scholarly journals DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 684
Author(s):  
Loredana Poeta ◽  
Denise Drongitis ◽  
Lucia Verrillo ◽  
Maria Giuseppina Miano
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Fragile X ◽  
Neuromuscular Diseases ◽  
Transcriptional Silencing ◽  
Common Disease ◽  
Dna Hypermethylation ◽  
Disease Modifier

Unstable repeat disorders comprise a variable group of incurable human neurological and neuromuscular diseases caused by an increase in the copy number of tandem repeats located in various regions of their resident genes. It has become clear that dense DNA methylation in hyperexpanded non-coding repeats induces transcriptional silencing and, subsequently, insufficient protein synthesis. However, the ramifications of this paradigm reveal a far more profound role in disease pathogenesis. This review will summarize the significant progress made in a subset of non-coding repeat diseases demonstrating the role of dense landscapes of 5-methylcytosine (5mC) as a common disease modifier. However, the emerging findings suggest context-dependent models of 5mC-mediated silencing with distinct effects of excessive DNA methylation. An in-depth understanding of the molecular mechanisms underlying this peculiar group of human diseases constitutes a prerequisite that could help to discover novel pathogenic repeat loci, as well as to determine potential therapeutic targets. In this regard, we report on a brief description of advanced strategies in DNA methylation profiling for the identification of unstable Guanine-Cytosine (GC)-rich regions and on promising examples of molecular targeted therapies for Fragile X disease (FXS) and Friedrich ataxia (FRDA) that could pave the way for the application of this technique in other hypermethylated expansion disorders.

scholarly journals DNA Methylation, Mechanisms of FMR1 Inactivation and Therapeutic Perspectives for Fragile X Syndrome

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 296
Author(s):  
Veronica Nobile ◽  
Cecilia Pucci ◽  
Pietro Chiurazzi ◽  
Giovanni Neri ◽  
Elisabetta Tabolacci
Keyword(s):  
Dna Methylation ◽  
Fragile X Syndrome ◽  
Intellectual Development ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Fragile X ◽  
Fmr1 Gene ◽  
Critical Question ◽  
Cgg Repeat

Among the inherited causes of intellectual disability and autism, Fragile X syndrome (FXS) is the most frequent form, for which there is currently no cure. In most FXS patients, the FMR1 gene is epigenetically inactivated following the expansion over 200 triplets of a CGG repeat (FM: full mutation). FMR1 encodes the Fragile X Mental Retardation Protein (FMRP), which binds several mRNAs, mainly in the brain. When the FM becomes methylated at 10–12 weeks of gestation, the FMR1 gene is transcriptionally silent. The molecular mechanisms involved in the epigenetic silencing are not fully elucidated. Among FXS families, there is a rare occurrence of males carrying a FM, which remains active because it is not methylated, thus ensuring enough FMRPs to allow for an intellectual development within normal range. Which mechanisms are responsible for sparing these individuals from being affected by FXS? In order to answer this critical question, which may have possible implications for FXS therapy, several potential epigenetic mechanisms have been described. Here, we focus on current knowledge about the role of DNA methylation and other epigenetic modifications in FMR1 gene silencing.

scholarly journals Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing

2021 ◽  
Author(s):  
Igor Stevanovski ◽  
Sanjog R. Chintalaphani ◽  
Hasindu Gamaarachchi ◽  
James M. Ferguson ◽  
Sandy S. Pineda ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Fragile X ◽  
Genetic Diagnosis ◽  
Neuromuscular Diseases ◽  
Nanopore Sequencing ◽  
Molecular Tests ◽  
Genetic Landscape ◽  
Long Read ◽  
Short Tandem

