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1.
Neuron ; 109(1): 11-26, 2021 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-33412093

RESUMO

Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.


Assuntos
Encéfalo/metabolismo , Epigenoma/fisiologia , Análise de Célula Única/métodos , Transcriptoma/fisiologia , Metilação de DNA/fisiologia , Epigenômica/métodos , Humanos , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos
2.
Ecotoxicol Environ Saf ; 211: 111919, 2021 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-33476853

RESUMO

The aim of this study was to elucidate the effect of pH on bacterial resistance mechanisms to copper (Cu) stress by genomic and transcriptomic analysis. Klebsiella michiganensis cells were exposed to 0.5 mM CuCl2 at pH 4 and 5. Lower pH (pH < 4) strongly inhibited K. michiganensis growth, while Cu stress and higher pH (pH > 5) induced Cu precipitation in the medium. Transcriptomic analyses indicated that two groups of genes related to quorum sensing (QS) systems (lsrABCDFGKR) and type II secretion systems (T2SS) (gspCDEFGHIJKLM) were significantly up-regulated at pH 4 only. These results suggest that T2SS may be induced and controlled by QS, thereby contributing to the formation of extracellular polymeric substances (EPS) and the secretion of proteins to prevent Cu ions from entering cells. Six Cu resistance genes (cusABF, copA, cueO, and gene05308) were more significantly up-regulated at pH 4 than at pH 5. In addition, the relative expression (log2|FC=) of the sulfur assimilation genes cysHJIK was relatively higher at pH 4 than at pH 5, while the gene encoding organic sulfur metabolism, tauB, was also significantly up-regulated at only pH 4. These results indicate that the Cu efflux system can remove intracellular Cu ions from cells, and that the sulfur assimilation system is related to the detoxification of Cu ions. Furthermore, increased free Cu ions at lower pH (4) could induce communication signals among cells, thereby stimulating the response of T2SS-related genes in K. michiganensis to tolerate Cu stress. Consequently, the resistance of K. michiganensis to Cu stress is a multisystem collaborative process composed of intracellular and extracellular components.


Assuntos
Cobre/toxicidade , Poluentes Ambientais/toxicidade , Klebsiella/fisiologia , Transcriptoma/fisiologia , Cobre/metabolismo , Perfilação da Expressão Gênica , Íons , Klebsiella/genética
3.
Ecotoxicol Environ Saf ; 211: 111945, 2021 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-33516137

RESUMO

OBJECTIVE: The study aimed to recognize potential molecular targets and signal pathways whereby phenolic environmental estrogen promotes the proliferation of uterine leiomyoma cells. METHODS: Primary cultured cell lines of uterine leiomyoma were treated with 0.1% DMSO, 10.0µmol/L Bisphenol A (BPA), and 32.0µmol/L Nonylphenol (NP) for 48 h before RNA-seq was performed. Those genes affected by BPA and NP were identified. Then, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and Protein-protein Interaction (PPI) analysis were performed. Quantitative real-time polymerase chain reaction (q-PCR) and western blot were used to verify the differentially expressed gene and protein. RESULTS: Compared to with the control group, 739 differentially expressed genes were identified in both the BPA group and the NP group. GO enrichment analysis showed that the most enriched GO terms were connective tissue development and G1/S transition of mitotic cell cycle, and extracellular matrix. The results of KEGG enrichment analysis showed that differentially expressed mRNA were enriched mainly in three primary pathways, including environmental information processing, human diseases, and cellular processes. The cell cycle, PI3K-Akt signaling pathway are significantly enriched. The q-PCR and western blot verified the cell cycle associated genes and proteins were upregulated in both BPA group and NP group. Both BPA and NP activated the PI3K-AKT signaling pathway. CONCLUSION: Phenolic environmental estrogens may promote the proliferation and cell cycle progression of uterine leiomyoma cells through rapid non-genomic ER signaling, which leads to disordered cell cycle regulation and accelerates the transition of the cell cycle from G0/G1 phase to S phase. In addition, as an external stimulant, phenolic estrogen promotes the upregulation of inflammatory factors in uterine leiomyomas.


