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1.
FASEB J ; 36(10): e22520, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36065633

RESUMO

Hypoxia-inducible factors (HIFs) are core regulators of the hypoxia response. HIF signaling is activated in the local physiological and pathological hypoxic environment, acting on downstream target genes to synthesize the corresponding proteins and regulate the hypoxic stress response. HIFs belong to the hypoxia-activated transcription family and contain two heterodimeric transcription factors, HIF-α and HIF-ß. Under hypoxia, the dimer formed by HIF-α binding to HIF-ß translocates into the nucleus and binds to the hypoxia response element (HRE) to induce transcription of a series of genes. HIF-1α plays an important role in innate bone development and acquired bone regeneration. HIF-1α promotes bone regeneration mainly through the following two pathways: (1) By regulating angiogenesis-osteoblast coupling to promote bone regeneration; and (2) by inducing metabolic reprogramming in osteoblasts, promoting cellular anaerobic glycolysis, ensuring the energy supply of osteoblasts under hypoxic conditions, and further promoting bone regeneration and repair. This article reviews recent basic research on HIF-1α and its role in promoting osteogenesis, discusses the possible molecular mechanisms, introduces the hypoxia-independent role of HIF-1α and reviews the application prospects of HIF-1α in tissue engineering.


Assuntos
Regeneração Óssea , Osteoblastos , Hipóxia Celular , Humanos , Hipóxia/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Osteoblastos/metabolismo , Osteogênese , Elementos de Resposta
2.
PLoS One ; 17(9): e0274338, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36084008

RESUMO

Gene expression is regulated through cis-regulatory elements (CREs), among which are promoters, enhancers, Polycomb/Trithorax Response Elements (PREs), silencers and insulators. Computational prediction of CREs can be achieved using a variety of statistical and machine learning methods combined with different feature space formulations. Although Python packages for DNA sequence feature sets and for machine learning are available, no existing package facilitates the combination of DNA sequence feature sets with machine learning methods for the genome-wide prediction of candidate CREs. We here present Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences by providing extensible APIs and implementing the glue required for combining feature sets and models for genome-wide prediction. Gnocis implements a variety of base feature sets, including motif pair occurrence frequencies and the k-spectrum mismatch kernel. It integrates with Scikit-learn and TensorFlow for state-of-the-art machine learning. Gnocis additionally implements a broad suite of tools for the handling and preparation of sequence, region and curve data, which can be useful for general DNA bioinformatics in Python. We also present Deep-MOCCA, a neural network architecture inspired by SVM-MOCCA that achieves moderate to high generalization without prior motif knowledge. To demonstrate the use of Gnocis, we applied multiple machine learning methods to the modelling of D. melanogaster PREs, including a Convolutional Neural Network (CNN), making this the first study to model PREs with CNNs. The models are readily adapted to new CRE modelling problems and to other organisms. In order to produce a high-performance, compiled package for Python 3, we implemented Gnocis in Cython. Gnocis can be installed using the PyPI package manager by running 'pip install gnocis'. The source code is available on GitHub, at https://github.com/bjornbredesen/gnocis.


Assuntos
Drosophila melanogaster , Software , Algoritmos , Animais , DNA/genética , Drosophila melanogaster/genética , Redes Neurais de Computação , Elementos de Resposta
3.
Gene ; 845: 146832, 2022 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-36007803

RESUMO

Polycomb and Trithorax group proteins (PcG, TrxG) epigenetically regulate developmental genes. These proteins bind with specific DNA elements, the Polycomb Response Element (PRE). Apart from mutations in polycomb/ trithorax proteins, altered cis-elements like PRE underlie the modified function and thus disease etiology. PREs are well studied in Drosophila, while only a few human PREs have been reported. We have identified a polycomb responsive DNA element, hPRE-HoxA3, in the intron of the HoxA3 gene. The hPRE-HoxA3 represses luciferase reporter activity in a PcG-dependent manner. The endogenous hPRE-HoxA3 element recruits PcG proteins and is enriched with repressive H3K27me3 marks, demonstrating that hPRE-HoxA3 is a part of the PcG-dependent gene regulatory network. Furthermore, it interacts with D11-12, the well-known PRE in the human Hox cluster. hPRE-Hox3 is a part of the 3-dimensional chromosomal domain organization as it is involved in the long-range interaction with other PcG enriched regions of Hox A, B, C, and D clusters.


