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1.
Arch Virol ; 166(3): 755-766, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33420627

RESUMEN

MicroRNAs (miRNAs) are important host molecules involved in human immunodeficiency virus type 1 (HIV-1) infection. Antiretroviral therapy (ART) can affect the miRNA expression profile, but differentially expressed miRNAs still remain to be identified. In this study, we used gene chips to analyze miRNA expression profiles in peripheral blood mononuclear cells from ART-naive HIV-1 patients and those receiving ART, as well as from uninfected individuals. We measured differences in miRNA expression by quantitative polymerase chain reaction (qPCR) in an expanded sample. We found significant differences in the expression of has-miR-191-5p among the three groups (P < 0.05). Furthermore, we showed that hsa-miR-191-5p has an inhibitory effect on HIV-1 replication in cell models in vitro. We identified CCR1 and NUP50 as target molecules of hsa-miR-191-5p and found that hsa-miR-191-5p inhibits the expression of CCR1 and NUP50. Knockdown of NUP50 resulted in significant inhibition of HIV-1 replication. In summary, our research shows that hsa-miR-191-5p expression is reduced in HIV-1-infected patients and acts an inhibitor of HIV-1 infection via a mechanism that may involve targeted repression of NUP50 expression.


Asunto(s)
Regulación de la Expresión Génica/genética , VIH-1/metabolismo , MicroARNs/genética , Proteínas de Complejo Poro Nuclear/biosíntesis , Proteínas Nucleares/biosíntesis , Receptores CCR1/biosíntesis , Adulto , Línea Celular , Regulación hacia Abajo , Femenino , Perfilación de la Expresión Génica , Células HEK293 , Humanos , Células Jurkat , Masculino , Persona de Mediana Edad , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Reacción en Cadena en Tiempo Real de la Polimerasa , Replicación Viral/genética , Adulto Joven
2.
Nucleic Acids Res ; 49(2): 818-831, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33410890

RESUMEN

Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the significance of codon usage effect on gene expression. Here we show that gene-specific regulation reduces the genome-wide codon usage and mRNA correlations: Constitutively expressed genes exhibit much higher genome-wide correlations than differentially expressed genes from fungi to human cells. Using Drosophila S2 cells as a model system, we showed that the effect of codon usage on mRNA expression level is promoter-dependent. Regions downstream of the core promoters of differentially expressed genes can repress the codon usage effects on mRNA expression. An element in the Hsp70 promoter was identified to be necessary and sufficient for this inhibitory effect. The promoter-dependent codon usage effects on mRNA levels are regulated at the transcriptional level through modulation of histone modifications, nucleosome densities and premature termination. Together, our results demonstrate that promoters play a major role in determining whether codon usage influences gene expression and further establish the transcription-dependent codon usage effects on gene expression.


Asunto(s)
Uso de Codones , Drosophila melanogaster/genética , Regulación de la Expresión Génica/genética , Regiones Promotoras Genéticas/genética , Acetilación , Animales , Composición de Base , Línea Celular , Cromatina/genética , Cromatina/ultraestructura , Codón sin Sentido , Proteínas de Drosophila/fisiología , Drosophila melanogaster/citología , Genes Reporteros , Código de Histonas , Humanos , Luciferasas de Renilla/biosíntesis , Luciferasas de Renilla/genética , Ratones , Neurospora crassa/genética , Nucleosomas/metabolismo , Procesamiento Proteico-Postraduccional , Estabilidad del ARN , ARN Mensajero/biosíntesis , ARN Mensajero/genética , Saccharomyces cerevisiae/genética , Especificidad de la Especie
3.
Nat Commun ; 12(1): 567, 2021 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-33495464

RESUMEN

The regulatory elements controlling gene expression during acute inflammation are not fully elucidated. Here we report the identification of a set of NF-κB-bound elements and common chromatin landscapes underlying the acute inflammatory response across cell-types and mammalian species. Using primary vascular endothelial cells (human/mouse/bovine) treated with the pro-inflammatory cytokine, Tumor Necrosis Factor-α, we identify extensive (~30%) conserved orthologous binding of NF-κB to accessible, as well as nucleosome-occluded chromatin. Regions with the highest NF-κB occupancy pre-stimulation show dramatic increases in NF-κB binding and chromatin accessibility post-stimulation. These 'pre-bound' regions are typically conserved (~56%), contain multiple NF-κB motifs, are utilized by diverse cell types, and overlap rare non-coding mutations and common genetic variation associated with both inflammatory and cardiovascular phenotypes. Genetic ablation of conserved, 'pre-bound' NF-κB regions within the super-enhancer associated with the chemokine-encoding CCL2 gene and elsewhere supports the functional relevance of these elements.


