Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum

Abstract Background Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. Results A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. Conclusions We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.

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Genome-wide analysis of microRNAs expression profiling in patients with primary IgA nephropathy

Genome ◽

10.1139/gen-2012-0159 ◽

2013 ◽

Vol 56 (3) ◽

pp. 161-169 ◽

Cited By ~ 27

Author(s):

Kuibi Tan ◽

Jing Chen ◽

Wuxian Li ◽

Yuyu Chen ◽

Weiguo Sui ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Immunoglobulin A ◽

Differentially Expressed ◽

Control Group ◽

Pathological Changes ◽

Genome Wide ◽

Differentially Expressed Mirnas ◽

Specific Tissue ◽

Mirnas Expression

The aim of this study was to investigate the differential expression characteristics and the roles of the genome-wide microRNAs (miRNAs) in immunoglobulin A nephropathy (IgAN) kidney tissues. We used Illumina high-throughput sequencing technology to evaluate the miRNAs expression of six biopsy tissues from IgAN and six normal renal cortex specimens from patients with renal cell carcinoma. We observed a total of 85 miRNAs that were differentially expressed in the six IgAN patients, of which 11 miRNAs were up-regulated and 74 miRNAs were down-regulated in patients' tissues compared with control tissues. Additionally, we identified 55 candidate novel miRNAs in our study, which comprised seven candidates who were detected in the IgAN group and 49 candidates who were detected in the control group. Only one candidate (miR-n-9) was expressed in both groups. The bioinformatics showed that the regulated target genes of differentially expressed miRNAs were associated with immune and renal pathological changes. The identification of specific tissue miRNAs in our study not only helped clarify the genetics or immunology mechanisms involved in the pathogenesis of IgAN but also helped explain the pathological changes in the kidney tissues. We hypothesize that some significant miRNAs might potentially serve as novel diagnostic biomarkers in IgAN patients.

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Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽

10.1530/rep-18-0631 ◽

2019 ◽

Vol 157 (6) ◽

pp. 525-534 ◽

Cited By ~ 4

Author(s):

Hang Qi ◽

Guiling Liang ◽

Jin Yu ◽

Xiaofeng Wang ◽

Yan Liang ◽

...

Keyword(s):

Pathway Analysis ◽

Mirna Expression ◽

Gene Networks ◽

Target Genes ◽

Expression Profiles ◽

Expression Patterns ◽

Mirna Gene ◽

Differentially Expressed ◽

Signal Pathways ◽

Differentially Expressed Mirnas

MicroRNA (miRNA) expression proﬁles in tubal endometriosis (EM) are still poorly understood. In this study, we analyzed the differential expression of miRNAs and the related gene networks and signaling pathways in tubal EM. Four tubal epithelium samples from tubal EM patients and five normal tubal epithelium samples from uterine leiomyoma patients were collected for miRNA microarray. Bioinformatics analyses, including Ingenuity Pathway Analysis (IPA), Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of five miRNAs was performed in six tubal epithelium samples from tubal EM and six from control. A total of 17 significantly differentially expressed miRNAs and 4343 potential miRNA-target genes involved in tubal EM were identified (fold change >1.5 and FDR-adjustedPvalue <0.05). IPA indicated connections between miRNAs, target genes and other gynecological diseases like endometrial carcinoma. GO and KEGG analysis revealed that most of the identified genes were involved in the mTOR signaling pathway, SNARE interactions in vesicular transport and endocytosis. We constructed an miRNA-gene-disease network using target gene prediction. Functional analysis showed that the mTOR pathway was connected closely to tubal EM. Our results demonstrate for the first time the differentially expressed miRNAs and the related signal pathways involved in the pathogenesis of tubal EM which contribute to elucidating the pathogenic mechanism of tubal EM-related infertility.

