Harnessing targeted DNA methylation and demethylation using dCas9

2019 ◽  
Vol 63 (6) ◽  
pp. 813-825 ◽  
Author(s):  
Christian Pflueger ◽  
Tessa Swain ◽  
Ryan Lister
Keyword(s):  
Dna Methylation ◽  
Disease Modeling ◽  
Aberrant Methylation ◽  
Dna Modification ◽  
Future Directions ◽  
Disease States ◽  
Genome Regulation ◽  
Fundamental Understanding ◽  
Functional Relevance

Abstract DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.

scholarly journals FOLIC ACID, VITAMIN B12, AND DNA METHYLATION: AN UPDATE.

2018 ◽  
Vol 11 (1) ◽  
pp. 17 ◽  
Author(s):  
Bhongir Aparna Varma ◽  
Srilatha Bashetti ◽  
Rajagopalan Vijayaraghavan ◽  
Kumar Sai Sailesh
Keyword(s):  
Dna Methylation ◽  
Folic Acid ◽  
Vitamin B12 ◽  
The Body ◽  
Aberrant Methylation ◽  
Restricted Diet ◽  
Current Review ◽  
Folate And Vitamin B12 ◽  
Methylation Patterns

 Epigenetics is one of the exciting and fastest expanding fields of biology; this is above genetics. Methylation is the process involved in the transfer of methyl group to amino acids, proteins, enzymes and DNA of all the cells, and tissues of the body. During cell-division low folate availability may result in decreased production of thymidine wherein uracil may be substituted in the place of thymidine in the DNA sequence. It was reported that folate and Vitamin B12 restricted diet resulted in aberrant methylation patterns. The current review was undertaken to explore the role of folic acid and Vitamin B12 in DNA methylation.

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.

scholarly journals The Role of Aberrant DNA Methylation in Misregulation of Gene Expression in Gonadotroph Nonfunctioning Pituitary Tumors

Cancers ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1650 ◽  
Author(s):  
Paulina Kober ◽  
Joanna Boresowicz ◽  
Natalia Rusetska ◽  
Maria Maksymowicz ◽  
Agnieszka Paziewska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Pituitary Tumors ◽  
Aberrant Methylation ◽  
Qrt Pcr ◽  
Open Sea ◽  
Aberrant Dna Methylation ◽  
Positive Correlations ◽  
Affect Gene Expression

Gonadotroph nonfunctioning pituitary adenomas (NFPAs) are common intracranial tumors, but the role of aberrant epigenetic regulation in their development remains poorly understood. In this study, we investigated the effect of impaired CpG methylation in NFPAs. We determined DNA methylation and transcriptomic profiles in 32 NFPAs and normal pituitary sections using methylation arrays and sequencing, respectively. Ten percent of differentially methylated CpGs were correlated with gene expression, and the affected genes are involved in a variety of tumorigenesis-related pathways. Different proportions of gene body and promoter region localization were observed in CpGs with negative and positive correlations between methylation and gene expression, and different proportions of CpGs were located in ‘open sea’ and ‘shelf/shore’ regions. The expression of ~8% of genes differentially expressed in NFPAs was related to aberrant methylation. Methylation levels of seven CpGs located in the regulatory regions of FAM163A, HIF3A and PRSS8 were determined by pyrosequencing, and gene expression was measured by qRT-PCR and immunohistochemistry in 83 independent NFPAs. The results clearly confirmed the negative correlation between methylation and gene expression for these genes. By identifying which aberrantly methylated CpGs affect gene expression in gonadotrophinomas, our data confirm the role of aberrant methylation in pathogenesis of gonadotroph NFPAs.

scholarly journals Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases

2017 ◽  
Vol 1 (4) ◽  
pp. 333-349 ◽  
Author(s):  
Ian O'Neill ◽  
Zoe Schofield ◽  
Lindsay J. Hall
Keyword(s):  
Critical Period ◽  
Immune Modulation ◽  
Future Directions ◽  
Immune Development ◽  
Disease States ◽  
Physiological Processes ◽  
Inflammatory Bowel ◽  
Different Strains ◽  
Immune Maturation

The gut-associated microbiota is essential for multiple physiological processes, including immune development. Acquisition of our initial pioneer microbial communities, including the dominant early life genus Bifidobacterium, occurs at a critical period of immune maturation and programming. Bifidobacteria are resident microbiota members throughout our lifetime and have been shown to modulate specific immune cells and pathways. Notably, reductions in this genus have been associated with several diseases, including inflammatory bowel disease. In this review, we provide an overview of bifidobacteria profiles throughout life and how different strains of bifidobacteria have been implicated in immune modulation in disease states. The focus will be examining preclinical models and outcomes from clinical trials on immune-linked chronic conditions. Finally, we highlight some of the important unresolved questions in relation to Bifidobacterium-mediated immune modulation and implications for future directions, trials, and development of new therapies.

scholarly journals FOLIC ACID, VITAMIN B12, AND DNA METHYLATION: AN UPDATE.