Asunto(s)
Cromatina/genética , Células Endoteliales/metabolismo , Regulación de la Expresión Génica/genética , Inflamación/genética , FN-kappa B/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos/genética , Enfermedad Aguda , Animales , Sitios de Unión/genética , Bovinos , Células Cultivadas , Quimiocina CCL2/genética , Quimiocina CCL2/metabolismo , Cromatina/metabolismo , Secuencia Conservada/genética , Células Endoteliales/citología , Células Endoteliales/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Inflamación/metabolismo , Inflamación/patología , Lógica , Ratones , Modelos Genéticos , Unión Proteica , Factor de Necrosis Tumoral alfa/genética , Factor de Necrosis Tumoral alfa/farmacología
4.
BMC Bioinformatics ; 22(1): 5, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407064

RESUMEN

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) enables the possibility of many in-depth transcriptomic analyses at a single-cell resolution. It's already widely used for exploring the dynamic development process of life, studying the gene regulation mechanism, and discovering new cell types. However, the low RNA capture rate, which cause highly sparse expression with dropout, makes it difficult to do downstream analyses. RESULTS: We propose a new method SCC to impute the dropouts of scRNA-seq data. Experiment results show that SCC gives competitive results compared to two existing methods while showing superiority in reducing the intra-class distance of cells and improving the clustering accuracy in both simulation and real data. CONCLUSIONS: SCC is an effective tool to resolve the dropout noise in scRNA-seq data. The code is freely accessible at https://github.com/nwpuzhengyan/SCC .


Asunto(s)
Perfilación de la Expresión Génica/métodos , ARN Citoplasmático Pequeño/genética , Análisis de la Célula Individual/métodos , Regulación de la Expresión Génica/genética , Genómica/métodos , Modelos Genéticos
5.
Gene ; 773: 145415, 2021 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-33444678

RESUMEN

Heat shock protein 27 (HSP27) plays an important role in protecting cells from various stress factors. This study aimed to investigate the function of HSP27 gene and its regulatory mechanism as infected by Escherichia coli (E. coli) at the tissue and cellular levels. Real-time PCR was used to detect the differential expression of HSP27 gene in F18 resistant and sensitive Sutai pigs and the differential expression upon E. coli F18ab, F18ac, K88ac bacterial supernatant, thallus infection and LPS induction in IPEC-J2. In addition, the HSP27 gene overexpression vector was constructed to detect the effect of the HSP27 gene overexpression on the adhesion of E. coli F18 to IPEC-J2, secretion of pro-inflammatory factors, and the expression of the upstream key genes in Mitogen-activated protein kinase (MAPK) pathway. Ribosomal S6 kinase (RSK2) is an important protein in the MAPK pathway. Therefore, the RSK2 gene overexpression vector was constructed and the number of colonies was counted after co-transfection of HSP27 and RSK2 gene. Results revealed that the expression level of HSP27 gene in resistant individuals in 11 tissues was higher than sensitive type. At the cellular level, the relative expression levels of HSP27 gene were increased after F18ab, F18ac bacterial supernatant, F18ab thallus infection, and LPS induction for 4 h (P < 0.01). The adhesion ability of E. coli F18ab to IPEC-J2 was significantly reduced after HSP27 gene overexpression (P < 0.01), and the concentration of pro-inflammatory factors in the HSP27 gene overexpression group was significantly reduced compared with the control group after F18ab infection (P < 0.05). Furthermore, the expression of RSK2 was significantly increased in HSP27 overexpression group upon F18ab infection (P < 0.01). The colonies quantitative results also showed that the number of colonies was significantly reduced after co-transfection of HSP27 and RSK2 gene. We indicated that the high expression of HSP27 gene may resist the inflammatory response caused by exogenous stress and enhance the ability of IPEC-J2 to resist E. coli F18 infection. RSK2 gene in the MAPK pathway may cooperate with HSP27 gene to participate in the immune response of the organism, which provides a theoretical basis for the study of the mechanism of anti-E. coli infection in piglets.


Asunto(s)
Resistencia a la Enfermedad/genética , Infecciones por Escherichia coli/genética , Escherichia coli/genética , Proteínas de Choque Térmico HSP27/genética , Animales , Adhesión Bacteriana/genética , Diarrea/genética , Diarrea/microbiología , Diarrea/veterinaria , Escherichia coli/patogenicidad , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/patología , Proteínas de Escherichia coli/genética , Regulación de la Expresión Génica/genética , Porcinos/genética , Porcinos/microbiología , Enfermedades de los Porcinos/genética , Enfermedades de los Porcinos/microbiología
6.
Gene ; 767: 145075, 2021 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-32858179

RESUMEN

Salidroside (Sal), a natural extract of Rhodiola rosea, shows a latent effect on protecting cardiovascular system. Our study explored the effect of salidroside on ischemia-reperfusion (I/R) injury in rat heart. I/R was performed on Wistar rat hearts, and Sal pretreatment was performed in I/R rats. Cardiac marker enzyme, myocardial infarct size, malondialdehyde (MDA) and superoxide dismutase (SOD) content were then measured. Compared with the untreated group, Sal pretreatment observably ameliorated the cardiac function, decreased the myocardial infarct size, reduced the levels of cardiac lactate creatine kinase-MB (CK-MB) and dehydrogenase (LDH), and inhibited the anti-oxidative stress. In addition, Sal treatment also significantly inhibited autophagy and apoptosis, which could be partially reversed by Rapamycin (RAPA), an autophagic agonist. Furthermore, Sal treatment attenuated autophagy by up-regulating the expression of hsa_circ_0000064 (circ-0000064) and Rapamycin (RAPA) treatment abolished it. Our study showed that Sal protected the heart from I/R injury, which might berelated to the upregulation of circ-0000064 and the inhibition of autophagy.


