized by multi-systemic proliferations of mature histiocytes in a background of inflammatory stroma. The inflammatory and neoplastic characteristics of the disease comprise a complex medical challenge for its diagnosis and treatment. MicroRNAs (miRNAs/miRs) are short non-coding RNAs (~22 nucleotides) that regulate gene expression in a sequence specific manner and play an important role in cancer development and progression. Since miRNAs are released into the blood by tumor cells, they may be used as biomarkers to distinguish between cancer patients and healthy individuals and to assist in determining treatment response. Moreover, miRNA-mRNA interactions can determine the molecular mechanism by which miRNAs and their target genes are involved in ECD and may suggest novel therapeutic options for these patients. To date, this is the first study elucidating the role of miRNA in ECD. Aims: The main focus of this study is to identify miRNAs that are differentially expressed in ECD patients compared to healthy controls and any clinical utility they have as potential biomarkers in ECD diagnosis, as well as to investigate their role in ECD pathogenesis, which may lead to new therapeutic options. Preliminary results: Using the nCounter Human miRNA Expression Assay (NanoString Technologies), we analyzed the plasma miRNA expression profiles of 6 ECD patients (BRAF V600E) compared to 6 healthy individuals. Of the 800 mature miRNAs analyzed, 234 miRNAs showed different expression levels in these samples. Principal component analysis (PCA) was applied to experimental quality control. The miRNAs from healthy donors were clustered separately from the ECD samples indicating a distinct miRNA expression pattern between these groups (Fig. 1A, 1B). Among the 131 miRNAs remaining in the final analysis (FDR<0.05),110 miRNAs were downregulated in ECD patients compared to those of healthy controls, and 21 miRNAs were upregulated in ECD samples compared to those of the controls. We validated the analysis method by quantitative real-time polymerase chain reaction (qRT-PCR) and found a positive correlation between miRs-15a, 16, 125a, 223, 21, 34a, 155 and miR-630 expression obtained by the NanoString array. This may indicate the potential use of miRNAs as biomarkers in ECD. To determine potential target genes and signaling pathways implicated in ECD, we analyzed the predicted pathways of the top 30 downregulated miRNAs that were differentially expressed between the two groups using the Ingenuity® Pathway Analysis (IPA) and DIANA-miRPath v3.0 database. Reassuringly, the analysis identified cancer, inflammatory disease, and inflammatory response (p<0.01) as the main disease and disorder related with the miRNA expression pattern, as well as oncogenic pathways such as MAPK, PI3K-AKT, RAS, ErbB, Hippo, and mTOR as the main molecular pathways related to the differentially-expressed miRNAs (p<0.009). This finding suggests that low expression of miRNAs results in up regulation of target genes that participate in cell survival signaling. These augmented pathways may be inhibited by novel therapeutic treatments such as PI3K inhibitors, mTOR pathway inhibitors, and MEK inhibitors in ECD patients. Next, we examined if there is any correlation between the predicted target genes of the miRNAs (obtained by IPA) and the experimentally validated gene expression pattern in ECD patients. To that end, we downloaded RNA-seq results of ECD patients from the GEO database (GSE74442 deposited by Diamond et al) and compared this list to our predicted miRNA targets in ECD patients, using Gene Set Enrichment Analysis (GSEA). We found a positive correlation between the gene expression reported in the literature and the predicted target of our deregulated miRNAs (Fig. 2), indicating that the predicted target genes are enriched in this data set, suggesting that the differentially expressed miRNAs might have a crucial role in the pathogenesis of ECD. Conclusions: Our preliminary data highlight the unique inflammatory and neoplastic features characteristic of ECD. These deregulated miRNAs may highlight new candidate gene targets allowing for a better understanding of the molecular mechanisms underlying the development of ECD and propose novel therapeutic treatments for these patients. Disclosures No relevant conflicts of interest to declare.

Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

2020 ◽  
Vol 15 ◽  
Author(s):  
Na Wang ◽  
Yukun Li ◽  
Sijing Liu ◽  
Liu Gao ◽  
Chang Liu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Functional Study ◽  
Regulation Network ◽  
Glucagon Like Peptide 1 ◽  
G Protein Coupled ◽  
Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

scholarly journals Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

2013 ◽  
Vol 40 (10) ◽  
pp. 1029 ◽  
Author(s):  
Aguida M. A. P. Morales ◽  
Jamie A. O'Rourke ◽  
Martijn van de Mortel ◽  
Katherine T. Scheider ◽  
Timothy J. Bancroft ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Silencing ◽  
Differentially Expressed ◽  
Soybean Rust ◽  
Phakopsora Pachyrhizi ◽  
R Gene ◽  
Virus Induced Gene Silencing ◽  
Asian Soybean Rust ◽  
Defence Responses

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.

scholarly journals Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia “Yuza 1” by High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Minjie Deng ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
Lu Yang ◽  
Yanfang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Target Genes ◽  
Reference Data ◽  
Relevant Information ◽  
Putative Target

Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.

scholarly journals FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Gaili Fan ◽  
Huawei Zheng ◽  
Kai Zhang ◽  
Veena Devi Ganeshan ◽  
Stephen Obol Opiyo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Family ◽  
Fusarium Graminearum ◽  
Target Genes ◽  
Homeobox Gene ◽  
Global Gene Expression ◽  
Binding Motifs ◽  
Content Type ◽  
Aerial Growth

ABSTRACT The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes. IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum. In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.

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