Assuntos
Poluentes Ambientais/toxicidade , Estrogênios/toxicidade , Fenóis/toxicidade , Transcriptoma/fisiologia , Compostos Benzidrílicos , Linhagem Celular Tumoral , Poluentes Ambientais/metabolismo , Feminino , Perfilação da Expressão Gênica , Ontologia Genética , Humanos , Leiomioma/genética , Leiomioma/metabolismo , Fenóis/metabolismo , Fosfatidilinositol 3-Quinases/metabolismo , Transdução de Sinais/efeitos dos fármacos , Transcriptoma/efeitos dos fármacos , Regulação para Cima/efeitos dos fármacos , Neoplasias Uterinas/genética , Neoplasias Uterinas/metabolismo
4.
Ecotoxicol Environ Saf ; 209: 111816, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33360213

RESUMO

As a non-essential heavy metal, cadmium (Cd) is toxic to plants. In the last 15 years, over 70 transcriptome studies have been published to decipher the molecular response mechanism against Cd stress in different plants. To extract generalization results from transcriptomic data across different plants and obtain some hub genes that respond to Cd stress, we carried out a meta-analysis of 32 published datasets. Cluster analysis revealed that plant species played a more decisive role than the media used and exposure time in the transcriptome patterns of plant roots response to Cd. The datasets from a Gramineae-like (GL) group were closer in clustering. 838 DEGs were commonly Cd-regulated in at least nine of 18 GL datasets. Gene ontology and KEGG pathway analyses revealed that oxidative stress-related terms and lignin synthesis-related terms were significantly enriched. Mapman analysis revealed that these common DEGs were mainly involved in regulation, cellular response, secondary metabolism, transport, cell wall and lipid metabolism. In Oryza sativa, 15 DEGs were up-regulated in at least four of five HM (As, Cr, Cd, Hg and Pb) groups, such as Os10g0517500 (methionine gamma-lyase) and Os01g0159800 (bHLH107). Moreover, our datasets can be used to retrieve log2FC value of specific genes across 29 studies (48 datasets), which provides data reference for the subsequent selection of HM-related genes. Our results provide the basis for further understanding of Cd tolerance mechanisms in plants.


Assuntos
Cádmio/toxicidade , Poaceae/fisiologia , Poluentes do Solo/toxicidade , Estresse Fisiológico/genética , Transcriptoma/fisiologia , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Metais Pesados/metabolismo , Oryza/metabolismo , Raízes de Plantas/metabolismo , Poaceae/metabolismo , Metabolismo Secundário
5.
Ecotoxicol Environ Saf ; 209: 111823, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33360594

RESUMO

Aflatoxin is a known mycotoxin that pollutes various grains widely in the environment. Aflatoxin B1 (AFB1) and Aflatoxin M1 (AFM1) have been shown to induce cytotoxicity in many cells, yet their effects on mammary epithelial cells remain unclear. In this study, we examined the toxicity and the effects of AFB1 and AFM1 on bovine mammary epithelial cells (BME cells). The cells were treated with AFB1 or AFM1 at a concentration of 0-10 mg/L for 24 or 48 h, followed by cytotoxicity assays, flow cytometry, and transcriptomics. Our results demonstrated that AFB1 and AFM1 induced cell proliferation inhibition, apoptosis and cell cycle arrest. However, the level of intracellular reactive oxygen species has no significant difference. The RNA-Seq results also showed that AFB1 and AFM1 changed many related gene expressions like apoptosis and oxidative stress, cycle, junction, and signaling pathway. Taken together, AFB1 and AFM1 were found to affect cytotoxicity and related gene changes in BME cells. Notably, this study reported that 2 mg/L of AFB1 and AFM1 affected the expression of methylation-related genes, and ultimately altered the rate of m6A methylation in RNA. It may provide a potential direction for toxins to indirectly regulate gene expression by affecting RNA methylation modification. Our research provides some novel insights and data about AFB1 and AFM1 toxicity in BME cells.