Assuntos
Proteínas de Drosophila , Histonas , Animais , Drosophila/genética , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Genômica , Histonas/genética , Histonas/metabolismo , Humanos , Luciferases/metabolismo , Complexo Repressor Polycomb 1/genética , Proteínas do Grupo Polycomb/genética , Proteínas do Grupo Polycomb/metabolismo , Elementos de Resposta , Fatores de Transcrição/genética
4.
Int J Mol Sci ; 23(15)2022 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-35955808

RESUMO

The Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded ORF50 protein is a potent transcriptional activator essential for triggering KSHV lytic reactivation. Despite extensive studies, little is known about whether ORF50 possesses the ability to repress gene expression or has an antagonistic action to cellular transcription factors. Previously, we demonstrated that human oncoprotein MDM2 can promote the degradation of ORF50 protein. Herein, we show that abundant ORF50 expression in cells can conversely downregulate MDM2 expression via repressing both the upstream (P1) and internal (P2) promoters of the MDM2 gene. Deletion analysis of the MDM2 P1 promoter revealed that there were two ORF50-dependent negative response elements located from -102 to -63 and from -39 to +1, which contain Sp1-binding sites. For the MDM2 P2 promoter, the ORF50-dependent negative response element was identified in the region from -110 to -25, which is coincident with the location of two known p53-binding sites. Importantly, we further demonstrated that overexpression of Sp1 or p53 in cells indeed upregulated MDM2 expression; however, coexpression with ORF50 protein remarkably reduced the Sp1- or p53-mediated MDM2 upregulation. Collectively, our findings propose a reciprocal negative regulation between ORF50 and MDM2 and uncover that ORF50 decreases MDM2 expression through repressing Sp1- and p53-mediated transactivation.


Assuntos
Herpesvirus Humano 8 , Regulação Viral da Expressão Gênica , Herpesvirus Humano 8/genética , Humanos , Regiões Promotoras Genéticas , Proteínas Proto-Oncogênicas c-mdm2/genética , Proteínas Proto-Oncogênicas c-mdm2/metabolismo , Elementos de Resposta , Fator de Transcrição Sp1/genética , Fator de Transcrição Sp1/metabolismo , Fatores de Transcrição/metabolismo , Ativação Transcricional , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo , Proteínas Virais
5.
Clin Transl Med ; 12(8): e1003, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35917404

RESUMO

BACKGROUND: Human Tau (hTau) accumulation and synapse loss are two pathological hallmarks of tauopathies. However, whether and how hTau exerts toxic effects on synapses remain elusive. METHODS: Mutated hTau (P301S) was overexpressed in the N2a cell line, primary hippocampal neurons and hippocampal CA3. Western blotting and quantitative polymerase chain reaction were applied to examine the protein and mRNA levels of synaptic proteins. The protein interaction was tested by co-immunoprecipitation and proximity ligation assays. Memory and emotion status were evaluated by a series of behavioural tests. The transcriptional activity of nuclear factor-erythroid 2-related factor 2 (NRF2) was detected by dual luciferase reporter assay. Electrophoresis mobility shift assay and chromosome immunoprecipitation were conducted to examine the combination of NRF2 to specific anti-oxidative response element (ARE) sequences. Neuronal morphology was analysed after Golgi staining. RESULTS: Overexpressing P301S decreased the protein levels of post-synaptic density protein 93 (PSD93), PSD95 and synapsin 1 (SYN1). Simultaneously, NRF2 was decreased, whereas Kelch-like ECH-associated protein 1 (KEAP1) was elevated. Further, we found that NRF2 could bind to the specific AREs of DLG2, DLG4 and SYN1 genes, which encode PSD93, PSD95 and SYN1, respectively, to promote their expression. Overexpressing NRF2 ameliorated P301S-reduced synaptic proteins and synapse. By means of acetylation at K312, P301S increased the protein level of KEAP1 via inhibiting KEAP1 degradation from ubiquitin-proteasome pathway, thereby decreasing NRF2 and reducing synapse. Blocking the P301S-KEAP1 interaction at K312 rescued the P301S-suppressed expression of synaptic proteins and memory deficits with anxiety efficiently. CONCLUSIONS: P301S-hTau could acetylate KEAP1 to trigger synaptic toxicity via inhibiting the NRF2/ARE pathway. These findings provide a novel and potential target for the therapeutic intervention of tauopathies.


