Positive Transcriptional Regulator Research Articles

LINC00346 promotes pancreatic cancer progression through the CTCF-mediated Myc transcription.

Although multiple factors are known to contribute to pancreatic ductal adenocarcinoma (PDAC) progression, the role of long non-coding RNAs (lncRNAs) in PDAC remains largely unknown. In this study, we present data that long intergenic non-coding RNA 346 (LINC00346) functions as a promoting factor for PDAC development. We first show that LINC00346 is highly expressed in pancreatic tumor specimens as compared to normal pancreatic tissue based on interrogation of The Cancer Genome Atlas (TCGA) pancreatic adenocarcinoma dataset. Of significance, this upregulation of LINC00346 is associated with overall survival (OS) and disease-free survival (DFS), respectively. We further show that knockout (KO) of LINC00346 impairs pancreatic cancer cell proliferation, tumorigenesis, migration, and invasion ability. Importantly, these phenotypes can be restored by LINC00346 re-expression in KO cells (i.e., rescue experiment). RNA precipitation assays combined with mass spectrometry analysis indicate that LINC00346 interacts with CCCTC-binding factor (CTCF), a known transcriptional repressor of c-Myc. This interaction between LINC00346 and CTCF prevents the binding of CTCF to c-Myc promoter, relieving the CTCF-mediated repression of c-Myc. Thus, LINC00346 functions as a positive transcriptional regulator of c-Myc. Together, these results suggest that LINC00346 contributes to PDAC pathogenesis by activating c-Myc, and as such, LINC00346 may serve as a potential biomarker and therapeutic target for PDAC.

Functional characterization of interferon regulatory factor 2 and its role in the transcription of interferon a3 in golden pompano Trachinotus ovatus (Linnaeus 1758)

Similar to mammals, fish possess interferon (IFN) regulatory factor 2 (IRF2)-dependent type I IFN responses. Nevertheless, the detailed mechanism through which IRF2 regulates type I IFNa3 remains largely unknown. In the present study, we first identified two genes from golden pompano (Trachinotus ovatus), IRF2 (ToIRF2) and IFNa3 (ToIFNa3), in the IFN/IRF-based signalling pathway. The open reading frame (ORF) sequence of ToIRF2 encoded 335 amino acids possessing four typical characteristic domains, including a conserved DNA-binding domain (DBD), an interferon association domain 2 (IAD2), a transcriptional activation domain (TAD), and a transcriptional repression domain (TRD). Furthermore, transcripts of ToIRF2 were significantly upregulated after stimulation by polyinosinic: polycytidylic acid [poly (I:C)], lipopolysaccharide (LPS) and flagellin in immune-related tissues (blood, liver, and head-kidney). Moreover, to investigate whether ToIRF2 was a regulator of ToIFNa3, promoter analysis was performed. The results showed that the region from −896 bp to −200 bp is defined as the core promoter using progressive deletion mutations of IFNa3. Additionally, ToIRF2 overexpression led to a clear time-dependent enhancement of ToIFNa3 promoter expression in HEK293T cells. Mutation analyses indicated that the activity of the ToIFNa3 promoter significantly decreased after targeted mutation of M4/5 binding sites. Electrophoretic mobile shift assays (EMSAs) verified that IRF2 interacted with the binding site of the ToIFNa3 promoter region to regulate ToIFNa3 transcription. Last, the promoter activity of ToIFNa3-2 was more responsive to treatment with poly (I:C) than LPS and flagellin. Furthermore, overexpression of ToIRF2 in vitro obviously increased the expression of several IFN/IRF-based signalling pathway genes after poly (I:C) abduction. In conclusion, the present study provides the first evidence of the positive regulation of ToIFNa3 transcription by ToIRF2 and contributes to a better understanding of the transcriptional mechanisms of ToIRF2 in fish.