Asunto(s)
Glucósidos/metabolismo , Miocitos Cardíacos/metabolismo , Fenoles/metabolismo , ARN Circular/genética , Animales , Apoptosis/efectos de los fármacos , Autofagia/efectos de los fármacos , Regulación de la Expresión Génica/genética , Glucósidos/farmacología , Masculino , Malondialdehído/metabolismo , Infarto del Miocardio/metabolismo , Daño por Reperfusión Miocárdica/metabolismo , Estrés Oxidativo/efectos de los fármacos , Fenoles/farmacología , Extractos Vegetales , ARN Circular/metabolismo , Ratas , Ratas Wistar , Daño por Reperfusión/tratamiento farmacológico , Rhodiola , Superóxido Dismutasa/metabolismo
7.
Gene ; 767: 145148, 2021 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-32949698

RESUMEN

Ischemic stroke is a common clinical cardiovascular disease and often accompanied by central nervous system injury. It often causes paralysis or loss of motor function after central nervous system injury and significantly reduces the patient's quality of life. At present, there is no effective treatment strategy for nerve damage caused by ischemic stroke. Therefore, it is urgently need to explore effective treatment targets. The protein expression of SOX5, VEGF and apoptosis related proteins were measured by western blot. The mRNA expression of SOX5 and VEGF were detected by RT-qPCR. The concentration of S100B and GFAP which are related to nerve damage were detected using ELISA assay. The transcriptional regulation of SOX5 on VEGF was detected using ChIP-PCR and dual luciferase reporter gene assays. The cell apoptosis was measured by TUNEL assay and cell viability was detected by CCK-8 assay. In our study, we found that the expression of SOX5 was significantly reduced when LPS induced apoptosis in PC-12 cells. Overexpression of SOX5 repaired LPS-induced apoptosis. SOX5 promotes VEGF expression as a transcription factor to activate the PI3K/AKT pathway. VEGF also repairs nerve injury and brain tissue injury caused by ischemic stroke. In conclusion, SOX5 transcription regulates the expression of VEGF to activate the PI3K/AKT pathway, which repaired nerve damage caused by ischemic stroke. Therefore, SOX5 could be a new targetto regulate VEGF which can repair nerve injury induced by ischemic stroke.


Asunto(s)
/tratamiento farmacológico , Factores de Transcripción SOXD/metabolismo , Animales , Apoptosis/fisiología , Isquemia Encefálica/genética , Isquemia Encefálica/metabolismo , Muerte Celular , Proliferación Celular , Regulación de la Expresión Génica/genética , Fármacos Neuroprotectores/metabolismo , Fármacos Neuroprotectores/uso terapéutico , Células PC12 , Fosfatidilinositol 3-Quinasas/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Ratas , Factores de Transcripción SOXD/genética , Factores de Transcripción SOXD/fisiología , Transducción de Señal/genética , Accidente Cerebrovascular/genética , Factor A de Crecimiento Endotelial Vascular/metabolismo , Factores de Crecimiento Endotelial Vascular/metabolismo
8.
Gene ; 767: 145162, 2021 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-32987105

RESUMEN

The mammalian Cytochrome P450 (Cyp) gene superfamily encodes enzymes involved in numerous metabolic pathways and are frequently expressed in the liver. Despite the remarkably high sequence similarity of Cyp2a4 and Cyp2a5 genes and their surrounding genomic regions, they exhibit differences in expression in the adult mouse liver. For example, Cyp2a4 is highly female-biased whereas Cyp2a5 is only moderately female-biased and Cyp2a4, but not Cyp2a5, is activated in liver cancer. We hypothesized that the limited sequence differences may help us identify the basis for this differential expression. An antisense expressed sequence tag had been uniquely annotated to the Cyp2a4 gene which led us to investigate this transcript as a possible regulator of this gene. We characterized the full-length antisense transcript and also discovered a similar transcript in the Cyp2a5 gene. These transcripts are nuclear long noncoding RNAs that are expressed similarly to their sense mRNA counterparts. This includes the sex-biased and liver tumor differences seen between the Cyp2a4 and Cyp2a5 genes, but we also find that these two genes and their antisense transcripts are expressed within different zones of the liver structure. Interestingly, while the differences in sex-biased expression of the mRNAs are established 1-2 months after birth, the antisense transcripts exhibit these expression differences earlier, at 3-4 weeks after birth. By analyzing published genomic data, we have identified candidate transcription factor binding sites that could account for differences in Cyp2a4/Cyp2a5 expression. Taken together, these studies characterize the first antisense RNAs within the Cyp supergene family and identify potential transcriptional and post-transcriptional mechanisms governing different Cyp2a4 and Cyp2a5 expression patterns in mouse liver.