Assuntos
Aflatoxina B1/toxicidade , Aflatoxina M1/toxicidade , Testes de Toxicidade , Transcriptoma/fisiologia , Animais , Apoptose/efeitos dos fármacos , Bovinos , Contagem de Células , Proliferação de Células , Células Epiteliais/efeitos dos fármacos , Feminino , Citometria de Fluxo , Estresse Oxidativo/efeitos dos fármacos , Espécies Reativas de Oxigênio
6.
Ecotoxicol Environ Saf ; 207: 111485, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-33254386

RESUMO

Polychlorinated biphenyls (PCBs) are well-known persistent organic pollutants; they have toxic effects on the immune system, reproductive system, and endocrine system by changing the metabolism of the body. To elucidate the underlying molecular mechanism, the clam Meretrix meretrix was exposed to 10 and 1000 ng/L Aroclor 1254 and natural seawater (control). Samples from clams exposed to natural seawater and those exposed to Aroclor 1254 for 1 and 3 days were individually collected for transcriptome analysis. After assembly, more than 535,157 transcripts with a mean length of 949 bp and an N50 length of 1279 bp were obtained; a final set of 177,142 unigenes was generated. In the present study, 5101 differentially expressed genes were identified. The differentially expressed genes were related to detoxification metabolism, oxidative stress, immune response, and endocrine system disruption. Of these genes, under the Aroclor 1254 exposure, cytochrome P450 20A1 (2.06-4.46 folds), glutathione S-transferase (2.25-3.80 folds), multidrug resistance-associated protein 1-like (1.49-2.92 folds), peroxidase-like protein (1.33-4.26 folds), lysozyme (1.61-2.05 folds), bcl-2 like 1 protein (1.14-2.29 folds) and vitellogenin (1.09-1.19 folds) showed been significantly induced expressed. At the same time, some genes were down regulated, including cytochrome P450 2J5 (-1.20 ~ -2.86 folds), cytochrome P450 3A24 (-1.40 ~ -4.08 folds), C1q (-1.27 ~ -1.66 folds), Sulfotransferase (-1.51 ~ -1.84 folds), monocarboxylate transporter 10 (-1.30 ~ -4.70 folds), 3-beta hydroxysteroid dehydrogenase (-1.43 ~ -2.81 folds) and beta-galactosidase (-1.23 ~ -2.23 folds). Furthermore, it showed that the expression levels of CYP2J5, glutathione S-transferase, 3-beta hydroxysteroid dehydrogenase and beta-galactosidase had time responses and dose responses. The present study provided insights into the toxic effects of Aroclor 1254 exposure in M. meretrix.


Assuntos
Bivalves/fisiologia , Transcriptoma/fisiologia , Poluentes Químicos da Água/toxicidade , Animais , Bivalves/efeitos dos fármacos , Sistema Enzimático do Citocromo P-450/metabolismo , Glutationa Transferase/metabolismo , Oxirredução , Estresse Oxidativo , Bifenilos Policlorados
7.
Chemosphere ; 262: 127891, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32799150

RESUMO

Fluoride generally exists in the natural environment, and has been reported to induce serious environmental hazard to animals, plants, and even humans via ecological cycle. Silkworm, Bombyx mori, which showed significant growth and reproductivity reduction when exposed to fluoride, has become a model to evaluate the toxicity of fluoride. However, the detailed mechanism underlying fluoride toxicity and corresponding transport proteins remain unclear. In this study, we performed RNA-seq of the larval midgut and fat body with fluoride exposure and normal treatment. Differential analysis showed that there were 4405 differentially expressed genes in fat body and 4430 DEGs in midgut with fluoride stress. By Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified several key pathways involved in the fluoride exposure and poisoning. We focused on the oxidative phosphorylation and MAPK signal pathway. QRT-PCR confirmed that oxidative phosphorylation process was remarkably inhibited by fluoride exposure and resulted in the blocking of ATP synthesis. The MAPK signal pathway was stimulated via phosphorylation signal transduction. Moreover, by protein structure analysis combined with the DEGs, we screen 36 potential membrane proteins which might take part in transporting fluoride. Taken together, the results of our study expanded the underlying mechanisms of fluoride poisoning on silkworm larval growth and development, and implied potential fluoride transport proteins in silkworm.