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Genome-Wide Expression Profiling in Malaria Infection Reveals Transcriptional Changes Associated with Lethal and Nonlethal Outcomes

Infection and Immunity ◽

10.1128/iai.73.9.6091-6100.2005 ◽

2005 ◽

Vol 73 (9) ◽

pp. 6091-6100 ◽

Cited By ~ 24

Author(s):

Kurt Schaecher ◽

Sanjai Kumar ◽

Anjali Yadava ◽

Maryanne Vahey ◽

Christian F. Ockenhouse

Keyword(s):

Gene Expression ◽

Immune Responses ◽

Transcriptional Activation ◽

Malaria Infection ◽

Target Genes ◽

Expression Profiles ◽

Plasmodium Yoelii ◽

Differentially Expressed ◽

Genome Wide ◽

Study Gene Expression

ABSTRACT High-density oligonucleotide microarrays are widely used to study gene expression in cells exposed to a variety of pathogens. This study addressed the global genome-wide transcriptional activation of genes in hosts infected in vivo, which result in radically different clinical outcomes. We present an analysis of the gene expression profiles that identified a set of host biomarkers which distinguish between lethal and nonlethal blood stage Plasmodium yoelii malaria infections. Multiple biological replicates sampled during the course of infection were used to establish statistically valid sets of differentially expressed genes. These genes that correlated with the intensity of infection were used to identify pathways of cellular processes related to metabolic perturbations, erythropoiesis, and B-cell immune responses and other innate and cellular immune responses. The transcriptional apparatus that controls gene expression in erythropoiesis was also differentially expressed and regulated the expression of target genes involved in the host's response to malaria anemia. The biological systems approach provides unprecedented opportunities to explore the pathophysiology of host-pathogen interactions in experimental malaria infection and to decipher functionally complex networks of gene and protein interactions.

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MicroRNA (miRNA) Expression is Regulated by Butyrate-Induced Epigenetic Modulation of Gene Expression in Bovine Cells

Genetics & Epigenetics ◽

10.4137/geg.s6144 ◽

2010 ◽

Vol 3 ◽

pp. GEG.S6144 ◽

Cited By ~ 5

Author(s):

Cong-Jun Li ◽

Robert W. Li ◽

Theodore H. Elsasser

Keyword(s):

Gene Expression ◽

Histone Acetylation ◽

Mirna Expression ◽

Gene Networks ◽

Differentially Expressed ◽

Cellular Functions ◽

Differentially Expressed Mirnas ◽

Pathways Analysis ◽

Modulation Of Gene Expression ◽

Epigenetic Modulation

We present evidence that butyrate induced histone acetylation regulates miRNA expression. MicroRNA expression microarray profiling revealed that 35 miRNA transcripts are significantly ( P < 0.05) differentially expressed after cells were treated with 10 mM butyrate. Among them, 11 transcripts are differentially expressed very significantly ( P < 0.01). The functional and pathways analysis using MetaCore analytical suite shows differentially expressed miRNAs targeting some very important gene networks and differentially expressed miRNAs may interfere with butyrate induced modulation of gene expression and cellular functions. The data indicates the complicated interaction between miRNA and histone acetylation forms a highly integrated regulatory mechanism.

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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 ◽

10.1182/blood-2018-99-112388 ◽

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.

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Screening miRNA and their target genes related to tetralogy of Fallot with microarray

Cardiology in the Young ◽

10.1017/s104795111300053x ◽

2013 ◽

Vol 24 (3) ◽

pp. 442-446 ◽

Cited By ~ 6

Author(s):

Xian-min Wang ◽

Kui Zhang ◽

Yan Li ◽

Kun Shi ◽

Yi-ling Liu ◽

...

Keyword(s):

Gene Expression ◽

Functional Analysis ◽

Tetralogy Of Fallot ◽

Gene Expression Profile ◽

Target Genes ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Differentially Expressed Mirnas ◽

