scholarly journals Specific Roles of MicroRNAs in Their Interactions with Environmental Factors

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Juan Wang ◽  
Qinghua Cui
Keyword(s):  
Gene Expression ◽  
Cell Growth ◽  
Environmental Factors ◽  
Cigarette Smoking ◽  
Current Knowledge ◽  
Wide Spectrum ◽  
Exercise Stress ◽  
Biological Processes ◽  
Industrial Materials ◽  
Posttranscriptional Level

MicroRNAs (miRNAs) have emerged as critical regulators of gene expression by modulating numerous target mRNAs expression at posttranscriptional level. Extensive studies have shown that miRNAs are critical in various important biological processes, including cell growth, proliferation, differentiation, development, and apoptosis. In terms of their importance, miRNA dysfunction has been associated with a broad range of diseases. Increased number of studies have shown that miRNAs can functionally interact with a wide spectrum of environmental factors (EFs) including drugs, industrial materials, virus and bacterial pathogens, cigarette smoking, alcohol, nutrition, sleep, exercise, stress, and radiation. More importantly, the interactions between miRNAs and EFs have been shown to play critical roles in determining abnormal phenotypes and diseases. In this paper, we propose an outline of the current knowledge about specific roles of miRNAs in their interactions with various EFs and analyze the literatures detailing miRNAs-EFs interactions in the context of various of diseases.

scholarly journals Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities

2021 ◽  
Author(s):  
Yoo-Ah Kim ◽  
Ermin Hodzic ◽  
Ariella Saslafsky ◽  
Damian Wojtowicz ◽  
Bayarbaatar Amgalan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Environmental Factors ◽  
Disease Progression ◽  
Environmental Exposures ◽  
Biological Processes ◽  
Mutational Signatures ◽  
Mutational Signature ◽  
The Impact ◽  
Pathway Level

Background: Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases such as lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to measure, making it challenging to understand their impacts. On the other hand, some COVID-19 patients develop ARDS in an unfavorable disease progression and smoking has been suggested as a potential risk factor among others. Yet initial studies on COVID-19 cases reported contradictory results on the effects of smoking on the disease. Some suggest that smoking might have a protective effect against it while other studies report an increased risk. A better understanding of how the exposure to smoking and other environmental factors affect biological processes relevant to SARS-CoV-2 infection and unfavorable disease progression is needed. Approach: In this study, we utilize mutational signatures associated with environmental factors as sensors of their exposure level. Many environmental factors including smoking are mutagenic and leave characteristic patterns of mutations, called mutational signatures, in affected genomes. We postulated that analyzing mutational signatures, combined with gene expression, can shed light on the impact of the mutagenic environmental factors to the biological processes. In particular, we utilized mutational signatures from lung adenocarcinoma (LUAD) data set collected in TCGA to investigate the role of environmental factors in COVID-19 vulnerabilities. Integrating mutational signatures with gene expression in normal tissues and using a pathway level analysis, we examined how the exposure to smoking and other mutagenic environmental factors affects the infectivity of the virus and disease progression. Results: By delineating changes associated with smoking in pathway-level gene expression and cell type proportions, our study demonstrates that mutational signatures can be utilized to study the impact of exogenous mutagenic factors on them. Consistent with previous findings, our analysis showed that smoking mutational signature (SBS4) is associated with activation of cytokines mediated singling pathways, leading to inflammatory responses. Smoking related changes in cell composition were also observed, including the correlation of SBS4 with the expansion of goblet cells. On the other hand, increased basal cells and decreased ciliated cells in proportion were associated with the strength of a different mutational signature (SBS5), which is present abundantly but not exclusively in smokers. In addition, we found that smoking increases the expression levels of genes that are upregulated in severe COVID-19 cases. Jointly, these results suggest an unfavorable impact of smoking on the disease progression and also provide novel findings on how smoking impacts biological processes in lung.

scholarly journals A Comprehensive Profile of Mature MicroRNA in the Pig

2017 ◽  
Author(s):  
Xiliang Wang ◽  
David K.C. Cooper ◽  
Zhiming Cai ◽  
Lisha Mou
Keyword(s):  
Gene Expression ◽  
Critical Role ◽  
Mature Mirnas ◽  
Human Diseases ◽  
Meat Production ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Mature Microrna ◽  
And Function ◽  
Posttranscriptional Level

The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is non-coding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.

scholarly journals Expression and Regulation Profile of Mature MicroRNA in the Pig: Relevance to Xenotransplantation

2017 ◽  
Author(s):  
Zongpei Song ◽  
David K. C. Cooper ◽  
Zhiming Cai ◽  
Lisha Mou
Keyword(s):  
Gene Expression ◽  
Critical Role ◽  
Mature Mirnas ◽  
Human Diseases ◽  
Meat Production ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Mature Microrna ◽  
And Function ◽  
Posttranscriptional Level