Asunto(s)
Hidrocarburo de Aril Hidroxilasas/genética , Familia 2 del Citocromo P450/genética , Hígado/metabolismo , Esteroide Hidroxilasas/genética , Animales , Hidrocarburo de Aril Hidroxilasas/metabolismo , Sistema Enzimático del Citocromo P-450/genética , Familia 2 del Citocromo P450/metabolismo , Femenino , Regulación de la Expresión Génica/genética , Masculino , Ratones , Ratones Endogámicos C57BL , Unión Proteica , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , ARN Mensajero/genética , Esteroide Hidroxilasas/metabolismo
9.
Gene ; 767: 145285, 2021 Jan 30.
Artículo en Inglés | MEDLINE | ID: mdl-33144271

RESUMEN

The genus Takifugu is a group of approximately 20 species of puffer fishes living in a wide range of salinity environments around East Asian countries. This group presents a broad spectrum of evolutionary stages adapted to anadromy as a result of speciation that occurred a short time (2-5 million years) ago on an evolutionary timescale. This group thus can be considered as a model for studying the evolutionary mechanisms of anadromy. We firstly conducted a transfer experiment from seawater to low-salinity waters on five Takifugu species: two anadromous species T. obscurus and T. ocellatus, two euryhaline wanderer marine species T. rubripes and T. niphobles, and a strictly marine species T. snyderi, and confirmed that the capacity for acclimation to hypotonic environments was associated with their life history strategies. Next, transcriptomes of the gill and intestine of these species in hypotonic condition were compared to those under hypertonic condition for each species using RNA-Sequencing so as to determine possible candidate transporters playing an important role on freshwater adaptation. As this analysis suggested that cftr, encoding an important ion transporter for seawater acclimation in the gill, and ncc, encoding a transporter that is suggested to play important osmoregulatory roles in the intestine, are important candidates, their expression was validated by quantitative real-time PCR analysis. Expression of cftr was downregulated in the gills of the four euryhaline species under the hypotonic condition, but no change was detected in the gill of stenohaline T. snyderi, which may be one reason for the poor hypotonic acclimation capacity of T. snyderi. Expression of ncc was clearly upregulated in the intestines of the two anadromous species under the hypotonic condition, but not in other three species. Different ion transporter expression patterns between the five species indicate that the transcriptional regulation of cftr in the gill and ncc in the intestine may be important for the improvement of hypotonic acclimation capacity and evolution of anadromy in the Takifugu species.


Asunto(s)
Transporte Iónico/genética , Takifugu/genética , Takifugu/metabolismo , Aclimatación/genética , Adaptación Fisiológica/genética , Animales , Agua Dulce , Regulación de la Expresión Génica/genética , Branquias/metabolismo , Transporte Iónico/fisiología , Concentración Osmolar , Salinidad , Agua de Mar , ATPasa Intercambiadora de Sodio-Potasio/metabolismo , Transcriptoma/genética , Equilibrio Hidroelectrolítico/genética
10.
Gene ; 765: 145065, 2021 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-32889056

RESUMEN

PURPOSE: The aim of the present study was to investigate expression levels of circular RNA HIPK3 (circHIPK3) in mice with diabetic nephropathy (DN) and the role of circHIPK3 in rat mesangial cells (MCs). METHODS: Quantitative real-time polymerase chain reaction was performed to detect expression levels of circHIPK3, miR-185, cyclin D1, proliferating cell nuclear antigen (PCNA), transforming growth factor-ß1 (TGF-ß1), collagen Ⅰ (Col. Ⅰ), and fibronectin (FN) in mice with DN and rat mesangial cells. Luciferase assay was performed to investigate the binding sites of circHIPK3 and miR-185. Silencing cells of circHIPK3 and miR-185 were constructed using cell transfection assay. RESULTS: Our results revealed that the levels of 24-hour urinary albumin and urinary 8-hydroxy-2'-deoxyguanosine (8-OH-dG) from diabetic mice increased considerably. Up-regulation of circHIPK3 was observed in the renal tissues of mice with DN. Similarly, circHIPK3 expression in rat mesangial cells increased significantly in a microenvironment of high glucose. A loss-of-function experiment indicated that down-regulation of circHIPK3 inhibited cell proliferation and significantly decreased mRNA abundance of cyclin D1, PCNA, TGF-ß1, Col. I, and FN in MCs. Luciferase assay demonstrated that circHIPK3 can specifically sponge miR-185, and silencing of miR-185 can reverse the effects of knocking down circHIPK3 on cell proliferation and mRNA abundance of cyclin D1, PCNA, TGF-ß1, Col. I, and FN in MCs. CONCLUSION: Overall, circHIPK3 exhibits a promotive function in DN by sponging miR-185 and this evidence suggests that circHIPK3 might be a biomarker or therapeutic target for DN.