ABSTRACTShort-tandem repeat (STR) expansions are an important class of pathogenic genetic variants. Over forty neurological and neuromuscular diseases are caused by STR expansions, with 37 different genes implicated to date. Here we describe the use of programmable targeted long-read sequencing with Oxford Nanopore’s ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single, simple assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of expanded and non-expanded STR sites. In doing so, the assay correctly diagnoses all individuals in a cohort of patients (n = 27) with various neurogenetic diseases, including Huntington’s disease, fragile X syndrome and cerebellar ataxia (CANVAS) and others. Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing, and identifies non-canonical STR motif conformations and internal sequence interruptions. Even in our relatively small cohort, we observe a wide diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of STR expansion disorders. Finally, we show how the flexible inclusion of pharmacogenomics (PGx) genes as secondary ReadUntil targets can identify clinically actionable PGx genotypes to further inform patient care, at no extra cost. Our study addresses the need for improved techniques for genetic diagnosis of STR expansion disorders and illustrates the broad utility of programmable long-read sequencing for clinical genomics.One sentence summaryThis study describes the development and validation of a programmable targeted nanopore sequencing assay for parallel genetic diagnosis of all known pathogenic short-tandem repeats (STRs) in a single, simple test.

scholarly journals DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral modelAiptasia

2017 ◽  
Author(s):  
Yong Li ◽  
Yi Jin Liew ◽  
Guoxin Cui ◽  
Maha J Cziesielski ◽  
Noura Zahran ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Model System ◽  
Epigenetic Mechanism ◽  
Symbiotic Relationship ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
Spurious Transcription ◽  
Coral Reef Ecosystems

The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research is focusing on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, which have been implicated in transcriptional regulation and acclimation to environmental change, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model systemAiptasia. We find methylated genes are marked by histone H3K36me3 and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes such as immunity, apoptosis, phagocytosis recognition and phagosome formation, and unveil intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis during symbiosis.

scholarly journals Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Jing Shen ◽  
Shuang Wang ◽  
Abby B. Siegel ◽  
Helen Remotti ◽  
Qiao Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Potential Role ◽  
Dna Hypermethylation ◽  
Two Phase ◽  
Genome Wide ◽  
Phase Study ◽  
A Genome ◽  
Genome Wide Expression ◽  
Inactive Chromatin

Background.Previous studies, including ours, have examined the regulation of microRNAs (miRNAs) by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC) is unclear.Subjects/Methods.Using a two-phase study design, we conducted genome-wide screening for DNA methylation and miRNA expression to explore the potential role of methylation alterations in miRNAs regulation.Results.We found that expressions of 25 miRNAs were statistically significantly different between tumor and nontumor tissues and perfectly differentiated HCC tumor from nontumor. Six miRNAs were overexpressed, and 19 were repressed in tumors. Among 133 miRNAs with inverse correlations between methylation and expression, 8 miRNAs (6%) showed statistically significant differences in expression between tumor and nontumor tissues. Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells.Conclusion.These data suggest that the expressions of miR-125b and miR-199a are dramatically regulated by DNA hypermethylation that plays a key role in hepatocarcinogenesis.

scholarly journals ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Stefan Milosavljevic ◽  
Tony Kuo ◽  
Samuele Decarli ◽  
Lucas Mohn ◽  
Jun Sese ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Sequence Similarity ◽  
Ground Truth ◽  
Whole Genome ◽  
Initial Dataset ◽  
Quality Checks ◽  
Living Organisms ◽  
Set Up

Abstract Background Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid’s parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization. Results We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC’s performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO’s output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data. Conclusions The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO.

Semenogelin 1 Expression in Myeloma Cells: Interaction between DNA Methylation, MeCP2 Protein and Specific Cytokines.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2242-2242
Author(s):  
Yana Zhang ◽  
Zhiqing Wang ◽  
Jian Zhang ◽  
Benjamin Farmer ◽  
Seah H. Lim
Keyword(s):  
Dna Methylation ◽  
Protein Binding ◽  
Tumor Cells ◽  
Molecular Mechanisms ◽  
Hematologic Malignancies ◽  
Cytosine Residue ◽  
Normal Tissues ◽  
Mecp2 Protein ◽  
Cpg Dinucleotide