SP1-stimulated miR-545-3p inhibits osteogenesis via targeting LRP5-activated Wnt/beta-catenin signaling

Recently, the emerging role of microRNAs (miRNAs) has been identified in osteogenesis and the development of osteoporosis. Here, we found that miR-545-3p was decreased with the progression of osteogenic differentiation of MC3T3-E1 cells. Gain-of-function assay elucidated that ectopic expression of miR-545-3p led to abolishment on the levels of osteogenic differentiation markers including OC, ALP and Runx2, as well as increase on the expression of SOST, a negative regulator of osteogenic differentiation. Meanwhile, we explained that the inhibitory role of miR-545-3p in the proliferation of differentiated MC3T3-E1 cells was attributed to its induction on apoptosis. Furthermore, the mechanistic investigations validated that miR-545-3p inactivated Wnt/β-catenin signaling pathway by post-transcriptionally silencing LRP5. Importantly, we verified that miR-545-3p-confined osteogenic differentiation was mediated by the inhibition of LRP5-dependent Wnt/β-catenin pathway. Furthermore, it was identified that miR-545-3p downregulation in osteogenic differentiation was due to the positive transcriptional regulation by SP1, an osteoporosis-promoting transcription factor that was proved to be lessened along with osteoblastic differentiation. Jointly, this study elaborated that the SP1-modulated miR-545-3p functions as an osteogenesis-inhibitory factor through targeting LRP5 to inactivate Wnt/β-catenin signaling. Remarkably, strategies targeting miR-545-3p might be an innovative idea for the therapy of patients with osteoporosis.

T-box transcription factor eomesodermin/Tbr2 in Atlantic cod (Gadus morhua L.): Molecular characterization, promoter structure and function analysis

Eomesodermin (Eomes) is a member of T-box transcription factor family and plays an important role in the regulation of a wide variety of developmental processes and immune response in animals. Here we report cloning and characterization of the full-length cDNA of Atlantic cod Eomes (GmEomes), which possesses a TBOX_3 domain similar to its counterpart in mammals. The regulated expression was observed in head kidney and spleen in response to live Vibrio anguillarum infection in vivo, and spleen leukocytes in vitro after PMA and poly I:C stimulation. Furthermore, we determined a 694 bp sequence, upstream of the transcriptional start site (TSS), to contain a number of sequence motifs that matched known transcription factor-binding sites. Activities of the presumptive regulatory gene were assessed by transfecting different 5′-deletion constructs in CHSE-214 cells. The results showed that the basal promoters and positive transcriptional regulator activities of GmEomes were dependent by sequences located from −694 to −376 bp upstream of TSS. Furthermore, we found that some Eomes binding sites were present in the 5′-flanking regions of the cod IFNγ gene predicted by bioinformatics. However, Co-transfection of eomesodermin overexpression plasmids with INFγ reporter vector into CHSE-214 cells determined that Atlantic cod eomesodermin played a minor role in activation of the INFγ promoter.

Highlights From the Circulation Family of Journals

Highlights From the <i>Circulation</i> Family of Journals

Abstract 5225: Androgen deprivation upregulates SPINK1 expression and potentiates cellular plasticity in prostate cancer