Assuntos
Bombyx/fisiologia , Fluoretos/toxicidade , Substâncias Perigosas/toxicidade , Tecido Adiposo/metabolismo , Animais , Bombyx/metabolismo , Sistema Digestório/metabolismo , Corpo Adiposo/metabolismo , Perfilação da Expressão Gênica/métodos , Inativação Metabólica , Larva/genética , Transcriptoma/fisiologia
8.
PLoS One ; 15(10): e0239771, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33022020

RESUMO

Huanglongbing (HLB) is a deadly, incurable citrus disease putatively caused by the unculturable bacterium, 'Candidatus Liberibacter asiaticus' (CLas), and transmitted by Diaphorina citri. Prior studies suggest D. citri transmits CLas in a circulative and propagative manner; however, the precise interactions necessary for CLas transmission remain unknown, and the impact of insect sex on D. citri-CLas interactions is poorly understood despite reports of sex-dependent susceptibilities to CLas. We analyzed the transcriptome, proteome, metabolome, and microbiome of male and female adult D. citri reared on healthy or CLas-infected Citrus medica to determine shared and sex-specific responses of D. citri and its endosymbionts to CLas exposure. More sex-specific than shared D. citri responses to CLas were observed, despite there being no difference between males and females in CLas density or relative abundance. CLas exposure altered the abundance of proteins involved in immunity and cellular and oxidative stress in a sex-dependent manner. CLas exposure impacted cuticular proteins and enzymes involved in chitin degradation, as well as energy metabolism and abundance of the endosymbiont 'Candidatus Profftella armatura' in both sexes similarly. Notably, diaphorin, a toxic Profftella-derived metabolite, was more abundant in both sexes with CLas exposure. The responses reported here resulted from a combination of CLas colonization of D. citri as well as the effect of CLas infection on C. medica. Elucidating these impacts on D. citri and their endosymbionts contributes to our understanding of the HLB pathosystem and identifies the responses potentially critical to limiting or promoting CLas acquisition and propagation in both sexes.


Assuntos
Citrus/microbiologia , Hemípteros/microbiologia , Insetos Vetores/microbiologia , Doenças das Plantas/microbiologia , Rhizobiaceae/fisiologia , Rhizobiaceae/patogenicidade , Simbiose/fisiologia , Animais , Citrus/metabolismo , Citrus/fisiologia , Feminino , Hemípteros/metabolismo , Hemípteros/fisiologia , Insetos Vetores/metabolismo , Insetos Vetores/fisiologia , Masculino , Metaboloma/fisiologia , Microbiota/fisiologia , Estresse Oxidativo/fisiologia , Proteoma/metabolismo , Transcriptoma/fisiologia
9.
Nat Commun ; 11(1): 4678, 2020 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-32938916

RESUMO

Diabetic foot ulcers (DFUs) are a life-threatening disease that often result in lower limb amputations and a shortened lifespan. However, molecular mechanisms contributing to the pathogenesis of DFUs remain poorly understood. We use next-generation sequencing to generate a human dataset of pathogenic DFUs to compare to transcriptional profiles of human skin and oral acute wounds, oral as a model of "ideal" adult tissue repair due to accelerated closure without scarring. Here we identify major transcriptional networks deregulated in DFUs that result in decreased neutrophils and macrophages recruitment and overall poorly controlled inflammatory response. Transcription factors FOXM1 and STAT3, which function to activate and promote survival of immune cells, are inhibited in DFUs. Moreover, inhibition of FOXM1 in diabetic mouse models (STZ-induced and db/db) results in delayed wound healing and decreased neutrophil and macrophage recruitment in diabetic wounds in vivo. Our data underscore the role of a perturbed, ineffective inflammatory response as a major contributor to the pathogenesis of DFUs, which is facilitated by FOXM1-mediated deregulation of recruitment of neutrophils and macrophages, revealing a potential therapeutic strategy.