Assuntos
Fator 2 Relacionado a NF-E2 , Tauopatias , Hidrolases de Éster Carboxílico/metabolismo , Genes Reguladores , Humanos , Proteína 1 Associada a ECH Semelhante a Kelch/genética , Proteína 1 Associada a ECH Semelhante a Kelch/metabolismo , Fator 2 Relacionado a NF-E2/genética , Fator 2 Relacionado a NF-E2/metabolismo , Elementos de Resposta , Tauopatias/genética
6.
Cancer Biol Ther ; 23(1): 424-438, 2022 12 31.
Artigo em Inglês | MEDLINE | ID: mdl-35816613

RESUMO

Mounting evidence has demonstrated that fatty acid binding protein 5 (FABP5) is commonly upregulated in many human malignancies. However, the mechanisms explaining the involvement of FABP5 in hepatocellular carcinoma (HCC) remain unclear. In this study, we demonstrated the involvement of FABP5 and its downstream signaling molecules in HCC progression. We first confirmed that FABP5 expression was upregulated in HCC. Additionally, FABP5 promoted HCC cells proliferation, migration, and invasion. Mechanistic investigation showed that FABP5 could improve cAMP-response element binding protein (CREB) phosphorylation. Meanwhile, CREB, as a transcription factor, upregulated the miR-889-5p expression by binding to the miR-889-5p promoter region. Consequently, miR-889-5p led to downregulation of Krüppel-like factor 9 (KLF9) by binding to the 3'-UTR of the KLF9 mRNA, potentiating the PI3K/AKT signaling pathway and promoting the proliferation, migration, and invasion of HCC cells. Our findings have identified a FABP5/CREB/miR-889-5p/KLF9 axis for HCC progression, and we postulate that blocking this key signaling pathway may represent a promising strategy for HCC treatment.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , MicroRNAs , Regiões 3' não Traduzidas , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral , Movimento Celular/genética , Proliferação de Células/genética , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/genética , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/metabolismo , Proteínas de Ligação a Ácido Graxo/genética , Proteínas de Ligação a Ácido Graxo/metabolismo , Regulação Neoplásica da Expressão Gênica , Humanos , Fatores de Transcrição Kruppel-Like/genética , Fatores de Transcrição Kruppel-Like/metabolismo , Neoplasias Hepáticas/patologia , MicroRNAs/genética , MicroRNAs/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Elementos de Resposta
7.
Endocrinology ; 163(8)2022 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-35678380

RESUMO

When bound to thyroid hormone, the nuclear receptor TRα1 activates the transcription of a number of genes in many cell types. It mainly acts by binding DNA as a heterodimer with retinoid X receptors at specific response elements related to the DR4 consensus sequence. However, the number of DR4-like elements in the genome exceed by far the number of occupied sites, indicating that minor variations in nucleotides composition deeply influence the DNA-binding capacity and transactivation activity of TRα1. An improved protocol of synthetic self-transcribing active regulatory region sequencing was used to quantitatively assess the transcriptional activity of thousands of synthetic sites in parallel. This functional screen highlights a strong correlation between the affinity of the heterodimers for DNA and their capacity to mediate the thyroid hormone response.


Assuntos
Receptores do Ácido Retinoico , Receptores dos Hormônios Tireóideos , DNA/metabolismo , Receptores do Ácido Retinoico/genética , Receptores dos Hormônios Tireóideos/metabolismo , Elementos de Resposta , Receptores X de Retinoides/genética , Hormônios Tireóideos
8.
Cell Mol Life Sci ; 79(7): 353, 2022 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-35676368

RESUMO

The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.


Assuntos
Proteínas de Drosophila , Animais , Proteínas Argonauta/genética , Cromatina/metabolismo , DNA/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Drosophila/metabolismo , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Complexo Repressor Polycomb 1/genética , Complexo Repressor Polycomb 1/metabolismo , Proteínas do Grupo Polycomb/genética , Proteínas do Grupo Polycomb/metabolismo , Elementos de Resposta
9.
J Anim Sci ; 100(7)2022 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-35772747