Asunto(s)
Nefropatías Diabéticas/genética , MicroARNs/genética , Proteínas Serina-Treonina Quinasas/genética , Animales , Línea Celular Tumoral , Proliferación Celular/genética , Diabetes Mellitus Experimental/genética , Nefropatías Diabéticas/fisiopatología , Regulación de la Expresión Génica/genética , Regulación Neoplásica de la Expresión Génica , Flujo Génico/genética , Masculino , Ratones , Ratones Endogámicos C57BL , MicroARNs/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , ARN Circular/genética , Ratas , Factor de Crecimiento Transformador beta1/metabolismo
11.
Gene ; 765: 145131, 2021 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-32898608

RESUMEN

The inflammatory events related to prostaglandins may play an important role in the progression of vessel stenosis. The aim of this study was to investigate the monocyte PTGES and 15-PGDH gene expression levels and the serum 13,14-dihyro-15-keto-PGF2α value involved in PGE2 metabolism in patients with coronary artery stenosis and restenosis. Moreover, the effects of miR-520, miR-1297 and miR-34 were studied on the gene expression levels. A total of sixty subjects referred for coronary angiography including healthy controls (stenosis <5%), subjects with stent no restenosis) SNR, stenosis <5%) and subjects in stent restenosis (ISR, restenosis >70%) were participated in the study. The gene expression levels and the serum 13,14-dihyro-15-keto- PGF2α value were measured by RT-qPCR and ELISA techniques, respectively. Moreover, the effects of miRNAs on the gene expression levels were investigated by the monocyte transfection of miR/PEI complexes. The PTGES and 15-PGDH gene expression levels and serum 13,14-dihyro-15-keto- PGF2α value increased significantly (P <0.05). Based on the miR-520 and miR-34 expression levels, the miR/PEI transfection studies were confirmed significantly the gene expression changes. The monocyte PGE2 synthesis pathway is actively considered in the SNR and ISR patients and might be related to miR-34 and miR-520 functions.


Asunto(s)
Reestenosis Coronaria/metabolismo , Estenosis Coronaria/metabolismo , Dinoprostona/metabolismo , Adulto , Anciano , Angiografía Coronaria , Enfermedad de la Arteria Coronaria/sangre , Reestenosis Coronaria/fisiopatología , Estenosis Coronaria/fisiopatología , Dinoprost/análogos & derivados , Dinoprost/análisis , Dinoprost/sangre , Dinoprostona/genética , Femenino , Expresión Génica/genética , Regulación de la Expresión Génica/genética , Humanos , Hidroxiprostaglandina Deshidrogenasas/análisis , Masculino , MicroARNs/genética , Persona de Mediana Edad , Stents
12.
Gene ; 766: 145159, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-32971186

RESUMEN

Considering the relevance of insect α-amylases and natural α-amylase inhibitors present in plants to protect against insect damage, we investigated the effect of white bean and rapeseed protein extracts on digestive α-amylase gene expression of the Colorado potato beetle, Leptinotarsa decemlineata (Say). For this purpose, in vitro and in vivo trials were performed to determine the inhibitory activity of seed proteins on the third and fourth instar larvae. In both trials, the significant inhibitory effect of each extracts on the third and fourth instar larval α-amylase activity and considerable mortality in treatments were observed compared to control trials. In the RT-qPCR, expression ratio demonstrated that the α-amylase gene of two different larval stages grown on both proteins treated leaves had significantly differentiated expression and was up-regulated in third instar larvae and down-regulated in fourth instar larvae compared to control. Results suggest that the hyper-production of α-amylase in third instar larvae is elicited to compensate for the enzyme activity inhibition at an earlier stage and also down-regulation suggests the existence of a negative feedback of plant proteins on the last instar larvae via impaired food intake and digestive α-amylase activity in Colorado potato beetle. Therefore, disruption of the insect's digestive physiology by plant defensive proteins can be considered in the development of innovative controlling methods of this crucial potato pest.


