DNA methylation dynamics of long noncoding RNA during human fetal development

Epigenomics ◽  
2021 ◽  
Author(s):  
Xin Li ◽  
Yuanyuan Fu ◽  
Yue Gao ◽  
Shipeng Shang ◽  
Shuang Guo ◽  
...  

Aim: To determine whether the promoters of long noncoding RNAs (lncRNAs) undergo dynamic changes in DNA methylation during fetal development. Methods: ANOVA and the tissue specificity index were used to identify and validate tissue-specific methylation sites. Age-associated DNA methylation signatures were identified by applying the elastic net method. Results: The lncRNA methylome landscape was characterized in four types of fetal tissue and at three gestational time points, and specific characteristics relative to the tissue of origin and developmental age were identified. Higher levels of lncRNA methylation might be involved in tissue differentiation. LncRNAs harboring age-associated methylation signatures may participate in the fetal developmental process. Conclusion: This study provides novel insights into the role of lncRNA methylomes in fetal tissue specification and development.

PLoS Genetics ◽  
2015 ◽  
Vol 11 (10) ◽  
pp. e1005583 ◽  
Author(s):  
Roderick C. Slieker ◽  
Matthias S. Roost ◽  
Liesbeth van Iperen ◽  
H. Eka D. Suchiman ◽  
Elmar W. Tobi ◽  
...  

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Michele Lanza ◽  
Giuditta Benincasa ◽  
Dario Costa ◽  
Claudio Napoli

Network medicine is a molecular-bioinformatic approach analyzing gene-gene interactions that can perturb the human interactome. This review focuses on epigenetic changes involved in several ocular diseases, such as DNA methylation, histone and nonhistone post-translational modifications, and noncoding RNA regulators. Although changes in aberrant DNA methylation play a major role in the pathogenesis of most ocular diseases, histone modifications are seldom investigated. Hypermethylation in TGM-2 and hypomethylation in MMP-2/CD24 promoter genes may play a crucial role in pterygium development; hypermethylation in regulatory regions of GSTP1 and OGG1 genes appear to be diagnostic biomarkers of cataract; hypomethylation of TGF-β1 promoter may trigger glaucoma onset; hypermethylation of the LOXL1 gene might be associated with pseudoexfoliation syndrome. A large panel of upregulated micro-RNAs (miRNAs), including hsa-hsa-miR-494, hsa-let-7e, hsa-miR-513-1, hsa-miR-513-2, hsa-miR-518c, hsa-miR-129-1, hsa-miR-129-2, hsa-miR-198, hsa-miR-492, hsa-miR-498, hsa-miR-320, hsa-miR-503, and hsa-miR-373,∗ may have a putative role in the development of retinoblastoma. Hypermethylation of H3K4 and hypomethylation of H3K27 at the TGFBIp locus are putative pathogenic mechanisms involved in corneal dystrophies. Determining how, where, and when specific epigenetic changes trigger ocular diseases may provide useful clinical biomarkers for their prevention, diagnosis, and management, as well as innovative drug targets. PF-04523655, a 19-nucleotide methylated double-stranded siRNA targeting the RTP80 gene, showed a dose-related improvement in best-corrected visual acuity (BCVA) in patients affected by diabetic macular edema. The observed results support a clinical network-based research program aimed to clarify the role of epigenetic regulators in the development of ocular diseases and personalized therapy.


2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Tianle He ◽  
Qingyun Chen ◽  
Ke Tian ◽  
Yinzhao Xia ◽  
Guozhong Dong ◽  
...  

circRNAs are a class of endogenous noncoding RNA molecules with closed loop structures. They are mainly responsible for regulating gene expression in eukaryotic cells. With the emergence of high-throughput RNA sequencing (RNA-Seq) and new types of bioinformatics tools, thousands of circRNAs have been discovered, making circRNA one of the research hotspots. Recent studies have shown that circRNAs play an important regulatory role in the growth, reproduction, and formation of livestock products. They can not only regulate mammalian fetal growth and development but also have important regulatory effects on livestock muscle development and lactation. In this review, we briefly introduce the putative biogenic pathways and regulatory functions of circRNA and highlight our understanding of circRNA and its latest advances in fetal development, muscle development, and lactation biogenesis as well as expression in livestock. This review will provide a theoretical basis for the research and development of related industries.