Abstract The Serine Peptidase Inhibitor, Kazal type 1 (SPINK1) overexpression represents the second-largest prostate cancer (PCa) subtype associated with increased risk of recurrence and poor prognosis. Regardless of molecular subtype, androgen-deprivation therapy (ADT) remains the mainstay treatment for locally advanced and metastatic PCa patients. However, majority of the treated individuals eventually progress to castration-resistant stage and a subset of these patients develop ADT-induced neuroendocrine prostate cancer. Despite evidences of detrimental effects of ADT on PCa, possible role of androgen signaling in SPINK1-mediated prostate oncogenesis remains unexplored. Here, we show that androgen receptor (AR) functions as a direct transcriptional repressor of SPINK1, and blocking AR signaling relieves its repression, leading to upregulation of SPINK1. In agreement, we observe an inverse association between SPINK1 levels and AR expression across multiple patient cohorts, and in neuroendocrine differentiated LNCaP cells. We show that AR and its corepressor, the RE1-silencing transcription factor (REST), occupy SPINK1 promoter and inhibits its transcription. On the other hand, in the absence of AR, lineage reprogramming factor SOX2 in turn binds to SPINK1 promoter leading to its positive transcriptional regulation in androgen-deprived conditions with concomitant increase in neuroendocrine markers. Additionally, stable knockdown of SPINK1 results in reduced epithelial-mesenchymal transition, decreased stemness and drug resistance. Collectively, our findings provide a plausible explanation to the paradoxical clinical outcomes of ADT, arising due to increase in SPINK1 levels. Finally, we emphasize the need to take a well-informed decision prior to ADT and develop alternative therapeutic strategies for castrate-resistant PCa patients. Citation Format: Ritika Tiwari, Nishat Manzar, Vipul Bhatia, Anjali Yadav, Shannon Carskadon, Nilesh Gupta, Amina Zoubeidi, Nallasivam Palanisamy, Bushra Ateeq. Androgen deprivation upregulates SPINK1 expression and potentiates cellular plasticity in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5225.

Circular RNA sequencing reveals the molecular mechanism of the effects of acupuncture and moxibustion on endometrial receptivity in patients undergoing infertility treatment.

The present study aimed to determine the profile of differentially expressed circular RNAs (circRNAs) in infertile patients treated with acupuncture and moxibustion and verify the role of acupuncture and moxibustion in altering endometrial receptivity (ER). High‑throughput RNA sequencing and bioinformatics analysis of samples from six pairs of patients treated with or without acupuncture and moxibustion were conducted. The reliability of high‑throughput RNA sequencing was validated using reverse transcription‑quantitative PCR. The most significant circRNA functions and pathways were selected by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A circRNA‑miR‑mRNA interaction network was constructed to determine the connection between circRNAs, microRNAs (miRs), and mRNAs. High‑throughput RNA sequencing identified 2,653 circRNAs. A total of 86 circRNAs was differentially expressed, of which 57 were upregulated and 29 were downregulated, between the acupuncture and moxibustion group and the control group. In the GO analysis, the identified BP terms were chromatin modification, positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response, oxidative DNA demethylation, regulation of transcription from RNA polymerase II promoter in response to hypoxia, and regulation of smooth muscle cell differentiation. The identified CC terms were nucleoplasm, nucleolus, nucleus, histone acetyltransferase complex, and annulate lamellae. The identified MF terms were methylcytosine dioxygenase activity, chromatin binding, zinc ion binding, histone binding, and protein binding. In the KEGG pathway analysis, the identified pathways were protein processing in endoplasmic reticulum, degradation of aromatic compounds, shigellosis, mTOR signaling pathway, bacterial invasion of epithelial cells, and prostate cancer. Circ‑SFMBT2, circ‑BACH1, and circ‑LPAR1 were significantly upregulated (P<0.05) and associated with numerous miRs and mRNAs. Acupuncture and moxibustion could impact ER by regulating the expression of circRNAs.

Deciphering the crucial roles of transcriptional regulator GadR on gamma-aminobutyric acid production and acid resistance in Lactobacillus brevis