The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is non-coding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.

scholarly journals E.PAGE: A curated database and enrichment tool to predict modules associated with gene-environment interactions

2022 ◽  
Author(s):  
Sachin Muralidharan ◽  
Farah Zahir ◽  
Ahmed M. Mehdi
Keyword(s):  
Gene Expression ◽  
Statistical Analysis ◽  
Environmental Factors ◽  
Differentially Expressed Genes ◽  
R Package ◽  
Differentially Expressed ◽  
Toxic Chemicals ◽  
Biological Processes ◽  
Analysis Package ◽  
Gene Modules

Aims/hypothesis: The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. Methods: We followed a two-step process to achieve the objectives of this study. First, we conducted a systematic review of the existing gene expression datasets to identify the integrated genomic and environmental factors used in available studies. This enabled us to curate a comprehensive genomic-environmental database for four key environmental factors (smoking, diet, infections and toxic chemicals) associated with various autoimmune and chronic conditions. Second, we developed a statistical analysis package that allows users to understand the relationships between differentially expressed genes and environmental factors under different disease conditions. Results: The initial database search run on the Gene Expression Omnibus (GEO) and the Molecular Signature Database (MSigDB) retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 186 studies were selected. From those, 243 individual sets of genes, or gene modules, were obtained. We then curated a database containing four environmental factors, namely cigarette smoking, diet, infections and toxic chemicals, along with a total of 25789 genes that had an association with one or more of these factors. In 6 case studies, the database and statistical analysis package were then tested with lists of differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, cobalt exposure, COVID-19 and smoking. On testing, we uncovered statistically enriched biological processes, which could help us understand the pathways associated with environmental factors and gene modules. Conclusions: A novel curated database and software tool is provided as an R Package. Users can enter a list of genes to discover associated environmental factors under various disease conditions.

scholarly journals Emerging Roles of N6-Methyladenosine Modification in Neurodevelopment and Neurodegeneration

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2694
Author(s):  
Liqi Shu ◽  
Xiaoli Huang ◽  
Xuejun Cheng ◽  
Xuekun Li
Keyword(s):  
Gene Expression ◽  
Neurodegenerative Diseases ◽  
Neurological Disorders ◽  
Neuronal Development ◽  
Current Knowledge ◽  
Biological Processes ◽  
Messenger Rnas ◽  
Domain Family ◽  
Yth Domain ◽  
Essential Function

N6-methyladenosine (m6A), the most abundant modification in messenger RNAs (mRNAs), is deposited by methyltransferases (“writers”) Mettl3 and Mettl14 and erased by demethylases (“erasers”) Fto and Alkbh5. m6A can be recognized by m6A-binding proteins (“readers”), such as Yth domain family proteins (Ythdfs) and Yth domain-containing protein 1 (Ythdc1). Previous studies have indicated that m6A plays an essential function in various fundamental biological processes, including neurogenesis and neuronal development. Dysregulated m6A modification contributes to neurological disorders, including neurodegenerative diseases. In this review, we summarize the current knowledge about the roles of m6A machinery, including writers, erasers, and readers, in regulating gene expression and the function of m6A in neurodevelopment and neurodegeneration. We also discuss the perspectives for studying m6A methylation.

scholarly journals Effects of Methanol on Carotenoids as Well as Biomass and Fatty Acid Biosynthesis in Schizochytrium limacinum B4D1

2019 ◽  
Vol 85 (19) ◽  
Author(s):  
Huanmin Du ◽  
Xiaoping Liao ◽  
Zhengquan Gao ◽  
Yang Li ◽  
Yu Lei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Cell Growth ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Expression Profiles ◽  
Total Sterol ◽  
Transcriptomic Analysis ◽  
Schizochytrium Limacinum ◽  
Promising Source

