Research progress in predicting DNA methylation modifications and the relation with human diseases

2021 ◽  
Vol 28 ◽  
Author(s):  
Chunyan Ao ◽  
Lin Gao ◽  
Liang Yu
Keyword(s):  
Dna Methylation ◽  
Eukaryotic Cell ◽  
Machine Learning Algorithms ◽  
Research Progress ◽  
Epigenetic Mechanisms ◽  
Biological Processes ◽  
Prediction Tools ◽  
Transformation Mechanisms ◽  
The Relationship ◽  
Treatment And Diagnosis

: DNA methylation is an important mode of regulation in epigenetic mechanisms, and it is one of the research foci in the field of epigenetics. DNA methylation modification affects a series of biological processes, such as eukaryotic cell growth, differentiation and transformation mechanisms, by regulating gene expression. In this review, we systematically summarized the DNA methylation databases, prediction tools for DNA methylation modification, machine learning algorithms for predicting DNA methylation modification, and the relationship between DNA methylation modification and diseases such as hypertension, Alzheimer's disease, diabetic nephropathy, and cancer. An in-depth understanding of DNA methylation mechanisms can promote accurate prediction of DNA methylation modifications and the treatment and diagnosis of related diseases.

scholarly journals The Roles of Epigenetics Regulation in Bone Metabolism and Osteoporosis

2021 ◽  
Vol 8 ◽  
Author(s):  
Fei Xu ◽  
Wenhui Li ◽  
Xiao Yang ◽  
Lixin Na ◽  
Linjun Chen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Modification ◽  
Osteogenic Differentiation ◽  
Bone Metabolism ◽  
Bone Fragility ◽  
Research Progress ◽  
Epigenetic Mechanisms ◽  
Mineral Density ◽  
Transcriptional Regulatory ◽  
Non Coding Rnas

Osteoporosis is a metabolic disease characterized by decreased bone mineral density and the destruction of bone microstructure, which can lead to increased bone fragility and risk of fracture. In recent years, with the deepening of the research on the pathological mechanism of osteoporosis, the research on epigenetics has made significant progress. Epigenetics refers to changes in gene expression levels that are not caused by changes in gene sequences, mainly including DNA methylation, histone modification, and non-coding RNAs (lncRNA, microRNA, and circRNA). Epigenetics play mainly a post-transcriptional regulatory role and have important functions in the biological signal regulatory network. Studies have shown that epigenetic mechanisms are closely related to osteogenic differentiation, osteogenesis, bone remodeling and other bone metabolism-related processes. Abnormal epigenetic regulation can lead to a series of bone metabolism-related diseases, such as osteoporosis. Considering the important role of epigenetic mechanisms in the regulation of bone metabolism, we mainly review the research progress on epigenetic mechanisms (DNA methylation, histone modification, and non-coding RNAs) in the osteogenic differentiation and the pathogenesis of osteoporosis to provide a new direction for the treatment of bone metabolism-related diseases.

scholarly journals Regulation Is in the Air: The Relationship between Hypoxia and Epigenetics in Cancer

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 300 ◽  
Author(s):  
Diego Camuzi ◽  
Ísis de Amorim ◽  
Luis Ribeiro Pinto ◽  
Leonardo Oliveira Trivilin ◽  
André Mencalha ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Epigenetic Mechanisms ◽  
Prolyl Hydroxylases ◽  
Metabolic Intermediates ◽  
Cancer Hallmarks ◽  
Proliferation And Apoptosis ◽  
Histone Modifiers ◽  
Non Coding Rnas ◽  
Epigenetic Patterns ◽  
The Relationship

Hypoxia is an inherent condition of tumors and contributes to cancer development and progression. Hypoxia-inducible factors (HIFs) are the major transcription factors involved in response to low O2 levels, orchestrating the expression of hundreds of genes involved in cancer hallmarks’ acquisition and modulation of epigenetic mechanisms. Epigenetics refers to inheritable mechanisms responsible for regulating gene expression, including genes involved in the hypoxia response, without altering the sequence of DNA bases. The main epigenetic mechanisms are DNA methylation, non-coding RNAs, and histone modifications. These mechanisms are highly influenced by cell microenvironment, such as O2 levels. The balance and interaction between these pathways is essential for homeostasis and is directly linked to cellular metabolism. Some of the major players in the regulation of HIFs, such as prolyl hydroxylases, DNA methylation regulators, and histone modifiers require oxygen as a substrate, or have metabolic intermediates as cofactors, whose levels are altered during hypoxia. Furthermore, during pathological hypoxia, HIFs’ targets as well as alterations in epigenetic patterns impact several pathways linked to tumorigenesis, such as proliferation and apoptosis, among other hallmarks. Therefore, this review aims to elucidate the intricate relationship between hypoxia and epigenetic mechanisms, and its crucial impact on the acquisition of cancer hallmarks.

scholarly journals Methylation and Gene Expression Differences Between Reproductive Castes of Bumblebee Workers