Assuntos
Pé Diabético/genética , Pé Diabético/imunologia , Proteína Forkhead Box M1/imunologia , Cicatrização/imunologia , Adulto , Idoso , Animais , Proliferação de Células , Diabetes Mellitus Experimental/complicações , Diabetes Mellitus Experimental/imunologia , Pé Diabético/patologia , Modelos Animais de Doenças , Feminino , Proteína Forkhead Box M1/antagonistas & inibidores , Proteína Forkhead Box M1/metabolismo , Humanos , Inflamação/genética , Inflamação/imunologia , Masculino , Camundongos Endogâmicos , Pessoa de Meia-Idade , Mucosa Bucal/fisiologia , Piridinas/farmacologia , Tiofenos/farmacologia , Transcriptoma/fisiologia , Cicatrização/genética
11.
Anticancer Res ; 40(8): 4719-4727, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32727798

RESUMO

BACKGROUND/AIM: We investigated whether mastication affects microglia, whose activity is thought to be associated with cognition and brain tumor progression. MATERIALS AND METHODS: We kept mice by feeding either a hard or soft diet for 2, 4 or 8 months. After each period, we removed the whole brains and isolated microglia. The total RNA extracted from each brain's microglia was subjected to DNA microarray analysis. RESULTS: Many genes were found to be significantly differentially expressed between hard- and soft-diet-fed mice in each group of the same feeding period. The expression of several genes involved in the regulation of actin cytoskeleton was down-regulated in the soft-diet-fed mice. CONCLUSION: Mastication may affect microglia's roles in cognition as well as their neuroimmune activity through their activity of patrolling the brain.


Assuntos
Mastigação/fisiologia , Microglia/fisiologia , Transcriptoma/fisiologia , Animais , Encéfalo/fisiologia , Masculino , Camundongos , Camundongos Endogâmicos C3H
12.
Fertil Steril ; 114(1): 33-43, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32622411

RESUMO

OBJECTIVE: To identify cell types in the male and female reproductive systems at risk for SARS-CoV-2 infection because of the expression of host genes and proteins used by the virus for cell entry. DESIGN: Descriptive analysis of transcriptomic and proteomic data. SETTING: Academic research department and clinical diagnostic laboratory. PATIENT(S): Not applicable (focus was on previously generated gene and protein expression data). INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Identification of cell types coexpressing the key angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) genes and proteins as well as other candidates potentially involved in SARS-CoV-2 cell entry. RESULT(S): On the basis of single-cell RNA sequencing data, coexpression of ACE2 and TMPRSS2 was not detected in testicular cells, including sperm. A subpopulation of oocytes in nonhuman primate ovarian tissue was found to express ACE2 and TMPRSS2, but coexpression was not observed in ovarian somatic cells. RNA expression of TMPRSS2 in 18 samples of human cumulus cells was shown to be low or absent. There was general agreement between publicly available bulk RNA and protein datasets in terms of ACE2 and TMPRSS2 expression patterns in testis, ovary, endometrial, and placental cells. CONCLUSION(S): These analyses suggest that SARS-CoV-2 infection is unlikely to have long-term effects on male and female reproductive function. Although the results cannot be considered definitive, they imply that procedures in which oocytes are collected and fertilized in vitro are associated with very little risk of viral transmission from gametes to embryos and may indeed have the potential to minimize exposure of susceptible reproductive cell types to infection in comparison with natural conception.


Assuntos
Betacoronavirus/metabolismo , Infecções por Coronavirus/metabolismo , Fertilidade/fisiologia , Regulação Viral da Expressão Gênica/fisiologia , Pneumonia Viral/metabolismo , Reprodução/fisiologia , Internalização do Vírus , Adolescente , Adulto , Animais , Betacoronavirus/genética , Linhagem Celular , Infecções por Coronavirus/genética , Feminino , Humanos , Macaca fascicularis , Masculino , Ovário/citologia , Ovário/metabolismo , Ovário/virologia , Pandemias , Peptidil Dipeptidase A/biossíntese , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Gravidez , Proteômica/métodos , Serina Endopeptidases/biossíntese , Serina Endopeptidases/genética , Testículo/citologia , Testículo/metabolismo , Testículo/virologia , Transcriptoma/fisiologia , Adulto Jovem
13.
Proc Natl Acad Sci U S A ; 117(31): 18788-18798, 2020 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-32690678