RESUMO

Widespread regions of the southeast United States have soils, and hence forages, deficient in selenium (Se), necessitating Se supplementation to grazing cattle for optimal immune function, growth, and fertility. We have reported that supplementation with an isomolar 1:1 mix (MIX) of inorganic (ISe) and organic (OSe) forms of Se increases early luteal phase (LP) progesterone (P4) above that in cows on ISe alone. Increased early LP P4 advances embryonic development. Our objective was to determine the effect of form of Se on the transcriptome of the early LP corpus luteum (CL) with the goal of elucidating form of Se-regulated processes affecting luteal steroidogenesis and function. Non-lactating, 3-yr-old Angus-cross cows underwent 45-d Se-depletion, then repletion periods, and then at least 90 d of supplementation (TRT) with 35 ppm Se/d as either ISe (n = 5) or MIX (n = 5). CL were then recovered on day 7 of the estrous cycle, total RNA isolated, and the effect of TRT on the luteal transcriptome evaluated using bovine gene 1.0 ST arrays (Affymetrix, Inc., Santa Clara, CA). The abundance of transcripts in each CL was subjected to one-way ANOVA using Partek Genomic Suite software to determine TRT effects. Microarray analysis indicated a total of 887 transcripts that were differentially expressed and functionally annotated, with 423 and 464 up- and down-regulated (P < 0.05) in MIX vs. ISe CL, respectively. Bioinformatic analysis (Ingenuity Pathway Analysis) revealed the top TRT-affected canonical pathways to include seven specific to cholesterol biosynthesis and two to inflammatory responses. Results from the microarray analysis were corroborated by targeted real-time PCR. MIX CL had increased (P < 0.05) abundance of transcripts regulating cholesterol biosynthesis including DHCR7, DHCR24, and CYP51A1 (fold changes of 1.65, 1.48, and 1.40, respectively), suggesting MIX-induced increases in P4 to be due, in part, to increased availability of substrate to luteal cells. In addition, MIX CL had increased (P < 0.05) abundance of immune-response transcripts including C1QC, FAS, ILR8B, and IL1R1 (fold changes of 2.30, 1.74, 1.66, and 1.63, respectively). SREBF1 mRNA was also increased (1.32-fold, P < 0.05) in the MIX CL, which increases cholesterol synthesis and stimulates IL1B, linking effects of form of supplemental Se (TRT) on cholesterol biosynthesis and immune function in the CL.


In regions with soils deficient in selenium (Se), producers should supplement this trace mineral to the diet of forage-grazing cattle. We previously reported that circulating concentrations of progesterone (P4) are affected by the form of Se supplemented to cows. In this report, we aimed to determine how the form of Se affects the transcriptome of the bovine CL, with the goal of elucidating form of Se effects on luteal steroidogenesis. Cows were supplemented with the industry standard, an inorganic form of Se, or a 1:1 mix of organic and inorganic forms (MIX), with corpora lutea recovered on day 7 of the estrous cycle. The effect of TRT (form of Se) on the luteal transcriptome was then evaluated using bovine gene 1.0 ST arrays (Affymetrix, Inc., Santa Clara, CA), with the results of the microarray analysis corroborated by targeted qPCR. Treatment altered >800 transcripts in the CL, including those regulating cholesterol biosynthesis and immune function. The effect of form of Se on luteal steroidogenesis appears to be the result of changes in cholesterol biosynthesis and uptake by luteal cells, with cross talk between immune and cholesterol regulatory pathways also apparent.


Assuntos
Selênio , Ração Animal/análise , Animais , Bovinos , Colesterol , Corpo Lúteo , Feminino , Imunidade , Fase Luteal , Gravidez , Progesterona , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Elementos de Resposta , Selênio/farmacologia
10.
Proc Natl Acad Sci U S A ; 119(20): e2011665119, 2022 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-35549556

RESUMO

APOBEC3A (A3A) is a cytidine deaminase that inactivates a variety of viruses through introduction of lethal mutations to the viral genome. Additionally, A3A can suppress HIV-1 transcription in a deaminase-independent manner by binding to the long terminal repeat of proviral HIV-1. However, it is unknown whether A3A targets additional host genomic loci for repression. In this study, we found that A3A suppresses gene expression by binding TTTC doublets that are in close proximity to each other. However, one TTTC motif is sufficient for A3A binding. Because TTTC doublets are present in interferon (IFN)-stimulated response elements (ISRE), we hypothesized that A3A may impact IFN-stimulated gene (ISG) expression. After scanning the human genome for TTTC doublet occurrences, we discovered that these motifs are enriched in the proximal promoters of genes associated with antiviral responses and type I IFN (IFN-I) signaling. As a proof of principle, we examined whether A3A can impact ISG15 expression. We found that A3A binding to the ISRE inhibits phosphorylated STAT-1 binding and suppresses ISG15 induction in response to IFN-I treatment. Consistent with these data, our RNA-sequencing analyses indicate that A3A loss results in increased IFN-I­dependent induction of several ISGs. This study revealed that A3A plays an unexpected role in ISG regulation and suggests that A3A contributes to a negative feedback loop during IFN signaling.