Protein Localisation ◽

Relationship Of

AbstractOur aim is to screen miRNAs and genes related to tetralogy of Fallot and construct a co-expression network based on integrating miRNA and gene microarrays. We downloaded the gene expression profile GSE35490 (miRNA) and GSE35776 (mRNA) of tetralogy of Fallot from the Gene Expression Omnibus database, which includes eight normal and 15 disease samples from infants, and screened differentially expressed miRNAs and genes between normal and disease samples (cut-off: p < 0.05; FDR < 0.05; and log FC > 2 or log FC < −2); in addition, we downloaded human miRNA and their targets, which were collected in the miRNA targets prediction database TargetScan, and selected ones that also appeared in our differentially expressed miRNAs and their predicted targets (score >0.9) and then made a relationship of diff_miRNAs and diff_genes of our results. Finally, we uploaded all the diff_target genes into String, constructed a co-expression network regulated by diff_miRNAs, and performed functional analysis with the software DAVID. Comparing normal and disease lesion tissue, we got 32 and 875 differentially expressed miRNAs and genes, respectively, and found hsa-miR-124 with 34 diff_target genes and hsa-miR-138 with two diff_target genes. Then we constructed a co-expression network that contains 231 pairs of genes. Genes in the network were enriched into 14 function clusters, and the most significant one is protein localisation. We screened the tetralogy of Fallot-related hsa-miR-124 and hsa-miR-138 with their direct and indirect differentially expressed target genes, and found that protein localisation is the significant cause affecting tetralogy of Fallot. Our approach may provide the groundwork for a new therapy approach to treating tetralogy of Fallot.

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Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

Current Bioinformatics ◽

10.2174/1574893615666200207092410 ◽

2021 ◽

Vol 15 (8) ◽

pp. 927-936 ◽

Cited By ~ 3

Author(s):

Yan Peng ◽

Yuewu Liu ◽

Xinbo Chen

Keyword(s):

Drought Stress ◽

Target Genes ◽

Hot Spot ◽

Interaction Network ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Protein Protein Interaction ◽

Promising Tool ◽

Differentially Expressed Mirnas ◽

Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identiﬁed. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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

Scientific Reports ◽

10.1038/s41598-021-85245-y ◽

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.

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

Journal of Innate Immunity ◽

10.1159/000450681 ◽

2016 ◽

Vol 9 (2) ◽

pp. 126-144 ◽

Cited By ~ 6

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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Genome-Wide Analysis of Glucocorticoid-Responsive Transcripts in the Hypothalamic Paraventricular Region of Male Rats

Endocrinology ◽

10.1210/en.2018-00535 ◽

2018 ◽

Vol 160 (1) ◽

pp. 38-54 ◽

Cited By ~ 2

Author(s):

Keiichi Itoi ◽

Ikuko Motoike ◽

Ying Liu ◽

Sam Clokie ◽

Yasumasa Iwasaki ◽

...

Keyword(s):

Gene Expression ◽

Target Genes ◽

Receptor Gene ◽

Male Rats ◽

Regulatory Mechanisms ◽

High Dose ◽

Sequencing Analysis ◽

Reverse Transcription Pcr ◽

Genome Wide ◽

A Genome

Abstract Glucocorticoids (GCs) are essential for stress adaptation, acting centrally and in the periphery. Corticotropin-releasing factor (CRF), a major regulator of adrenal GC synthesis, is produced in the paraventricular nucleus of the hypothalamus (PVH), which contains multiple neuroendocrine and preautonomic neurons. GCs may be involved in diverse regulatory mechanisms in the PVH, but the target genes of GCs are largely unexplored except for the CRF gene (Crh), a well-known target for GC negative feedback. Using a genome-wide RNA-sequencing analysis, we identified transcripts that changed in response to either high-dose corticosterone (Cort) exposure for 12 days (12-day high Cort), corticoid deprivation for 7 days (7-day ADX), or acute Cort administration. Among others, canonical GC target genes were upregulated prominently by 12-day high Cort. Crh was upregulated or downregulated most prominently by either 7-day ADX or 12-day high Cort, emphasizing the recognized feedback effects of GC on the hypothalamic-pituitary-adrenal (HPA) axis. Concomitant changes in vasopressin and apelin receptor gene expression are likely to contribute to HPA repression. In keeping with the pleotropic cellular actions of GCs, 7-day ADX downregulated numerous genes of a broad functional spectrum. The transcriptome response signature differed markedly between acute Cort injection and 12-day high Cort. Remarkably, six immediate early genes were upregulated 1 hour after Cort injection, which was confirmed by quantitative reverse transcription PCR and semiquantitative in situ hybridization. This study may provide a useful database for studying the regulatory mechanisms of GC-dependent gene expression and repression in the PVH.

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