BackgroundIn lactic acid bacteria (LAB), acid stress leads to decreases of cell vitality and fermentation yield. Glutamate decarboxylase (GAD) system is regarded as one of the essential acid-resistance mechanisms in LAB. However, the regulation of GAD system is not well identified in the genus Lactobacillus. Although potential transcriptional regulator gene located upstream of GAD system genes was found in several Lactobacillus species, such as Lactobacillus (L.) brevis, the contribution of the regulator to acid resistance of the genus Lactobacillus has not been experimentally determined.ResultsThe potential transcriptional regulator gene gadR was disrupted by homologous recombination in L. brevis ATCC 367, leading to the decreased expression of gadC and gadB. The inactivation of GadR completely eliminated γ-aminobutyric acid (GABA) production and decreased the glutamate-dependent acid resistance. Moreover, expression of gadC and gadB in the presence of glutamate was increased and glutamate also stimulated the expression of gadR. In addition, L. brevis D17, a strain screened from acidic fermented grains of Chinese liquor production, had much higher expression level of gadR than the typical strain L. brevis ATCC 367. Under the pH-controlled and mixed-feed fermentation, L. brevis D17 achieved a titer of 177.74 g/L and a productivity of 4.94 g/L/h of GABA within 36 h. However, the L. brevis ATCC 367 only achieved a titer of 6.44 g/L and 0.18 g/L/h of GABA although the same fermentation control approach was employed.ConclusionsGadR is a positive transcriptional regulator controlling GABA conversion and acid resistance in L. brevis. L. brevis strains with hyper-expressing of gadR are excellent candidates for GABA production in industrial scale.

MZF1 and SCAND1 Reciprocally Regulate CDC37 Gene Expression in Prostate Cancer.

Cell division control 37 (CDC37) increases the stability of heat shock protein 90 (HSP90) client proteins and is thus essential for numerous intracellular oncogenic signaling pathways, playing a key role in prostate oncogenesis. Notably, elevated expression of CDC37 was found in prostate cancer cells, although the regulatory mechanisms through which CDC37 expression becomes increased are unknown. Here we show both positive and negative regulation of CDC37 gene transcription by two members of the SREZBP-CTfin51-AW1-Number 18 cDNA (SCAN) transcription factor family—MZF1 and SCAND1, respectively. Consensus DNA-binding motifs for myeloid zinc finger 1 (MZF1/ZSCAN6) were abundant in the CDC37 promoter region. MZF1 became bound to these regulatory sites and trans-activated the CDC37 gene whereas MZF1 depletion decreased CDC37 transcription and reduced the tumorigenesis of prostate cancer cells. On the other hand, SCAND1, a zinc fingerless SCAN box protein that potentially inhibits MZF1, accumulated at MZF1-binding sites in the CDC37 gene, negatively regulated the CDC37 gene and inhibited tumorigenesis. SCAND1 was abundantly expressed in normal prostate cells but was reduced in prostate cancer cells, suggesting a potential tumor suppressor role of SCAND1 in prostate cancer. These findings indicate that CDC37, a crucial protein in prostate cancer progression, is regulated reciprocally by MZF1 and SCAND1.

Genome-Wide Association Study-Driven Gene-Set Analyses, Genetic, and Functional Follow-Up Suggest GLIS1 as a Susceptibility Gene for Mitral Valve Prolapse.

Background Mitral valve prolapse (MVP) is a common heart valve disease, the most frequent indication for valve repair or replacement. MVP is characterized by excess extracellular matrix secretion and cellular disorganization, which leads to bulky valves that are unable to coapt correctly during ventricular systole resulting in mitral regurgitation, and it is associated with sudden cardiac death. Here we aim to characterize globally the biological mechanisms underlying genetic susceptibility to MVP to better characterize its triggering mechanisms. Methods We applied i-GSEA4GWAS and DEPICT, two pathway enrichment tools to MVP genome-wide association studies. We followed-up the association with MVP in an independent dataset of cases and controls. This research was conducted using the UK Biobank Resource. Immunohistochemistry staining for Glis1 (GLIS family zinc finger 1) was conducted in developing heart of mice. Knockdown of Glis1 using morpholinos was performed in zebrafish animals 72 hours postfertilization. Results We show that genes at risk loci are involved in biological functions relevant to actin filament organization, cytoskeleton biology, and cardiac development. The enrichment for positive regulation of transcription, cell proliferation, and migration motivated the follow-up of GLIS1, a transcription factor from the Krüppel-like zinc finger family. In combination with previously available data, we now report a genome-wide significant association with MVP (odds ratio, 1.20; P=4.36×10-10), indicating that Glis1 is expressed during embryonic development predominantly in nuclei of endothelial and interstitial cells of mitral valves in mouse. We also show that Glis1 knockdown causes atrioventricular regurgitation in developing hearts in zebrafish. Conclusions Our findings define globally molecular and cellular mechanisms underlying common genetic susceptibility to MVP and implicate established and unprecedented mechanisms. Through the GLIS1 association and function, we point at regulatory functions during cardiac development as common mechanisms to mitral valve degeneration.