Abstract Semenogelin (SEMG) 1 is a protein of semen coagulum with limited expression in normal tissues. It plays an important role in sperm clotting and is normally degraded into smaller fragments by prostate-specific antigen. The gene encoding SEMG 1 has been localized to the long arm of chromosome 20, a region of chromosome 20 that is frequently deleted in myeloproliferative diseases and myelodysplastic syndrome. We previously found SEMG 1 to be aberrantly expressed by tumor cells of hematologic malignancies, including multiple myeloma (MM). The aberrant expression of SEMG 1 in tumor cells of hematologic malignancies is associated in vivo with the generation of high titers IgG directed at SEMG 1 protein, suggesting the immunogenicity of the protein in the cancer-bearing patients. The combination of being immunogenic in cancer patients and limited expression in normal tissue expression makes SEMG 1 a potential candidate protein for tumor vaccines. In this study, we have set out to determine the molecular mechanisms associated with SEMG 1 expression in MM. Treatment of SEMG 1-positive MM cells with IL-4 and IL-6 resulted in the upregulation of SEMG 1 expression. In SEMG 1-negative MM cells, SEMG 1 expression could only be upregulated by IL-4 and IL-6 after pre-treatment with 5-azacytidine, suggesting that DNA methylation is likely the primary regulatory mechanism for SEMG 1 expression. Treatment of SEMG 1-negative MM cells induced SEMG 1 gene and protein expression. SEMG 1 promoter only has one CpG dinucleotide, located at position -11 of the gene. Bisulfite conversion and nucleotide sequencing was carried out on the genomic DNA from MM cells. MM cells that did not express SEMG 1 were 100% methylated. In contrast, 100% of the sequences obtained from SEMG 1-positive MM cells were unmethylated at the cytosine residue of the CpG dinucleotide. Induction of SEMG 1 expression by 5-azacytidine was associated with a decrease in the % of methylation of this cytosine residue, from 100% to 20%. These results, therefore, further implicate the role of DNA methylation in the primary regulation of SEMG 1 expression. Applying antibodies directed at MeCP2 in chromatin immunoprecipiation, MeCP2 protein binding to the SEMG 1 promoter sequence of MM cell lines and fresh MM cells was correlated to SEMG 1 gene silencing, suggesting the likely role of the MeCP2 protein in SEMG 1 gene repression. Further analysis by promoter truncation studies indicated the dependence of the promoter function on the sequence spanning the two putative GATA-1 binding sites within the gene. Using a reporter gene expression system, both IL-4 and IL-6 were found to upregulate SEMG 1 via their effect on the hypomethylated promoter gene. The effects of IL-4 and IL-6 on the function of the SEMG 1 promoter were dose dependent. In conclusion, the present study demonstrates that SEMG 1 expression in MM cells is regulated through the interaction between primary regulatory effect of promoter methylation, MeCP2 protein binding and the secondary effect of specific cytokines. Our findings provide insight into the molecular mechanisms affecting SEMG 1 expression and suggest the possible use of hypomethylating agents to upregulate SEMG 1 expression in tumor cells. Obviously, it remains to be determined whether or not there is a differential dose response among the different normal tissues in their sensitivity to the antigen-inducing effect of these agents.

scholarly journals SLC4A11 and MFSD3 Gene Expression Changes in Deoxynivalenol Treated IPEC-J2 Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Yafei Xu ◽  
Xiaolei Chen ◽  
Luchen Yu ◽  
Yi Wang ◽  
Haifei Wang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Methylation ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
The Novel ◽  
Animal Cells ◽  
Cytotoxic Effects ◽  
M Phase ◽  
Detection Of Biomarkers