Assuntos
Citidina Desaminase , Citocinas , Regulação da Expressão Gênica , Interferon-alfa , Ubiquitinas , Citidina Desaminase/genética , Citidina Desaminase/metabolismo , Citocinas/genética , Humanos , Interferon-alfa/metabolismo , Interferon-alfa/farmacologia , Elementos de Resposta , Ubiquitinas/genética
11.
J Biol Chem ; 298(7): 102059, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35605663

RESUMO

Retinoid orphan nuclear receptor alpha (RORα) is a member of the orphan nuclear factor family and regulates gene expression by binding to ROR response elements (ROREs). RORα has been identified as a potential tumor suppressor; however, how downregulation of RORα promotes cancer progression is not fully understood. Here, we showed that protein levels of RORα were downregulated during the Snail-, Twist-, or transforming growth factor-ß-induced epithelial-mesenchymal transition (EMT). We found that silencing of RORα induced expression of mesenchymal markers in MCF10A cells, accompanied by enhanced cell invasion, migration, and mammosphere formation. Furthermore, ectopic expression of RORα suppressed transforming growth factor-ß-induced EMT processes in MCF10A and HMLE cells. These results indicate that downregulation of RORα is crucial for the induction of EMT in mammary epithelial cells. By analyzing gene expression profiles in control and RORα-expressing cells, we also identified Snail, a key regulator of EMT, as a potential target of RORα. We show that RORα expression significantly inhibits Snail transcription in breast cancer cells. Chromatin immunoprecipitation analysis demonstrated that RORα bound to the ROREs in promoter region of SNAI1 gene, and using the luciferase reporter assay, we showed that binding to the ROREs was critical for RORα to repress Snail transcription. Finally, rescue experiments substantiated that Snail mediates RORα function in suppressing EMT and mammosphere formation. These results reveal a novel function of RORα in suppressing EMT and identify Snail as a direct target of RORα in mammary epithelial cells.


Assuntos
Transição Epitelial-Mesenquimal , Membro 1 do Grupo F da Subfamília 1 de Receptores Nucleares , Receptores Nucleares Órfãos , Fatores de Transcrição da Família Snail , Linhagem Celular Tumoral , Transição Epitelial-Mesenquimal/fisiologia , Humanos , Membro 1 do Grupo F da Subfamília 1 de Receptores Nucleares/genética , Membro 1 do Grupo F da Subfamília 1 de Receptores Nucleares/metabolismo , Elementos de Resposta , Receptor alfa de Ácido Retinoico/genética , Retinoides , Fatores de Transcrição da Família Snail/genética , Fator de Crescimento Transformador beta/genética
12.
Virulence ; 13(1): 714-726, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-35465839

RESUMO

Hypoxia frequently occurs in aquatic environments, especially in aquaculture areas. However, research on the relationship between hypoxic aquatic environments with viral diseases outbreak is limited, and its underlying mechanisms remain elusive. Herein, we demonstrated that hypoxia directly triggers the outbreak of infectious spleen and kidney necrosis virus (ISKNV) disease. Hypoxia or activated hypoxia-inducible factor (HIF) pathway could remarkably increase the levels of viral genomic DNA, titers, and gene expression, indicating that ISKNV can response to hypoxia and HIF pathway. To reveal the mechanism of ISKNV respond to HIF pathway, we identified the viral hypoxia response elements (HREs) in ISKNV genome. Fifteen viral HREs were identified, and four related viral genes responded to the HIF pathway, in which the hre-orf077r promoter remarkably responded to the HIF pathway. The level of orf077r mRNA dramatically increased after the infected cells were treated with dimethyloxalylglycine (DMOG) or the infected cells/fish subjected to hypoxic conditions, and overexpressed orf077r could remarkably increase the ISKNV replication. These finding shows that hypoxic aquatic environments induce the expression of viral genes through the viral HREs to promote ISKNV replication, indicating that viral HREs might be important biomarkers for the evaluation of the sensitivity of aquatic animal viral response to hypoxia stress. Furthermore, the frequencies of viral HREs in 43 species aquatic viral genomes from 16 families were predicted and the results indicate that some aquatic animal viruses, such as Picornavirdea, Dicistronviridae, and Herpesviridae, may have a high risk to outbreak when the aquatic environment encounters hypoxic stress.