RhNAC31, a novel rose NAC transcription factor, enhances tolerance to multiple abiotic stresses in Arabidopsis

This work identifies a new rose NAM/CUC subgroup member, RhNAC31. Overexpression of RhNAC31 in Arabidopsis confers salt, cold, and drought tolerance along with enhanced ABA sensitivity. Plant-specific NAM, ATAF1/2, and CUC (NAC) transcription factors serve essential functions in plant development and plant responses to environmental cues. Yet, transcription factors specific to the rose (Rosa hybrida) NAM/CUC3 subfamily are poorly understood. Here, we identify a novel NAM/CUC3-subfamily transcription factor, RhNAC31, that is associated with flower opening and can be induced by increased salt, cold, and dehydration stress treatment. RhNAC31 has a transactivation region in its C-terminal region, and its overexpression is associated with enhanced cold tolerance in Arabidopsis, conferring a higher survival rate and reduced reactive oxygen (H2O2 and O2−) levels. Under salt stress conditions, plants overexpressing RhNAC31 displayed increased germination rates and lower levels of H2O2, malondiadehyde (MDA), peroxidase (POD), and superoxide dismutase (SOD). Moreover, RhNAC31 conferred enhanced drought resistance by reducing the rate of water loss through leaves. Further characterization revealed a higher sensitivity of RhNAC31 transgenic plants to abscisic acid (ABA) both during and post-germination, causing lower germination and root inhibition rates under ABA treatment. Quantitative PCR experiments showed that numerous abiotic stress-related genes were activated by RhNAC31 overexpression. Our results highlight RhNAC31 as a positive transcriptional regulator of tolerance to multiple abiotic pressures, and we conclude that RhNAC31 has potential for use in the molecular breeding of stress-tolerant crops.

Identification of significant genes with poor prognosis in ovarian cancer via bioinformatical analysis

Ovarian cancer (OC) is the highest frequent malignant gynecologic tumor with very complicated pathogenesis. The purpose of the present academic work was to identify significant genes with poor outcome and their underlying mechanisms. Gene expression profiles of GSE36668, GSE14407 and GSE18520 were available from GEO database. There are 69 OC tissues and 26 normal tissues in the three profile datasets. Differentially expressed genes (DEGs) between OC tissues and normal ovarian (OV) tissues were picked out by GEO2R tool and Venn diagram software. Next, we made use of the Database for Annotation, Visualization and Integrated Discovery (DAVID) to analyze Kyoto Encyclopedia of Gene and Genome (KEGG) pathway and gene ontology (GO). Then protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). There were total of 216 consistently expressed genes in the three datasets, including 110 up-regulated genes enriched in cell division, sister chromatid cohesion, mitotic nuclear division, regulation of cell cycle, protein localization to kinetochore, cell proliferation and Cell cycle, progesterone-mediated oocyte maturation and p53 signaling pathway, while 106 down-regulated genes enriched in palate development, blood coagulation, positive regulation of transcription from RNA polymerase II promoter, axonogenesis, receptor internalization, negative regulation of transcription from RNA polymerase II promoter and no significant signaling pathways. Of PPI network analyzed by Molecular Complex Detection (MCODE) plug-in, all 33 up-regulated genes were selected. Furthermore, for the analysis of overall survival among those genes, Kaplan–Meier analysis was implemented and 20 of 33 genes had a significantly worse prognosis. For validation in Gene Expression Profiling Interactive Analysis (GEPIA), 15 of 20 genes were discovered highly expressed in OC tissues compared to normal OV tissues. Furthermore, four genes (BUB1B, BUB1, TTK and CCNB1) were found to significantly enrich in the cell cycle pathway via re-analysis of DAVID. In conclusion, we have identified four significant up-regulated DEGs with poor prognosis in OC on the basis of integrated bioinformatical methods, which could be potential therapeutic targets for OC patients.