Deoxynivalenol (DON) caused serious cytotoxicity for animal cells. However, genes involved in regulating DON toxicity and the underlying molecular mechanisms remain largely unknown. This study explored the role of SLC4A11 and MFSD3 in alleviating DON toxicity and analyzed the DNA methylation changes of these two genes. Viability and cell cycle analysis showed that DON exposure decreased the IPEC-J2 viability (P < 0.01), blocked the cell cycle in the G2/M phase (P < 0.01), and increased the rate of apoptosis (P < 0.05). Expression of the SLC4A11 and MFSD3 genes was significantly downregulated upon DON exposure (P < 0.01). Overexpression of SLC4A11 and MFSD3 can enhance the cell viability (P < 0.01). DNA methylation assays indicated that promoter methylation of SLC4A11 (mC-1 and mC-23) and MFSD3 (mC-1 and mC-12) were significantly higher compared with those in the controls and correlated negatively with mRNA expression (P < 0.05). Further analysis showed that mC-1 of SLC4A11 and MFSD3 was located in transcription factor binding sites for NF-1 and Sp1. Our findings revealed the novel biological functions of porcine SLC4A11 and MFSD3 genes in regulating the cytotoxic effects induced by DON, and may contribute to the detection of biomarkers and drug targets for predicting and eliminating the potential toxicity of DON.

scholarly journals Novel Role of UHRF1 in DNA methylation-mediated repression of latent HIV-1

2021 ◽  
Author(s):  
Roxane Verdikt ◽  
Sophie Bouchat ◽  
Alexander O. Pasternak ◽  
Lorena Nestola ◽  
Gilles Darcis ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Ex Vivo ◽  
Proof Of Concept ◽  
Methylation Inhibitor ◽  
Dna Methylation Inhibitor ◽  
Latent Hiv ◽  
Hiv 1 ◽  
Patient Cell

The multiplicity, heterogeneity and dynamic nature of HIV-1 latency mechanisms are reflected in the current lack of functional cure for HIV-1 and in the various reported ex vivo potencies of latency-reversing agents. Here, we investigated the molecular mechanisms underlying the potency of the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC) in HIV-1 latency reversal. Doing so, we uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator UHRF1 to the HIV-1 promoter. We further demonstrated the role of UHRF1 in DNA methylation-mediated silencing of the latent HIV-1 promoter. As a proof-of-concept to this molecular characterization, we showed that pharmacological downregulation of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent reactivation of latent HIV-1. Together, we identify UHRF1 as a novel actor in HIV-1 gene silencing and highlight that it constitutes a new molecular target for HIV-1 curative strategies.

scholarly journals The impact of epigenetics on the development of neurodegenerative diseases

2021 ◽  
Author(s):  
Gustavo Hugo de Souza Faria
Keyword(s):  
Dna Methylation ◽  
Neurodegenerative Diseases ◽  
Molecular Mechanisms ◽  
Disease Onset ◽  
Specific Protein ◽  
Aberrant Methylation ◽  
Transcriptional Dysregulation ◽  
Altered Gene ◽  
The Impact

Introduction: Neurodegenerative diseases affect thousands of people in Brazil and have been increasing in frequency with the aging population. However, little is known about the molecular mechanisms and biomarkers of these diseases, which leads to a medical approach based on symptomatic and unresolving characteristics. Epigenetics, including DNA methylation, histone modifications, and changes in regulatory RNAs, emerges as a tool for prevention of neurodegenerative diseases. Objectives: To review studies that discuss the role of epigenetics in the development of neurodegenerative diseases. Methodology: This study involved an integrative review of papers published from 2016 to 2021 by searching PubMed and Scopus. Results: The studies showed that there is evidence that epigenetic mechanisms interfere with the development of major neurodegenerative diseases. Huntington’s disease presents an altered gene from birth, but transcriptional dysregulation is characteristic of the pathology that may be correlated to the age of disease onset in the cortex. In Parkinson’s disease dysregulation of expression of a specific protein is believed to play a central role in the disease and occurs through aberrant methylation that controls activation or suppression. In relation to Alzheimer’s disease, it has been found that deregulated DNA methylation and demethylation is linked to the onset and progression of the disease. In addition, these epigenetic factors are interfered with by diet, aging, and exercise. Conclusions: Investment in epigenetic studies is needed to understand possible markers of neurodegenerative diseases, for early diagnosis and the formation of epidrugs with the ability to treat.

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