Assuntos
Doenças dos Peixes , Iridoviridae , Animais , DNA Viral , Doenças dos Peixes/epidemiologia , Doenças dos Peixes/genética , Humanos , Hipóxia/genética , Iridoviridae/genética , Elementos de Resposta
13.
Endocr J ; 69(6): 605-612, 2022 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-35474028

RESUMO

Glucose is not only the energy fuel for most cells, but also the signaling molecule which affects gene expression via carbohydrate response element binding protein (ChREBP), a Mondo family transcription factor. In response to high glucose conditions, ChREBP regulates glycolytic and lipogenic genes by binding to carbohydrate response elements (ChoRE) in the regulatory region of its target genes, thus elucidating the role of ChREBP for converting excessively ingested carbohydrates to fatty acids as an energy storage in lipogenic tissues such as the liver and adipose tissue. While the pathophysiological roles of ChREBP for fatty liver and obesity in these tissues are well known, much of the physiological and pathophysiological roles of ChREBP in other tissues such as the kidney remains unclear despite its high levels of expression in them. This review will thus highlight the roles of ChREBP in the kidney and briefly introduce the latest research results that have been reported so far.


Assuntos
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos , Fatores de Transcrição , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Glucose/metabolismo , Rim/metabolismo , Fígado/metabolismo , Elementos de Resposta , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
14.
Mar Drugs ; 20(4)2022 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-35447906

RESUMO

Brevetoxins are a suite of marine neurotoxins that activate voltage-gated sodium channels (VGSCs) in cell membranes, with toxicity occurring from persistent activation of the channel at high doses. Lower doses, in contrast, have been shown to elicit neuroregeneration. Brevetoxins have thus been proposed as a novel treatment for patients after stroke, when neuron regrowth and repair is critical to recovery. However, findings from environmental exposures indicate that brevetoxins may cause inflammation, thus, there is concern for brevetoxins as a stroke therapy given the potential for neuroinflammation. In this study, we examined the inflammatory properties of several brevetoxin analogs, including those that do and do not bind strongly to VGSCs, as binding has classically indicated toxicity. We found that several analogs are toxic to monocytes, while others are not, and the degree of toxicity is not directly related to VGSC binding. Rather, results indicate that brevetoxins containing aldehyde groups were more likely to cause immunotoxicity, regardless of binding affinity to the VGSC. Our results demonstrate that different brevetoxin family members can elicit a spectrum of apoptosis and necrosis by multiple possible mechanisms of action in monocytes. As such, care should be taken in treating "brevetoxins" as a uniform group, particularly in stroke therapy research.


Assuntos
Oxocinas , Acidente Vascular Cerebral , Canais de Sódio Disparados por Voltagem , Apoptose , Humanos , Toxinas Marinhas , Monócitos , Oxocinas/toxicidade , Elementos de Resposta
15.
Evolution ; 76(6): 1331-1346, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35420699

RESUMO

In the males of many vertebrate species, sexual selection has led to the evolution of sexually dimorphic traits, which often are developmentally controlled by androgen signaling involving androgen response elements (AREs). Evolutionary changes in the number and genomic locations of AREs can modify patterns of receptor regulation and potentially alter gene expression. Here, we use recently sequenced primate genomes to evaluate the hypothesis that the strength of sexual selection is related to the genome-wide number of AREs in a diversifying lineage. In humans, we find a higher incidence of AREs near male-biased genes and androgen-responsive genes when compared to randomly selected genes from the genome. In a set of primates, we find that gains or losses of AREs proximal to genes are correlated with changes in male expression levels and the degree of sex-biased expression of those genes. In a larger set of primates, we find that increases in indicators of sexual selection are correlated with genome-wide ARE counts. Our results suggest that the responsiveness of the genome to androgens in humans and their close relatives has been shaped by sexual selection that arises from competition among males for mating access to females.