RESUMO

Humans display reproducible sex differences in cognition and behavior, which may partly reflect intrinsic sex differences in regional brain organization. However, the consistency, causes and consequences of sex differences in the human brain are poorly characterized and hotly debated. In contrast, recent studies in mice-a major model organism for studying neurobiological sex differences-have established: 1) highly consistent sex biases in regional gray matter volume (GMV) involving the cortex and classical subcortical foci, 2) a preponderance of regional GMV sex differences in brain circuits for social and reproductive behavior, and 3) a spatial coupling between regional GMV sex biases and brain expression of sex chromosome genes in adulthood. Here, we directly test translatability of rodent findings to humans. First, using two independent structural-neuroimaging datasets (n > 2,000), we find that the spatial map of sex-biased GMV in humans is highly reproducible (r > 0.8 within and across cohorts). Relative GMV is female biased in prefrontal and superior parietal cortices, and male biased in ventral occipitotemporal, and distributed subcortical regions. Second, through systematic comparison with functional neuroimaging meta-analyses, we establish a statistically significant concentration of human GMV sex differences within brain regions that subserve face processing. Finally, by imaging-transcriptomic analyses, we show that GMV sex differences in human adulthood are specifically and significantly coupled to regional expression of sex-chromosome (vs. autosomal) genes and enriched for distinct cell-type signatures. These findings establish conserved aspects of sex-biased brain development in humans and mice, and shed light on the consistency, candidate causes, and potential functional corollaries of sex-biased brain anatomy in humans.


Assuntos
Encéfalo , Caracteres Sexuais , Transcriptoma , Adulto , Encéfalo/anatomia & histologia , Encéfalo/diagnóstico por imagem , Encéfalo/metabolismo , Encéfalo/fisiologia , Feminino , Perfilação da Expressão Gênica , Humanos , Imagem por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Transcriptoma/genética , Transcriptoma/fisiologia , Adulto Jovem
14.
Am J Physiol Lung Cell Mol Physiol ; 319(3): L456-L470, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32639867

RESUMO

Mechanisms driving adaptive developmental responses to chronic high-altitude (HA) exposure are incompletely known. We developed a novel rat model mimicking the human condition of cardiopulmonary adaptation to HA starting at conception and spanning the in utero and postnatal timeframe. We assessed lung growth and cardiopulmonary structure and function and performed transcriptome analyses to identify mechanisms facilitating developmental adaptations to chronic hypoxia. To generate the model, breeding pairs of Sprague-Dawley rats were exposed to hypobaric hypoxia (equivalent to 9,000 ft elevation). Mating, pregnancy, and delivery occurred in hypoxic conditions. Six weeks postpartum, structural and functional data were collected in the offspring. RNA-Seq was performed on right ventricle (RV) and lung tissue. Age-matched breeding pairs and offspring under room air (RA) conditions served as controls. Hypoxic rats exhibited significantly lower body weights and higher hematocrit levels, alveolar volumes, pulmonary diffusion capacities, RV mass, and RV systolic pressure, as well as increased pulmonary artery remodeling. RNA-Seq analyses revealed multiple differentially expressed genes in lungs and RVs from hypoxic rats. Although there was considerable similarity between hypoxic lungs and RVs compared with RA controls, several upstream regulators unique to lung or RV were identified. We noted a pattern of immune downregulation and regulation patterns of immune and hormonal mediators similar to the genome from patients with pulmonary arterial hypertension. In summary, we developed a novel murine model of chronic hypoxia exposure that demonstrates functional and structural phenotypes similar to human adaptation. We identified transcriptomic alterations that suggest potential mechanisms for adaptation to chronic HA.


Assuntos
Adaptação Fisiológica/fisiologia , Altitude , Hipertensão Pulmonar/fisiopatologia , Hipóxia/fisiopatologia , Transcriptoma/fisiologia , Animais , Modelos Animais de Doenças , Pulmão/fisiopatologia , Ratos Sprague-Dawley , Remodelação Vascular/fisiologia
15.
Toxicol Appl Pharmacol ; 401: 115100, 2020 08 15.
Artigo em Inglês | MEDLINE | ID: mdl-32512070