Regulatory Network of Two Tumor-Suppressive Noncoding RNAs Interferes with the Growth and Metastasis of Renal Cell Carcinoma

Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long ncRNAs (lncRNAs) have been shown to function as pivotal regulators in the carcinogenesis of renal cell carcinoma (RCC). However, the functions and underlying mechanisms of most ncRNAs in RCC are still elusive, and the crosstalks of different layers of ncRNAs are seldom reported. Here we showed that miR-124 and maternally expressed gene 3 (MEG3) were both significantly reduced in RCC, and combined expression of miR-124 and MEG3 emerged as an independent prognostic factor in our RCC cohort. Overexpression of miR-124 or MEG3 inhibited cell proliferation, migration, and invasion in vitro, and restrained tumor growth in vivo. EZH2 knockdown induced the epigenetic silencing of miR-124 and MEG3 expression by H3K27me3. Besides, miR-124 directly targeted the TET1 transcript, and then the interaction resulted in the upregulation of MEG3. Furthermore, we demonstrated that MEG3 induced p53 protein accumulation, whereas p53 was a positive transcriptional regulator of the miR-124. In addition, tumor-suppressive PTPN11 was identified as a direct target of miR-124, as well as the MEG3- and p53-regulated gene. Our study identifies three crosstalks between miR-124 and MEG3, which provide a plausible link for these two ncRNAs in RCC. Both ncRNAs exert important antitumor effects in RCC pathogenesis and might serve as prognostic biomarkers and molecular therapeutic targets.

Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants.

Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.

Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs.

Ribosome biogenesis (RiBi) is an extremely energy intensive process that is critical for gene expression. It is thus highly regulated, including through the tightly coordinated expression of over 200 RiBi genes by positive and negative transcriptional regulators. We investigated RiBi regulation as cells initiated meiosis in budding yeast and noted early transcriptional activation of RiBi genes, followed by their apparent translational repression 1 hour (h) after stimulation to enter meiosis. Surprisingly, in the representative genes examined, measured translational repression depended on their promoters rather than mRNA regions. Further investigation revealed that the signature of this regulation in our data depended on pre-treating cells with the translation inhibitor, cycloheximide (CHX). This treatment, at 1 h in meiosis, but not earlier, rapidly resulted in accumulation of RiBi mRNAs that were not translated. This effect was also seen in with CHX pre-treatment of cells grown in media lacking amino acids. For NSR1, this effect depended on the –150 to –101 region of the promoter, as well as the RiBi transcriptional repressors Dot6 and Tod6. Condition-specific RiBi mRNA accumulation was also seen with translation inhibitors that are dissimilar from CHX, suggesting that this phenomenon might represent a feedback response to global translation inhibition.

Glucocorticoid‐Driven Transcriptomes in Human Airway Epithelial Cells: Commonalities, Differences and Functional Insight

RATIONALEGlucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease and during exacerbations indicates a need to improve ICS actions. Since ICS target the epithelium, glucocorticoid‐driven transcriptomes were compared between primary human bronchial epithelial (HBE) cells and common cell lines, pulmonary type II A549 and bronchial epithelial BEAS‐2B cells.METHODSGene expression profiling of RNA extracted from A549, BEAS‐2B and HBE cells following budesonide treatment was performed using Affymetrix PrimeView microarrays. Genes showing significant induction (fold ≥2, P ≤0.05) or repression (fold ≤0.5, P ≤0.05) compared to untreated cells, in any of the cell variants were used for further analyses.RESULTSIn BEAS‐2B cells, budesonide induced or, in a delayed fashion, repressed the expression of 63, 133, 240, and 257 or 15, 56, 236, and 344 mRNAs at 1, 2, 6, and 18 h, respectively. Within the early‐induced mRNAs were multiple transcriptional activators and repressors, thereby providing mechanisms for the subsequent modulation of gene expression. Using the above criteria, 17 (BCL6, BIRC3, CEBPD, ERRFI1, FBXL16, FKBP5, GADD45B, IRS2, KLF9, PDK4, PER1, RGCC, RGS2, SEC14L2, SLC16A12, TFCP2L1, TSC22D3) induced and 8 (ARL4C, FLRT2, IER3, IL11, PLAUR, SEMA3A, SLC4A7, SOX9) repressed mRNAs were common between A549, BEAS‐2B and HBE cells at 6 h. As absolute gene expression change showed greater commonality, lowering the cut‐off (≥1.25 or ≤0.8‐fold) within these groups produced 93 and 82 genes induced or repressed in common. Since large changes in few mRNAs and/or small changes in many mRNAs may drive function, gene ontology (GO)/pathway analyses were performed using both stringency criteria. Budesonide‐induced genes showed GO term enrichment for positive and negative regulation of transcription, signaling, proliferation, apoptosis, and movement, as well as FOXO and PI3K‐Akt signaling pathways. Repressed genes were enriched for inflammatory signaling pathways (TNF, NF‐κB) and GO terms for cytokine activity, chemotaxis and cell signaling. Reduced growth factor expression and effects on proliferation and apoptosis were highlighted.CONCLUSIONSWhile glucocorticoids repress mRNAs associated with inflammation, prior induction of transcriptional activators and repressors may explain longer‐term responses to these agents. Positive and negative effects on signaling, proliferation, migration and apoptosis were revealed. Since many such gene expression changes occurred in human airways post‐ICS inhalation, effects in cell lines and primary HBE cells in vitro may be relevant to ICS in vivo.Support or Funding InformationThis work was supported by: RN grants: Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council of Canada (NSERC) discovery grant, and AstraZeneca; MMM studentships: NSERC Postgraduate Scholarship – Doctoral, Queen Elizabeth II Doctoral scholarship, and The Lung Association – Alberta &amp; NWT studentship award.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Isolation, expression and function analysis of a bZIP transcription factor IbbZIP37 in sweetpotato (Ipomoea batatas L. [Lam

bZIP transcription factor play an important regulatory role in the response to multiple abiotic stresses. However, our knowledge of the stress tolerance functions of bZIP family genes in sweetpotato (Ipomoea batatas [L.] Lam) remains limited. In the present study, we isolated and functionally characterized an IbbZIP37 gene encoding an abiotic stress-inducible bZIP group A transcription factor. Sequence analysis showed that the IbbZIP37 contained a typical bZIP domain and five conserved Ser/Thr kinase phosphorylation sites (RXXS/T). The IbbZIP37 protein was localized in the nucleus and possessed transcriptional activation activity. The results of electrophoretic mobility shift assays indicated that IbbZIP37 can bind to the ABRE cis-element, not do to DRE cis-element in vitro. The IbbZIP37 gene showed the highest level of constitutive expression in root, especially in fibrous root and storage root body. Gene expression was induced by ABA and several environmental stresses including drought, salt and heat shock. Our results suggest that IbbZIP37 is a positive transcription regulator of the abiotic stresses response, which can be used as an excellent candidate for improving the stress tolerance of different crop plants.