Assuntos
Androgênios , Caracteres Sexuais , Androgênios/metabolismo , Animais , Proliferação de Células , Feminino , Masculino , Primatas/genética , Elementos de Resposta
16.
Mol Metab ; 61: 101501, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35452876

RESUMO

OBJECTIVE: Tamoxifen is widely used for inducible Cre-LoxP systems but has several undesirable side effects for researchers investigating metabolism or energy balance, including weight loss, lipoatrophy, and drug incorporation into lipid stores. For this reason, we sought to determine whether a doxycycline-inducible system would be more advantageous for adipocyte-specific Cre mouse models, but serendipitously discovered widespread ectopic tetracycline response element Cre (TRE-Cre) recombinase activity. METHODS: Adipocyte-specific tamoxifen- and doxycycline-inducible Cre mice were crossed to fluorescent Cre reporter mice and visualized by confocal microscopy to assess efficiency and background activity. TRE-Cre mice were crossed to stop-floxed diphtheria toxin mice to selectively ablate cells with background Cre activity. RESULTS: Tamoxifen- and doxycycline-inducible systems performed similarly in adipose tissues, but ectopic Cre recombination was evident in numerous other cell types of the latter, most notably neurons. The source of ectopic Cre activity was isolated to the TRE-Cre transgene, driven by the pTet (tetO7) tetracycline-inducible promoter. Ablation of cells with ectopic recombination in mice led to stunted growth, diminished survival, and reduced brain mass. CONCLUSIONS: These results indicate that tamoxifen- and doxycycline-inducible adipocyte-specific Cre mouse models are similarly efficient, but the TRE-Cre component of the latter is inherently leaky. TRE-Cre background activity is especially pronounced in the brain and peripheral nerve fibers, and selective ablation of these cells impairs mouse development and survival. Caution should be taken when pairing TRE-Cre with floxed alleles that have defined roles in neural function, and additional controls should be included when using this model system.


Assuntos
Doxiciclina , Transativadores , Animais , Antibacterianos , Doxiciclina/farmacologia , Integrases/genética , Integrases/metabolismo , Camundongos , Camundongos Transgênicos , Recombinação Genética , Elementos de Resposta , Tamoxifeno/farmacologia , Transativadores/metabolismo
17.
Mol Plant Microbe Interact ; 35(8): 650-658, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35343248

RESUMO

The establishment of the legume-rhizobia symbiosis, termed the root-nodule symbiosis (RNS), requires elaborate interactions at the molecular level. The host plant-derived transcription factor NODULE INCEPTION (NIN) is known to be crucial for RNS, regulating associated processes such as alteration of root hair morphology, infection thread formation, and cell division during nodulation. This emphasizes the importance of the precise spatiotemporal regulation of NIN expression for the establishment of RNS; however, the detailed role of NIN promoter sequences in this process remains unclear. The daphne mutant, a nin mutant allele containing a chromosomal translocation approximately 7 kb upstream of the start codon, does not form nodules but does form infection threads, indicating that the region within 7 kb of the NIN start codon contributes to NIN expression during infection thread formation. CYCLOPS binds to a CYCLOPS response element (CYC-RE) in the NIN promoter, and cyclops mutants are defective in infection thread formation. Here, we performed complementation analysis in nin mutants, using various truncated forms of the NIN promoter, and found that the CYC-RE is important for infection thread formation. Additionally, the CYC-RE deletion mutant, generated through CRISPR/Cas9 technology, displayed a significant reduction in infection thread formation, indicating that the CYC-RE is important for the fine-tuning of NIN expression during this process. However, the fact that infection thread formation is not completely abolished in the CYC-RE deletion mutant suggests that cis and trans factors other than CYCLOPS and the CYC-RE may cooperatively regulate NIN expression for the induction of infection thread formation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.


Assuntos
Lotus , Rhizobium , Códon de Iniciação/metabolismo , Regulação da Expressão Gênica de Plantas , Lotus/fisiologia , Minociclina/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Elementos de Resposta , Rhizobium/fisiologia , Nódulos Radiculares de Plantas/metabolismo , Simbiose/genética
18.
STAR Protoc ; 3(1): 101205, 2022 03 18.
Artigo em Inglês | MEDLINE | ID: mdl-35243382

RESUMO

Characterizing the noise modulation pattern of microRNA is valuable for both microRNA function analysis and synthetic biology applications. Here we propose a coarse-grained model to simulate how the properties of microRNAs, competing RNAs, and microRNA response elements affect gene expression noise. We also detail an experimental protocol based on synthetic gene circuits and flow cytometry to quantify the noise. This framework is easy-to-use for the study and application of both microRNA and gene expression noise. For complete details on the use and execution of this protocol, please refer to Wei et al. (2021).