RESUMO

(-)-Epigallocatechin-3-gallate (EGCG) is the main bioactive component in tea (Camellia sinensis) catechins, and exhibits potential antitumor activity against colorectal cancer (CRC). However, the underlying mechanisms are largely unclear. We investigated the effects of EGCG on activities of CRC cells and the exact molecular mechanism. We used human colon cancer cells (HT-29) and exposed them to EGCG at various concentrations. The MTT assay, flow cytometry, and TUNEL staining were used to study the underlying mechanisms of EGCG (proliferation, apoptosis, autophagy). Western blotting was used to measure expression of marker proteins of the cell cycle, apoptosis, and autophagy. Using a combined microarray-based transcriptomic and ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight tandem mass spectrometry (UHPLC-QTOF/MS)-based metabolomic approach, we investigated the perturbed pathways induced by EGCG treatment at transcript and metabolite levels. Transcriptomic analyses showed that 486 genes were differentially expressed between untreated and EGCG-treated cells. Also, 88 differentially expressed metabolites were identified between untreated and EGCG-treated cells. The altered metabolites were involved in the metabolism of glutathione, glycerophospholipids, starch, sucrose, amino sugars, and nucleotide sugars. There was substantial agreement between the results of transcriptomics and metabolomics analyses. Our data indicate that the anticancer activity of EGCG against HT-29 cells is mediated by induction of cell-cycle arrest, apoptosis, and autophagy. EGCG modulates cancer-cell metabolic pathways. These results provide a platform for future molecular mechanistic studies of EGCG.


Assuntos
Anticarcinógenos/farmacologia , Catequina/análogos & derivados , Neoplasias do Colo/genética , Neoplasias do Colo/metabolismo , Metabolômica/métodos , Transcriptoma/efeitos dos fármacos , Anticarcinógenos/uso terapêutico , Catequina/farmacologia , Catequina/uso terapêutico , Proliferação de Células/efeitos dos fármacos , Proliferação de Células/fisiologia , Neoplasias do Colo/tratamento farmacológico , Células HT29 , Humanos , Transcriptoma/fisiologia
16.
Proc Natl Acad Sci U S A ; 117(27): 15581-15590, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32576685

RESUMO

Protein synthesis represents a major metabolic activity of the cell. However, how it is affected by aging and how this in turn impacts cell function remains largely unexplored. To address this question, herein we characterized age-related changes in both the transcriptome and translatome of mouse tissues over the entire life span. We showed that the transcriptome changes govern those in the translatome and are associated with altered expression of genes involved in inflammation, extracellular matrix, and lipid metabolism. We also identified genes that may serve as candidate biomarkers of aging. At the translational level, we uncovered sustained down-regulation of a set of 5'-terminal oligopyrimidine (5'-TOP) transcripts encoding protein synthesis and ribosome biogenesis machinery and regulated by the mTOR pathway. For many of them, ribosome occupancy dropped twofold or even more. Moreover, with age, ribosome coverage gradually decreased in the vicinity of start codons and increased near stop codons, revealing complex age-related changes in the translation process. Taken together, our results reveal systematic and multidimensional deregulation of protein synthesis, showing how this major cellular process declines with age.


Assuntos
Envelhecimento/fisiologia , Regulação da Expressão Gênica/fisiologia , Biossíntese de Proteínas/fisiologia , Ribossomos/metabolismo , Animais , Códon de Iniciação/metabolismo , Biologia Computacional , Masculino , Camundongos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA-Seq , Ribossomos/genética , Transdução de Sinais/fisiologia , Serina-Treonina Quinases TOR/metabolismo , Transcriptoma/fisiologia
17.
PLoS Genet ; 16(6): e1008831, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32555673

RESUMO

Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.


Assuntos
Comportamento Animal/fisiologia , Encéfalo/fisiologia , Peixes/fisiologia , Regulação da Expressão Gênica/fisiologia , Transcriptoma/fisiologia , Agressão , Animais , Técnicas de Observação do Comportamento , Comportamento Cooperativo , Relações Interpessoais , Transporte de Íons/fisiologia , Aprendizagem/fisiologia , Masculino , Memória/fisiologia , RNA-Seq , Gravação em Vídeo
18.
PLoS One ; 15(4): e0231450, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32302342