2019 ◽  
Author(s):  
Hollie Marshall ◽  
Zoë N. Lonsdale ◽  
Eamonn B. Mallon
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Social Insects ◽  
Social Insect ◽  
Bombus Terrestris ◽  
Epigenetic Mechanisms ◽  
Biological Processes ◽  
Caste Determination ◽  
Differentially Methylated Genes

AbstractPhenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on it’s role in other bee species. In this study we analysed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found genome-wide methylation in B. terrestris is similar to other social insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high inter-colony variation in methylation. These findings suggest methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste specific methylome as well as it’s interaction with gene expression and caste specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in social insects.Impact SummarySocial insects, such as ants, termites, bees and wasps, can produce individuals with extreme physical and behavioural differences within the same colony known as castes (e.g. workers/soldiers/queens). These individuals have similar genomes and many studies have associated epigenetic mechanisms with the differences observed. Epigenetic modifications are changes that affect how genes are expressed without changing the underlying DNA code. Here we investigated differences in DNA methylation (a well researched modified base) between different reproductive castes of the bumblebee, Bombus terrestris, an economically and environmentally important pollinator species. We found B. terrestris has a similar methylation profile to other social insect species in terms of the distribution of methylation throughout the genome and the relationship between methylation and gene expression. Genes that have differences in methylation between reproductive castes are involved in multiple biological processes, including reproduction, suggesting methylation may hold multiple functions in this species. These differentially methylated genes are also different to differentially methylated genes identified between honeybee reproductive castes, again suggesting methylation may have a variable function. These findings provide greater understanding of the role of methylation in caste determination in social insect species.

CASC15：A tumor-associated long non-coding RNA

2020 ◽  
Vol 26 ◽  
Author(s):  
Bei Wang ◽  
Wen Xu ◽  
Yuxuan Cai ◽  
Chong Guo ◽  
Gang Zhou ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Therapeutic Target ◽  
Cancer Colorectal ◽  
Tumor Development ◽  
Pathophysiological Mechanism ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Cancer Côlon ◽  
The Relationship ◽  
Long Non Coding Rna

Background: CASC15, one of long non-coding RNA, is involved in the regulation of many tumor biological processes, and is expected to become a new biological therapeutic target. This paper aims to elucidate the pathophysiological function of CASC15 in various tumors. Methods: The relationship between CASC15 and tumors was analyzed by searching references, and summarizes the specific pathophysiological mechanism of CASC15. Results: LncRNA CASC15 is closely related to tumor development, and has been shown to be abnormally high expressed in all kinds of tumors, including breast cancer, cervical cancer, lung cancer, hepatocellular carcinoma, gastric cancer, bladder cancer, colon cancer, colorectal cancer, cardiac hypertrophy, intrahepatic cholangiocarcinoma, leukemia, melanoma, tongue squamous cell carcinoma, nasopharyngeal carcinoma. However, CASC15 has been found to be downexpressed abnormally in ovarian cancer, glioma and neuroblastoma. Besides, it is identified that CASC15 can affect the proliferation, invasion and apoptosis of tumors. Conclusion: LncRNA CASC15 has the potential to become a new therapeutic target or marker for a variety of tumors.

Epigenetic Mechanisms of Maternal Dietary Protein and Amino Acids Affecting Growth and Development of Offspring

2019 ◽  
Vol 20 (7) ◽  
pp. 727-735 ◽  
Author(s):  
Yi Wu ◽  
Zhibin Cheng ◽  
Yueyu Bai ◽  
Xi Ma
Keyword(s):  
Amino Acids ◽  
Dna Methylation ◽  
Dietary Protein ◽  
Growth And Development ◽  
Later Life ◽  
Biological Macromolecules ◽  
Epigenetic Mechanisms ◽  
Maternal Circulation ◽  
Energy Processing ◽  
Living Organisms

Nutrients can regulate metabolic activities of living organisms through epigenetic mechanisms, including DNA methylation, histone modification, and RNA regulation. Since the nutrients required for early embryos and postpartum lactation are derived in whole or in part from maternal and lactating nutrition, the maternal nutritional level affects the growth and development of fetus and creates a profound relationship between disease development and early environmental exposure in the offspring’s later life. Protein is one of the most important biological macromolecules, involved in almost every process of life, such as information transmission, energy processing and material metabolism. Maternal protein intake levels may affect the integrity of the fetal genome and alter DNA methylation and gene expression. Most amino acids are supplied to the fetus from the maternal circulation through active transport of placenta. Some amino acids, such as methionine, as dietary methyl donor, play an important role in DNA methylation and body’s one-carbon metabolism. The purpose of this review is to describe effects of maternal dietary protein and amino acid intake on fetal and neonatal growth and development through epigenetic mechanisms, with examples in humans and animals.