Assuntos
MicroRNAs , Expressão Gênica , Redes Reguladoras de Genes , MicroRNAs/genética , Elementos de Resposta , Biologia Sintética/métodos
19.
New Phytol ; 235(3): 1196-1211, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35318667

RESUMO

Early gene expression in arbuscular mycorrhiza (AM) and the nitrogen-fixing root nodule symbiosis (RNS) is governed by a shared regulatory complex. Yet many symbiosis-induced genes are specifically activated in only one of the two symbioses. The Lotus japonicus T-DNA insertion line T90, carrying a promoterless uidA (GUS) gene in the promoter of Calcium Binding Protein 1 (CBP1) is exceptional as it exhibits GUS activity in both root endosymbioses. To identify the responsible cis- and trans-acting factors, we subjected deletion/modification series of CBP1 promoter : reporter fusions to transactivation and spatio-temporal expression analysis and screened ethyl methanesulphonate (EMS)-mutagenized T90 populations for aberrant GUS expression. We identified one cis-regulatory element required for GUS expression in the epidermis and a second element, necessary and sufficient for transactivation by the calcium and calmodulin-dependent protein kinase (CCaMK) in combination with the transcription factor Cyclops and conferring gene expression during both AM and RNS. Lack of GUS expression in T90 white mutants could be traced to DNA hypermethylation detected in and around this element. We concluded that the CCaMK/Cyclops complex can contribute to at least three distinct gene expression patterns on its direct target promoters NIN (RNS), RAM1 (AM), and CBP1 (AM and RNS), calling for yet-to-be identified specificity-conferring factors.


Assuntos
Lotus , Micorrizas , Proteínas de Ligação ao Cálcio/metabolismo , Regulação da Expressão Gênica de Plantas , Lotus/metabolismo , Minociclina/metabolismo , Micorrizas/fisiologia , Proteínas de Plantas/metabolismo , Elementos de Resposta , Simbiose/genética , Ativação Transcricional/genética
20.
Mol Carcinog ; 61(5): 494-507, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35107180

RESUMO

Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers. Dysregulation of S100A2 has recently been found in many cancers including HCC. However, its regulatory mechanism in HCC remains poorly understood, especially in hypoxia. In this study, we found that S100A2 is upregulated and correlated with the clinicopathological features of HCC patients. Moreover, the elevated S100A2 showed worse overall survival. Functionally, S100A2 inhibition decreased the proliferation and migration of HepG2 cells. Interestingly, we found that HIF-1α directly binds to hypoxia response elements (HREs) of the S100A2 promoter region. S100A2 expression could be induced in an HIF-1α-dependent manner under hypoxia. Furthermore, S100A2 silencing significantly suppressed HCC cell proliferation and invasion under hypoxia. Mechanistically, pyrosequencing results showed that the hypomethylation status of CpG located in the HRE at the S100A2 promoter was correlated with S100A2 induction. Additionally, HIF-1α- mediated S100A2 activation was associated with TET2-related epigenetic inactivation. TET2 was enriched in the HRE of the S100A2 promoter in HepG2 cells. Finally, S100A2 methylation-related genes and pathways were analyzed. We found that the methylation of S100A2 is correlated with ANXA2, PPP1R15A, and FOS, which include in a hypoxia-related gene set from the GSEA database. Moreover, some EMT-related genes are associated with the methylation of S100A2 in HCC. Conclusively, our study thus uncovered a novel mechanism showing that hypoxia/HIF-1α signaling associated with DNA methylation enhances S100A2 expression in HCC. S100A2 may be useful as a target for facilitating novel diagnostic and therapeutic strategies in liver cancer.


Assuntos
Carcinoma Hepatocelular , Subunidade alfa do Fator 1 Induzível por Hipóxia , Neoplasias Hepáticas , Proteínas S100 , Carcinoma Hepatocelular/patologia , Hipóxia Celular/genética , Linhagem Celular Tumoral , Fatores Quimiotáticos/metabolismo , Regulação Neoplásica da Expressão Gênica , Células Hep G2 , Humanos , Hipóxia/genética , Hipóxia/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Neoplasias Hepáticas/patologia , Elementos de Resposta , Proteínas S100/genética , Proteínas S100/metabolismo , Ativação Transcricional
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