Asunto(s)
Escarabajos/efectos de los fármacos , Escarabajos/genética , Regulación de la Expresión Génica/efectos de los fármacos , Larva/efectos de los fármacos , Extractos Vegetales/farmacología , Proteínas de Plantas/farmacología , alfa-Amilasas/genética , Animales , Digestión/efectos de los fármacos , Digestión/genética , Regulación de la Expresión Génica/genética , Larva/genética , Hojas de la Planta/química , Solanum tuberosum/parasitología
13.
Gene ; 773: 145381, 2021 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-33383116

RESUMEN

We have previously found and characterized two pairs of enhancer elements, E1 and E2, in the type II collagen alpha 1 chain (COL2A1) gene. Subsequent studies have suggested that these enhancers function differently in the regulation of gene expression. For example, histone deacetylase 10 modifies only the E2 enhancer region to affect gene expression. Therefore, in this study, we aimed to clarify the transcriptional complex formed at each enhancer region by identifying transcription factors that specifically bind to each enhancer element. To this end, we used chondrocytic cell lines established using our unique silent reporter system and overexpressed candidate transcription factors in these cells. We found two transcription factors, other than the SOX trio, that directly bound to COL2A1 and regulated its expression. The first was Kruppel-like factor-4 (KLF4), which bound to the promoter proximal region, and the second was AT-rich interactive domain 5B (ARID5B) which bound to the E1 enhancer element. Further studies are needed to identify factors that specifically bind to the E2 enhancer element. In any case, our findings provide an important insight into the molecular mechanisms underlying the regulation of COL2A1. In this paper, we reevaluated the previous analysis of transcription factors involved in the regulation of COL2A1 expression.


Asunto(s)
Colágeno Tipo II/genética , Proteínas de Unión al ADN/genética , Factores de Transcripción de Tipo Kruppel/genética , Factores de Transcripción/genética , Animales , Diferenciación Celular/genética , Condrocitos/metabolismo , Elementos de Facilitación Genéticos/genética , Regulación de la Expresión Génica/genética , Humanos , Ratones , Regiones Promotoras Genéticas/genética , Unión Proteica/genética , Ratas , Factor de Transcripción SOX9
14.
Gene ; 773: 145383, 2021 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-33383118

RESUMEN

Alternative splicing (AS) is a key process to expand the diversity of mRNA and protein from the genome and it is crucial for fate determination of embryonic stem cells (ESCs) by encoding isoforms with different functions to regulate the balance between pluripotency maintenance and differentiation. Since the role of the Hippo pathway in ESCs is controversial, there may be novel isoforms of Taz, a key effector of the Hippo pathway, previously unknown to us. Here, we identified three variants of Taz in mESCs. Apart from the canonical Taz1185, there were also two novel variants, Taz402 and Taz1086. We found their structure and subcellular localization to be different, while they could all interact with TEAD2 with similar binding affinities and activate transcription. Under the LIFlow condition, overexpression of them all induced apoptosis and differentiation of mESCs, among which the phenotype of Taz1086 was the most dramatic. Taken together, we discovered novel variants of Taz and compared their structure and functional differences in mESC pluripotency maintenance. These findings will help us to understand the Taz gene and clarify its role in mESC.


Asunto(s)
Empalme Alternativo/genética , Proteínas de Unión al ADN/genética , Células Madre Embrionarias de Ratones/metabolismo , Transactivadores/genética , Factores de Transcripción/genética , Animales , Apoptosis/genética , Diferenciación Celular/genética , Regulación de la Expresión Génica/genética , Ratones , Células Madre Pluripotentes/metabolismo , Isoformas de Proteínas/genética , ARN Mensajero/genética
15.
Front Immunol ; 11: 603507, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33312178

RESUMEN

Defective IFN production and exacerbated inflammatory and pro-fibrotic responses are hallmarks of SARS-CoV-2 infection in severe COVID-19. Based on these hallmarks, and considering the pivotal role of macrophages in COVID-19 pathogenesis, we hypothesize that the transcription factors MAFB and MAF critically contribute to COVID-19 progression by shaping the response of macrophages to SARS-CoV-2. Our proposal stems from the recent identification of pathogenic lung macrophage subsets in severe COVID-19, and takes into consideration the previously reported ability of MAFB to dampen IFN type I production, as well as the critical role of MAFB and MAF in the acquisition and maintenance of the transcriptional signature of M-CSF-conditioned human macrophages. Solid evidences are presented that link overexpression of MAFB and silencing of MAF expression with clinical and biological features of severe COVID-19. As a whole, we propose that a high MAFB/MAF expression ratio in lung macrophages could serve as an accurate diagnostic tool for COVID-19 progression. Indeed, reversing the macrophage MAFB/MAF expression ratio might impair the exacerbated inflammatory and profibrotic responses, and restore the defective IFN type I production, thus becoming a potential strategy to limit severity of COVID-19.