Epigenetics, Nutrition, Disease and Drug Development

2019 ◽  
Vol 16 (4) ◽  
pp. 386-391 ◽  
Author(s):  
Kenneth Lundstrom
Keyword(s):  
Dna Methylation ◽  
Drug Discovery ◽  
Rna Interference ◽  
Nutritional Requirements ◽  
Signal Pathways ◽  
Disease Development ◽  
Epigenetic Mechanisms ◽  
Epigenetic Changes ◽  
Health And Disease ◽  
Novel Drug

Epigenetic mechanisms comprising of DNA methylation, histone modifications and gene silencing by RNA interference have been strongly linked to the development and progression of various diseases. These findings have triggered research on epigenetic functions and signal pathways as targets for novel drug discovery. Dietary intake has also presented significant influence on human health and disease development and nutritional modifications have proven important in prevention, but also the treatment of disease. Moreover, a strong link between nutrition and epigenetic changes has been established. Therefore, in attempts to develop novel safer and more efficacious drugs, both nutritional requirements and epigenetic mechanisms need to be addressed.

scholarly journals New Aspects of the Epigenetics of Pancreatic Carcinogenesis

Epigenomes ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 18
Author(s):  
Murat Toruner ◽  
Martin E. Fernandez-Zapico ◽  
Christopher L. Pin
Keyword(s):  
Pancreatic Cancer ◽  
Dna Methylation ◽  
Survival Rate ◽  
Epigenetic Mechanisms ◽  
Therapeutic Approaches ◽  
Cancer Epigenetics ◽  
Pancreatic Carcinogenesis ◽  
New Therapeutic Approaches ◽  
Environmental Events ◽  
Underlying Pathogenesis

Pancreatic cancer remains among the deadliest forms of cancer with a 5 year survival rate less than 10%. With increasing numbers being observed, there is an urgent need to elucidate the pathogenesis of pancreatic cancer. While both contribute to disease progression, neither genetic nor environmental factors completely explain susceptibility or pathogenesis. Defining the links between genetic and environmental events represents an opportunity to understand the pathogenesis of pancreatic cancer. Epigenetics, the study of mitotically heritable changes in genome function without a change in nucleotide sequence, is an emerging field of research in pancreatic cancer. The main epigenetic mechanisms include DNA methylation, histone modifications and RNA interference, all of which are altered by changes to the environment. Epigenetic mechanisms are being investigated to clarify the underlying pathogenesis of pancreatic cancer including an increasing number of studies examining the role as possible diagnostic and prognostic biomarkers. These mechanisms also provide targets for promising new therapeutic approaches for this devastating malignancy.

scholarly journals NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pep Amengual-Rigo ◽  
Victor Guallar
Keyword(s):  
Open Source ◽  
Antigen Processing ◽  
High Accuracy ◽  
Biological Processes ◽  
Mhc I ◽  
Mhc Ii ◽  
Prediction Tools ◽  
Immunogenic Peptides ◽  
Physicochemical Descriptors ◽  
Peptide Presentation

AbstractAntigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we present NetCleave, an open-source and retrainable algorithm for the prediction of the C-terminal antigen processing for both MHC-I and MHC-II pathways. NetCleave architecture consists of a neural network trained on 46 different physicochemical descriptors of the cleavage site amino acids. Our results demonstrate that prediction of C-terminal antigen processing achieves high accuracy on MHC-I (AUC of 0.91), while it remains challenging for MHC-II (AUC of 0.66). Moreover, we evaluated the performance of NetCleave and other prediction tools for the evaluation of four independent immunogenicity datasets (H2-Db, H2-Kb, HLA-A*02:01 and HLA-B:07:02). Overall, we demonstrate that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, and we provide one of the first evidence that C-terminal processing predictions may help in the discovery of immunogenic peptides.

scholarly journals Research Progress of Desertification and Its Prevention in Mongolia

2021 ◽  
Vol 13 (12) ◽  
pp. 6861
Author(s):  
Xiya Liang ◽  
Pengfei Li ◽  
Juanle Wang ◽  
Faith Ka Shun Chan ◽  
Chuluun Togtokh ◽  
...  
Keyword(s):  
Model Development ◽  
Mitigation Strategies ◽  
Research Progress ◽  
Prevention Measures ◽  
Interdisciplinary Approaches ◽  
The World ◽  
Impacting Factors ◽  
Decoupling Analysis ◽  
And Control ◽  
The Relationship

Mongolia is a globally crucial region that has been suffering from land desertification. However, current understanding on Mongolia’s desertification is limited, constraining the desertification control and sustainable development in Mongolia and even other parts of the world. This paper studied spatiotemporal patterns, driving factors, mitigation strategies, and research methods of desertification in Mongolia through an extensive review of literature. Results showed that: (i) remote sensing monitoring of desertification in Mongolia has been subject to a relatively low spatial resolution and considerable time delay, and thus high-resolution and timely data are needed to perform a more precise and timely study; (ii) the contribution of desertification impacting factors has not been quantitatively assessed, and a decoupling analysis is desirable to quantify the contribution of factors in different regions of Mongolia; (iii) existing desertification prevention measures should be strengthened in the future. In particular, the relationship between grassland changes and husbandry development needs to be considered during the development of desertification prevention measures; (iv) the multi-method study (particularly interdisciplinary approaches) and desertification model development should be enhanced to facilitate an in-depth desertification research in Mongolia. This study provides a useful reference for desertification research and control in Mongolia and other regions of the world.

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