LBX2-AS1 is activated by ZEB1 and promotes the development of esophageal squamous cell carcinoma by interacting with HNRNPC to enhance the stability of ZEB1 and ZEB2 mRNAs

Long non-coding RNAs (lncRNAs) are a group of transcripts, which can regulate the progression of esophageal squamous cell carcinoma (ESCC). According to the data of TCGA, Ladybird homeobox 2 antisense RNA 1 (LBX2-AS1) is a highly expressed lncRNA in ESCC samples. Herein, we chose it for further study. Furtherly, dysregulation of LBX2-AS1 was identified in ESCC tissues with metastasis. Loss-of function assays were conducted and revealed that LBX2-AS1 knockdown suppressed ESCC cell migration and epithelial-mesenchymal transition (EMT). Zinc finger E-box binding homeobox 1 (ZEB1) and zinc finger E-box binding homeobox 2 (ZEB2) are two EMT-related transcription factors. Since LBX2-AS1 promoted the EMT progress and simultaneously enhanced the level of ZEB1 and ZEB2, we further investigated whether LBX2-AS1 promoted cell migration and EMT in ESCC by regulating ZEB1 and ZEB2. Mechanism investigations revealed that RNA binding protein heterogeneous nuclear ribonucleoprotein C (HNRNPC) could interact with LBX2-AS1, ZEB1 and ZEB2, simultaneously. The similar function of HNRNPC in regulating migration and EMT process was demonstrated. ZEB1 has been reported as a positive transcriptional regulator of lncRNA. Therefore, further mechanism analysis was made to demonstrate whether ZEB1 could regulate the transcription of LBX2-AS1. Collectively, our data showed that ZEB1-induced upregulation of LBX2-AS1 promoted cell migration and EMT process in ESCC via enhancing the stability of ZEB1 and ZEB2.

Genome-wide investigation of microsatellite polymorphism in coding region of the giant panda (Ailuropoda melanoleuca) genome: a resource for study of phenotype diversity and abnormal traits

Repeat number variations of coding simple sequence repeats (coding SSRs) generate phenotype diversity for environmental adaptation and rapid adaptive evolution. Despite the positive potential of coding SSR mutations, the repeat variations have also been shown to cause hereditary disorders and severe diseases. However, there have been few reports on the analysis of SSR polymorphism in genome-wide coding regions. We identified 1016 coding SSRs, of which 283 SSRs (27.9%) were polymorphic with 2 to 8 alleles, using 33 re-sequenced giant panda genomes. The 283 polymorphic coding SSRs were mapped on 260 genes, which were assigned into 547 GO terms. Functional analysis of 260 genes showed that four significantly enriched pathways: thyroid hormone signaling pathway, pancreatic secretion, gastric acid secretion, and thyroid hormone synthesis, were relevant to digestion and metabolism. The comparison analysis of gene functions exhibited positive regulation of transcription, DNA-templated term (GO:0045893), the poly(A) RNA-binding term (GO:0008270), and zinc ion–binding term (GO:0044822) which were only significantly enriched in genes containing polymorphic coding SSRs. This indicates coding SSR polymorphism may be involved in binding and regulation functions that can affect the expression of their downstream genes and contribute to diverse phenotypes. Our results provide a solid foundation for further study regarding the effect of coding SSR polymorphism on the adaptation, adaptive evolution, and abnormal traits of the giant panda.

The magic 'hammer' of TOR: the multiple faces of a single pathway in the metabolic regulation of plant growth and development.

The target of rapamycin (TOR) pathway has emerged as a central hub synchronizing plant growth according to the nutrient/energy status and environmental inputs. Molecular mechanisms through which TOR promotes plant growth involve the positive regulation of transcription of cell proliferation-associated genes, mRNA translation initiation and ribosome biogenesis, to cite a few examples. Phytohormones, light, sugars, and sulfur have been found to broadly regulate TOR activity. TOR operates as a metabolic homeostat to fine-tune anabolic processes and efficiently enable plant growth under different circumstances. However, little is known about the multiple effectors that act up- and downstream of TOR. Here, we mainly discuss recent findings related to the TOR pathway in the context of plant metabolism and highlight areas of interest that need to be addressed to keep unravelling the intricate networks governing the regulation of TOR and its function in controlling biosynthetic growth.