ABSTRACT Schizochytrium is a promising source for the production of docosahexaenoic acid and astaxanthin. The effects of different methanol concentrations on astaxanthin, biomass, and production of the lipids, squalene, and total sterol in Schizochytrium limacinum B4D1 were investigated. Astaxanthin began to accumulate when the methanol concentration reached 3.2% and peaked at 5.6% methanol, with a 2,000-fold increase over that in the control. However, under cultivation with 5.6% methanol, the biomass, lipids, squalene, and total sterol decreased to various degrees. Transcriptomic analysis was performed to explore the effects of different methanol concentrations (0%, 3.2%, and 5.6%) on the expression profile of B4D1. Three key signaling pathways were found to play important roles in regulating cell growth and metabolism under cultivation with methanol. Five central carbon metabolism-associated genes were significantly downregulated in response to 5.6% methanol and thus were expected to result in less ATP and NADPH being available for cell growth and synthesis. High methanol conditions significantly downregulated three genes involved in fatty acid and squalene/sterol precursor biosynthesis but significantly upregulated geranylgeranyl diphosphate synthase, lycopene β-cyclase, and β-carotene 3-hydroxylase, which are involved in astaxanthin synthesis, thus resulting in an increase in the levels of precursors and the final production of astaxanthin. Additionally, the transcriptional levels of three stress response genes were upregulated. This study investigates gene expression profiles in the astaxanthin producer Schizochytrium when grown under various methanol concentrations. These results broaden current knowledge regarding genetic expression and provide important information for promoting astaxanthin biosynthesis in Schizochytrium. IMPORTANCE Schizochytrium strains are usually studied as oil-producing strains, but they can also synthesize other secondary metabolites, such as astaxanthin. In this study, methanol was used as an inducer, and we explored its effects on the production of astaxanthin, a highly valuable substance in Schizochytrium. Methanol induced Schizochytrium to synthesize large amounts of astaxanthin. Transcriptomic analysis was used to investigate the regulation of signaling and metabolic pathways (mainly relative gene expression) in Schizochytrium grown in the presence of various concentrations of methanol. These results contribute to the understanding of the underlying molecular mechanisms and may aid in the future optimization of Schizochytrium for astaxanthin biosynthesis.

scholarly journals Effects of Dietary Fatty Acids on Gene Expression and Biological Processes in Different Tissues of Pigs: A Review

2021 ◽  
Author(s):  
Simara Larissa Fanalli ◽  
Bruna Pereira Martins da Silva ◽  
Bruna Petry ◽  
Miguel Henrique de Almeida Santana ◽  
Guilherme Henrique Gebim Polizel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acids ◽  
Production Systems ◽  
Current Knowledge ◽  
Dietary Fatty Acids ◽  
Regulation Of Transcription ◽  
Biological Processes ◽  
Finishing Pigs ◽  
Production Traits ◽  
Different Tissues

Studies on the influence of dietary components and their effects are fundamental for nutrigenomics, or the study of how nutrients can be cellular sensors, how they affect biological processes and gene expression in different tissues. Lipids are an important source of fatty acids (FA) and energy and are fundamental to biological processes and influence the regulation of transcription. Pigs are excellent model to study nutrigenomics, particularly lipid metabolism because the deposition and composition of FA in their tissues reflect the composition of FA in their diet. Recent studies show that FA supplementation is important in production systems, such as growing and finishing pigs, as it can improve the energy value of the feed, help reduce costs, improve animal welfare, and influence the nutritional value of the meat. Studies show that oleic (OA), linoleic (LA), docosahexaenoic (DHA), and eicosapentaenoic (EPA) acids are associated with the regulation of transcription in tissues such as muscle, liver, adipose tissue, and brain. Other studies indicate that EPA and DHA are associated with changes in specific signaling pathways, altering gene expression and biophysical properties of membranes. This review, therefore, focuses on the current knowledge of the effects of dietary FA on production traits and gene expression.

The physiological and pathophysiological roles of adipocyte miRNAs

2013 ◽  
Vol 91 (4) ◽  
pp. 195-202 ◽  
Author(s):  
Hongyan Ling ◽  
Xing Li ◽  
Chao Hua Yao ◽  
Bi Hu ◽  
Duanfang Liao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipocyte Differentiation ◽  
Noncoding Rnas ◽  
Biological Processes ◽  
Insulin Production ◽  
Regulate Gene Expression ◽  
Small Noncoding Rnas ◽  
And Function ◽  
Posttranscriptional Level ◽  
Regulate Gene

MicroRNAs (miRNAs) are highly conserved, small, noncoding RNAs that regulate gene expression at the posttranscriptional level. Their actions affect numerous important biological processes, including adipocyte differentiation and function, sugar and lipid metabolism, and insulin production and secretion. Recent reports suggest miRNAs may also be involved in the pathogenic processes of obesity, diabetes, and insulin resistance. In this review, we summarize research progresses on adipocyte miRNAs and their physiological and pathological implications.

scholarly journals Expression and Regulation Profile of Mature MicroRNA in the Pig: Relevance to Xenotransplantation

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Zongpei Song ◽  
David K. C. Cooper ◽  
Zhiming Cai ◽  
Lisha Mou
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Critical Role ◽  
Mature Mirnas ◽  
Human Diseases ◽  
Meat Production ◽  
Biological Processes ◽  
Mature Microrna ◽  
And Function ◽  
Posttranscriptional Level

The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is noncoding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.

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