RESUMO

RNA-binding proteins (RBPs) control many types of post-transcriptional regulation, including mRNA splicing, mRNA stability, and translational efficiency, by directly binding to their target RNAs and their mutation and dysfunction are often associated with several human neurological diseases and tumorigenesis. Crosslinking immunoprecipitation (CLIP), coupled with high-throughput sequencing (HITS-CLIP), is a powerful technique for investigating the molecular mechanisms underlying disease pathogenesis by comprehensive identification of RBP target sequences at the transcriptome level. However, HITS-CLIP protocol is still required for some optimization due to experimental complication, low efficiency and time-consuming, whose library has to be generated from very small amounts of RNAs. Here we improved a more efficient, rapid, and reproducible CLIP method by optimizing BrdU-CLIP. Our protocol produced a 10-fold greater yield of pre-amplified CLIP library, which resulted in a low duplicate rate of CLIP-tag reads because the number of PCR cycles required for library amplification was reduced. Variance of the yields was also reduced, and the experimental period was shortened by 2 days. Using this, we validated IL-6 expression by a nuclear RBP, HNRNPU, which directly binds the 3'-UTR of IL-6 mRNA in HeLa cells. Importantly, this interaction was only observed in the cytoplasmic fraction, suggesting a role of cytoplasmic HNRNPU in mRNA stability control. This optimized method enables us to accurately identify target genes and provides a snapshot of the protein-RNA interactions of nucleocytoplasmic shuttling RBPs.


Assuntos
Núcleo Celular/metabolismo , Citoplasma/metabolismo , Proteínas de Ligação a RNA/metabolismo , RNA/metabolismo , Regiões 3' não Traduzidas/fisiologia , Transporte Ativo do Núcleo Celular/fisiologia , Linhagem Celular Tumoral , Sequenciamento de Cromatina por Imunoprecipitação/métodos , Perfilação da Expressão Gênica/métodos , Biblioteca Gênica , Células HeLa , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Imunoprecipitação/métodos , Interleucina-6/metabolismo , Processamento de RNA/fisiologia , RNA Mensageiro/metabolismo , Análise de Sequência de RNA/métodos , Transcriptoma/fisiologia
19.
Gene ; 746: 144660, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32275998

RESUMO

Bougainvillea spectabilis is known as a vital medicinal, ornamental as well as an essential oil producing plant. It is also a rich source of important secondary metabolites with several therapeutic properties. Various studies on its pharmacological and toxicological aspects have been published but there is no genomic or transcriptomic resource available in the public databases. To address this important issue, the de-novo transcriptome assembly of B. spectabilis leaf tissue has been done for the identification of genes involved in various important secondary metabolites, Single nucleotide polymorphism (SNPs) and Simple sequence repeats (SSRs). The transcriptome sequencing of B. spectabilis leaf tissue generated 79,811,024 raw reads with GC value 42.77%. The transcriptomic assembly was performed by Trinity software which generated 100,374 transcripts and 99,793 unigenes with minimum and maximum length of 201 bp and 13,237 bp and N50 value of 1470 and 1472 respectively. Annotation of these unigenes was performed using seven databases including NR, PFAM, GO and KEGG. Approximately, 44,302 unigenes were annotated in GO database. The KEGG pathway analysis revealed 23,102 unigenes in which 19,054 genes were assigned to five groups in KEGG and 130 biochemical pathways. The highest group among the five groups was Metabolism with 9230 unigenes. Moreover, about 63,226 SNPs and 30,333 SSRs in the leaf transcriptome of B. spectabilis were identified. To the best of my understanding it will be the first comprehensive transcriptome analysis of B. spectabilis from family Nyctaginaceae which will help as a reference line for further genomic and transcriptomic studies.


Assuntos
Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/fisiologia , Folhas de Planta , Polimorfismo de Nucleotídeo Único , Software , Transcriptoma/fisiologia , Nyctaginaceae/genética , Nyctaginaceae/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo
20.
Sci Rep ; 10(1): 4044, 2020 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-32132613

RESUMO

The ankyrin (ANK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. It is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding ANK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. Next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. Phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. Our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper.


Assuntos
Capsicum , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/fisiologia , Família Multigênica/fisiologia , Proteínas de Plantas , Transcriptoma/fisiologia , Repetição de Anquirina/fisiologia , Capsicum/genética , Capsicum/metabolismo , Estudo de Associação Genômica Ampla , Proteínas de Plantas/biossíntese , Proteínas de Plantas/genética , Especificidade da Espécie
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