2021 ◽  
Vol 22 (16) ◽  
pp. 8921
Author(s):  
Émile Bélanger ◽  
Catherine Laprise

Epigenetics is a field of study investigating changes in gene expression that do not alter the DNA sequence. These changes are often influenced by environmental or social factors and are reversible. Epigenetic mechanisms include DNA methylation, histone modification, and noncoding RNA. Understanding the role of these epigenetic mechanisms in human diseases provides useful information with regard to disease severity and development. Several studies have searched for the epigenetic mechanisms that regulate allergies and asthma; however, only few studies have used samples of eosinophil, a proinflammatory cell type known to be largely recruited during allergic or asthmatic inflammation. Such studies would enable us to better understand the factors that influence the massive recruitment of eosinophils during allergic and asthmatic symptoms. In this review, we sought to summarize different studies that aimed to discover differential patterns of histone modifications, DNA methylation, and noncoding RNAs in eosinophil samples of individuals with certain diseases, with a particular focus on those with asthma or allergic diseases.


2020 ◽  
Vol 21 (4) ◽  
pp. 1375
Author(s):  
Zhuang Miao ◽  
Yan Wang ◽  
Zhongsheng Sun

Brain-derived neurotrophic factor (BDNF), a critical member of the neurotrophic family, plays an important role in multiple stress-related mental disorders. Although alterations in BDNF in multiple brain regions of individuals experiencing stress have been demonstrated in previous studies, it appears that a set of elements are involved in the complex regulation. In this review, we summarize the specific brain regions with altered BDNF expression during stress exposure. How various environmental factors, including both physical and psychological stress, affect the expression of BDNF in specific brain regions are further summarized. Moreover, epigenetic regulation of BDNF, including DNA methylation, histone modification, and noncoding RNA, in response to diverse types of stress, as well as sex differences in the sensitivity of BDNF to the stress response, is also summarized. Clarification of the underlying role of BDNF in the stress process will promote our understanding of the pathology of stress-linked mental disorders and provide a potent target for the future treatment of stress-related illness.


2020 ◽  
Vol 5 (2) ◽  
pp. 51
Author(s):  
Hafiz Ghulam Muhu-Din Ahmed ◽  
Aziz Ullah ◽  
Abdul Malik ◽  
Babar Islam

The epigenetic alterations are central to numerous human diseases, counting cancer. Typically, cancer has been seen as a hereditary infection, and it is presently getting to be clear that the onset of cancer is gone before by epigenetic anomalies. Examiners within the quickly growing field of epigenetics have recorded broad genomic reconstructing in cancer cells, counting methylation of deoxyribonucleic acid (DNA), chemical alteration of the histone proteins, and RNA-dependent control. Recognizing that carcinogenesis includes both hereditary and epigenetic alterations have driven to distant better an understanding of the molecular pathways that oversee the advancement of cancer and to changes in diagnosing and foreseeing the result of different sorts of cancer. Thinks about of the mechanism (s) of epigenetic control and its reversibility have brought about within the recognizable proof of novel targets which will be valuable in creating unused methodologies for the avoidance and treatment of cancer. Cancer is the appearance of both hereditary and epigenetic adjustments. In spite of the fact that cancer start and movement is overwhelmingly driven by procured hereditary modifications, it is getting to be clear that microenvironment mediated epigenetic annoyances play critical parts in neoplastic advancement. Epigenetics is characterized as heritable changes in quality expression, movement and expression that happen without change in DNA arrangements but which are adequately capable to control the flow of quality expression. The key forms that are mindful for epigenetic control are DNA methylation, adjustments in chromatin (covalent adjustment of center histones), nucleosome situating (physical modification), and post-transcriptional quality direction by noncoding RNA (micro-RNAs). A number of well characterized epigenetic adjustments are connected to distorted quality capacities and modified designs of quality expression that play basic parts within the patho-biology of cancer


2019 ◽  
Vol 25 (6) ◽  
pp. 777-801 ◽  
Author(s):  
Maria Argyraki ◽  
Pauliina Damdimopoulou ◽  
Katerina Chatzimeletiou ◽  
Grigoris F Grimbizis ◽  
Basil C Tarlatzis ◽  
...  