Asunto(s)
/inmunología , Macrófagos/inmunología , Factores de Transcripción Maf/inmunología , Factor de Transcripción MafB/inmunología , /inmunología , /genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/genética , Regulación de la Expresión Génica/inmunología , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Humanos , Macrófagos/metabolismo , Factores de Transcripción Maf/genética , Factores de Transcripción Maf/metabolismo , Factor de Transcripción MafB/genética , Factor de Transcripción MafB/metabolismo , Índice de Severidad de la Enfermedad
16.
PLoS One ; 15(12): e0236771, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33320849

RESUMEN

BACKGROUNDS: Sevoflurane is a most frequently used volatile anesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis. METHODS: Eight-week old mice were exposed to sevoflurane. RNA from medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted and their gene ontology terms were analysed using Metascape. These our anesthetized mouse data and the transcriptome array data of the cerebral cortex of sleeping mice were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes. RESULTS: The gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in each region of brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anesthetized mice. Focusing on individual genes, sevoflurane induced Klf4 upregulation in all sampled parts of brain. wPGSA supported the function of KLF4 as a transcription factor, and KLF4-binding motifs were present in many regulatory regions of the differentially expressed genes. CONCLUSIONS: Klf4 was upregulated by sevoflurane inhalation in the mouse brain. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.


Asunto(s)
Encéfalo/efectos de los fármacos , Regulación de la Expresión Génica/efectos de los fármacos , Sevoflurano/farmacología , Transcriptoma/efectos de los fármacos , Animales , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/genética , Ontología de Genes , Masculino , Ratones , Ratones Endogámicos C57BL , Neuronas/efectos de los fármacos , Factores de Transcripción/genética , Transcriptoma/genética , Regulación hacia Arriba/efectos de los fármacos , Regulación hacia Arriba/genética
17.
PLoS One ; 15(12): e0243911, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33326461

RESUMEN

Peroxisome proliferator-activated receptor α/δ (PPAR α/δ), regulating glucolipid metabolism and immune inflammation, has been identified as an effective therapeutic target in non-alcoholic steatohepatitis (NASH). Dual PPAR α/δ agonist, such as GFT505 (also known as elafibranor), demonstrated potential therapeutic effect for NASH in clinical trials. To profile the regulatory network of PPAR α/δ agonist in NASH, the choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) induced NASH model was used to test the pharmacodynamics and transcriptome regulation of GFT505 in this study. The results showed that GFT505 ameliorated hepatic steatosis, inflammation and fibrosis in CDAHFD mice model. RNA-sequencing yielded 3995 up-regulated and 3576 down-regulated genes with GFT505 treatment. And the most significant differentialy expressed genes involved in glucolipid metabolism (Pparα, Acox1, Cpt1b, Fabp4, Ehhadh, Fabp3), inflammation (Ccl6, Ccl9, Cxcl14) and fibrosis (Timp1, Lamc3, Timp2, Col3a1, Col1a2, Col1a1, Hapln4, Timp3, Pik3r5, Pdgfα, Pdgfß, Tgfß1, Tgfß2) were confirmed by RT-qPCR. The down-regulated genes were enriched in cytokine-cytokine receptor interaction pathway and ECM-receptor interaction pathway, while the up-regulated genes were enriched in PPAR signaling pathway and fatty acid degradation pathway. This study provides clues and basis for further understanding on the mechanism of PPAR α/δ agonist on NASH.


Asunto(s)
Deficiencia de Colina/genética , Enfermedad del Hígado Graso no Alcohólico/genética , PPAR alfa/genética , Receptores Citoplasmáticos y Nucleares/genética , Aminoácidos/metabolismo , Animales , Chalconas/farmacología , Colina/genética , Deficiencia de Colina/patología , Dieta Alta en Grasa/efectos adversos , Modelos Animales de Enfermedad , Regulación de la Expresión Génica/genética , Humanos , Ratones , Enfermedad del Hígado Graso no Alcohólico/tratamiento farmacológico , Enfermedad del Hígado Graso no Alcohólico/patología , PPAR alfa/agonistas , Propionatos/farmacología , Receptores Citoplasmáticos y Nucleares/agonistas , Transducción de Señal/genética
18.
PLoS Biol ; 18(12): e3000982, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33332353

RESUMEN

Toll-like receptors (TLRs) play a crucial role in the innate immune response. Although endosomal TLR7 recognizes single-stranded RNAs, their endogenous RNA ligands have not been fully explored. Here, we report 5'-tRNA half molecules as abundant activators of TLR7. Mycobacterial infection and accompanying surface TLR activation up-regulate the expression of 5'-tRNA half molecules in human monocyte-derived macrophages (HMDMs). The abundant accumulation of 5'-tRNA halves also occur in HMDM-secreted extracellular vehicles (EVs); the abundance of EV-5'-tRNAHisGUG half molecules is >200-fold higher than that of the most abundant EV-microRNA (miRNA). Sequence identification of the 5'-tRNA halves using cP-RNA-seq revealed abundant and selective packaging of specific 5'-tRNA half species into EVs. The EV-5'-tRNAHisGUG half was experimentally demonstrated to be delivered into endosomes in recipient cells and to activate endosomal TLR7. Up-regulation of the 5'-tRNA half molecules was also observed in the plasma of patients infected with Mycobacterium tuberculosis. These results unveil a novel tRNA-engaged pathway in the innate immune response and assign the role of "immune activators" to 5'-tRNA half molecules.