AbstractBACKGROUNDGenomic imprinting is an epigenetic gene regulatory mechanism; disruption of this process during early embryonic development can have major consequences on both fetal and placental development. The periconceptional period and intrauterine life are crucial for determining long-term susceptibility to diseases. Treatments and procedures in assisted reproductive technologies (ART) and adverse in-utero environments may modify the methylation levels of genomic imprinting regions, including insulin-like growth factor 2 (IGF2)/H19, mesoderm-specific transcript (MEST), and paternally expressed gene 10 (PEG10), affecting the development of the fetus. ART, maternal psychological stress, and gestational exposures to chemicals are common stressors suspected to alter global epigenetic patterns including imprinted genes.OBJECTIVE AND RATIONALEOur objective is to highlight the effect of conception mode and maternal psychological stress on fetal development. Specifically, we monitor fetal programming, regulation of imprinted genes, fetal growth, and long-term disease risk, using the imprinted genes IGF2/H19, MEST, and PEG10 as examples. The possible role of environmental chemicals in genomic imprinting is also discussed.SEARCH METHODSA PubMed search of articles published mostly from 2005 to 2019 was conducted using search terms IGF2/H19, MEST, PEG10, imprinted genes, DNA methylation, gene expression, and imprinting disorders (IDs). Studies focusing on maternal prenatal stress, psychological well-being, environmental chemicals, ART, and placental/fetal development were evaluated and included in this review.OUTCOMESIGF2/H19, MEST, and PEG10 imprinted genes have a broad developmental effect on fetal growth and birth weight variation. Their disruption is linked to pregnancy complications, metabolic disorders, cognitive impairment, and cancer. Adverse early environment has a major impact on the developing fetus, affecting mostly growth, the structure, and subsequent function of the hypothalamic–pituitary–adrenal axis and neurodevelopment. Extensive evidence suggests that the gestational environment has an impact on epigenetic patterns including imprinting, which can lead to adverse long-term outcomes in the offspring. Environmental stressors such as maternal prenatal psychological stress have been found to associate with altered DNA methylation patterns in placenta and to affect fetal development. Studies conducted during the past decades have suggested that ART pregnancies are at a higher risk for a number of complications such as birth defects and IDs. ART procedures involve multiple steps that are conducted during critical windows for imprinting establishment and maintenance, necessitating long-term evaluation of children conceived through ART. Exposure to environmental chemicals can affect placental imprinting and fetal growth both in humans and in experimental animals. Therefore, their role in imprinting should be better elucidated, considering the ubiquitous exposure to these chemicals.WIDER IMPLICATIONSDysregulation of imprinted genes is a plausible mechanism linking stressors such as maternal psychological stress, conception using ART, and chemical exposures with fetal growth. It is expected that a greater understanding of the role of imprinted genes and their regulation in fetal development will provide insights for clinical prevention and management of growth and IDs. In a broader context, evidence connecting impaired imprinted gene function to common diseases such as cancer is increasing. This implies early regulation of imprinting may enable control of long-term human health, reducing the burden of disease in the population in years to come.


2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.


2020 ◽  
Vol 26 (6) ◽  
pp. 1283-1296
Author(s):  
K.A. Omarieva ◽  
P.G. Isaeva

Subject. The article addresses problems and prospects for the banking supervision development in the Russian Federation under modern conditions. Objectives. We review the essence and methods of organization of the banking supervision, and identify the main problems and prospects for its development. Methods. To provide valid, reliable and reasoned recommendations, we apply normative and integrated approaches to the study of the banking supervision effectiveness in the current circumstances. Results. The paper investigates main problems and development prospects for the Russian banking supervision. The essential importance of supervision comes from the main role of the banking system in maintaining accounts of economic entities and making settlements. Even minor failures or delays in operations can lead to negative outcomes and disastrous consequences for the entire monetary system and the national economy. Therefore, we highlight issues that require attention, and make proposals for further development of the banking supervision. Conclusions. In the context of dynamically developing economy, the banking practice is becoming more complex. As a result, there is a need for new financial instruments that can reduce risks, increase the speed and efficiency of operations and document flow, and help achieve the world levels of introduced standards.


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