Asunto(s)
Vesículas Extracelulares/genética , ARN de Transferencia de Histidina/metabolismo , Receptor Toll-Like 7/metabolismo , Endosomas/metabolismo , Vesículas Extracelulares/metabolismo , Regulación de la Expresión Génica/genética , Humanos , Inmunidad Innata/genética , Inmunidad Innata/fisiología , Macrófagos/metabolismo , ARN de Transferencia/metabolismo , ARN de Transferencia de Histidina/genética , ARN de Transferencia de Histidina/fisiología , Células THP-1 , Receptor Toll-Like 7/fisiología
19.
PLoS Pathog ; 16(12): e1008504, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33362245

RESUMEN

Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia/lymphoma (ATLL), and the neurological disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The HTLV-1 Tax protein persistently activates the NF-κB pathway to enhance the proliferation and survival of HTLV-1 infected T cells. Lysine 63 (K63)-linked polyubiquitination of Tax provides an important regulatory mechanism that promotes Tax-mediated interaction with the IKK complex and activation of NF-κB; however, the host proteins regulating Tax ubiquitination are largely unknown. To identify new Tax interacting proteins that may regulate its ubiquitination we conducted a yeast two-hybrid screen using Tax as bait. This screen yielded the E3/E4 ubiquitin conjugation factor UBE4B as a novel binding partner for Tax. Here, we confirmed the interaction between Tax and UBE4B in mammalian cells by co-immunoprecipitation assays and demonstrated colocalization by proximity ligation assay and confocal microscopy. Overexpression of UBE4B specifically enhanced Tax-induced NF-κB activation, whereas knockdown of UBE4B impaired Tax-induced NF-κB activation and the induction of NF-κB target genes in T cells and ATLL cell lines. Furthermore, depletion of UBE4B with shRNA resulted in apoptotic cell death and diminished the proliferation of ATLL cell lines. Finally, overexpression of UBE4B enhanced Tax polyubiquitination, and knockdown or CRISPR/Cas9-mediated knockout of UBE4B attenuated both K48- and K63-linked polyubiquitination of Tax. Collectively, these results implicate UBE4B in HTLV-1 Tax polyubiquitination and downstream NF-κB activation.


Asunto(s)
Productos del Gen tax/metabolismo , FN-kappa B/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Regulación de la Expresión Génica/genética , Genes pX/fisiología , Células HEK293 , Virus Linfotrópico T Tipo 1 Humano/metabolismo , Virus Linfotrópico T Tipo 1 Humano/patogenicidad , Humanos , FN-kappa B/fisiología , Transducción de Señal/fisiología , Linfocitos T/metabolismo , Ubiquitina-Proteína Ligasas/fisiología , Ubiquitinación , Ubiquitinas/metabolismo
20.
PLoS Genet ; 16(9): e1008934, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32870927

RESUMEN

Significant association signals from genome-wide association studies (GWAS) point to genomic regions of interest. However, for most loci the causative genetic variant remains undefined. Determining expression quantitative trait loci (eQTL) in a disease relevant tissue is an excellent approach to zoom in on disease- or trait-associated association signals and hitherto on relevant disease mechanisms. To this end, we explored regulation of gene expression in healthy retina (n = 311) and generated the largest cis-eQTL data set available to date. Genotype- and RNA-Seq data underwent rigorous quality control protocols before FastQTL was applied to assess the influence of genetic markers on local (cis) gene expression. Our analysis identified 403,151 significant eQTL variants (eVariants) that regulate 3,007 genes (eGenes) (Q-Value < 0.05). A conditional analysis revealed 744 independent secondary eQTL signals for 598 of the 3,007 eGenes. Interestingly, 99,165 (24.71%) of all unique eVariants regulate the expression of more than one eGene. Filtering the dataset for eVariants regulating three or more eGenes revealed 96 potential regulatory clusters. Of these, 31 harbour 130 genes which are partially regulated by the same genetic signal. To correlate eQTL and association signals, GWAS data from twelve complex eye diseases or traits were included and resulted in identification of 80 eGenes with potential association. Remarkably, expression of 10 genes is regulated by eVariants associated with multiple eye diseases or traits. In conclusion, we generated a unique catalogue of gene expression regulation in healthy retinal tissue and applied this resource to identify potentially pleiotropic effects in highly prevalent human eye diseases. Our study provides an excellent basis to further explore mechanisms of various retinal disease etiologies.


Asunto(s)
Retina/metabolismo , Retina/fisiología , Enfermedades de la Retina/genética , Autopsia , Expresión Génica/genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica/genética , Predisposición Genética a la Enfermedad/genética , Variación Genética/genética , Estudio de Asociación del Genoma Completo/métodos , Genómica/métodos , Genotipo , Voluntarios Sanos , Humanos , Fenotipo , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genética
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