2018 ◽  
Vol 11 (1) ◽  
pp. 17
Author(s):  
Bhongir Aparna Varma ◽  
Srilatha Bashetti ◽  
Rajagopalan Vijayaraghavan ◽  
Kumar Sai Sailesh
Keyword(s):  
Dna Methylation ◽  
Folic Acid ◽  
Vitamin B12 ◽  
The Body ◽  
Aberrant Methylation ◽  
Restricted Diet ◽  
Current Review ◽  
Folate And Vitamin B12 ◽  
Methylation Patterns

 Epigenetics is one of the exciting and fastest expanding fields of biology; this is above genetics. Methylation is the process involved in the transfer of methyl group to amino acids, proteins, enzymes and DNA of all the cells, and tissues of the body. During cell-division low folate availability may result in decreased production of thymidine wherein uracil may be substituted in the place of thymidine in the DNA sequence. It was reported that folate and Vitamin B12 restricted diet resulted in aberrant methylation patterns. The current review was undertaken to explore the role of folic acid and Vitamin B12 in DNA methylation.

scholarly journals Homologue Pairing in Flies and Mammals: Gene Regulation When Two Are Involved

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Manasi S. Apte ◽  
Victoria H. Meller
Keyword(s):  
Gene Expression ◽  
Chromosome Segregation ◽  
Germ Cells ◽  
Developmentally Regulated ◽  
X Chromosomes ◽  
Disease States ◽  
Genome Regulation ◽  
Normal Expression ◽  
Normal Pairing

Chromosome pairing is usually discussed in the context of meiosis. Association of homologues in germ cells enables chromosome segregation and is necessary for fertility. A few organisms, such as flies, also pair their entire genomes in somatic cells. Most others, including mammals, display little homologue pairing outside of the germline. Experimental evidence from both flies and mammals suggests that communication between homologues contributes to normal genome regulation. This paper will contrast the role of pairing in transmitting information between homologues in flies and mammals. In mammals, somatic homologue pairing is tightly regulated, occurring at specific loci and in a developmentally regulated fashion. Inappropriate pairing, or loss of normal pairing, is associated with gene misregulation in some disease states. While homologue pairing in flies is capable of influencing gene expression, the significance of this for normal expression remains unknown. The sex chromosomes pose a particularly interesting situation, as females are able to pair X chromosomes, but males cannot. The contribution of homologue pairing to the biology of the X chromosome will also be discussed.

scholarly journals Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Matthew WK Wong ◽  
Anbupalam Thalamuthu ◽  
Nady Braidy ◽  
Karen A Mather ◽  
Yue Liu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Lipids ◽  
Critical Role ◽  
Complex Interplay ◽  
Disease States ◽  
Twin Model ◽  
Genome Wide ◽  
Gene Transcripts ◽  
Health And Disease

The critical role of blood lipids in a broad range of health and disease states is well recognised but less explored is the interplay of genetics and environment within the broader blood lipidome. We examined heritability of the plasma lipidome among healthy older-aged twins (75 monozygotic/55 dizygotic pairs) enrolled in the Older Australian Twins Study (OATS) and explored corresponding gene expression and DNA methylation associations. 27/209 lipids (13.3%) detected by liquid chromatography-coupled mass spectrometry (LC-MS) were significantly heritable under the classical ACE twin model (h2 = 0.28–0.59), which included ceramides (Cer) and triglycerides (TG). Relative to non-significantly heritable TGs, heritable TGs had a greater number of associations with gene transcripts, not directly associated with lipid metabolism, but with immune function, signalling and transcriptional regulation. Genome-wide average DNA methylation (GWAM) levels accounted for variability in some non-heritable lipids. We reveal a complex interplay of genetic and environmental influences on the ageing plasma lipidome.

scholarly journals DNA methylation reprogramming during seed development and its functional relevance in seed size/weight determination in chickpea

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Mohan Singh Rajkumar ◽  
Khushboo Gupta ◽  
Niraj Kumar Khemka ◽  
Rohini Garg ◽  
Mukesh Jain
Keyword(s):  
Dna Methylation ◽  
Seed Development ◽  
Seed Size ◽  
Regulatory Networks ◽  
Differentially Methylated Region ◽  
Gene Body ◽  
Chickpea Cultivar ◽  
Gene Regulatory ◽  
Functional Relevance

AbstractSeed development is orchestrated via complex gene regulatory networks and pathways. Epigenetic factors may also govern seed development and seed size/weight. Here, we analyzed DNA methylation in a large-seeded chickpea cultivar (JGK 3) during seed development stages. Progressive gain of CHH context DNA methylation in transposable elements (TEs) and higher frequency of small RNAs in hypermethylated TEs during seed development suggested a role of the RNA-dependent DNA methylation pathway. Frequency of intragenic TEs was higher in CHH context differentially methylated region (DMR) associated differentially expressed genes (DEGs). CG context hyper/hypomethylation within the gene body was observed for most of DMR-associated DEGs in JGK 3 as compared to small-seeded chickpea cultivar (Himchana 1). We identified candidate genes involved in seed size/weight determination exhibiting CG context hypermethylation within the gene body and higher expression in JGK 3. This study provides insights into the role of DNA methylation in seed development and seed size/weight determination in chickpea.

scholarly journals THU0004 GENOME-WIDE DNA METHYLATION PROFILING IN MONOCYTES FROM PRIMARY ANTIPHOSPHOLIPID SYNDROME PATIENTS IDENTIFIES AN ABERRANT METHYLATION SIGNATURE ASSOCIATED WITH THEIR ATHEROTHROMBOTIC PHENOTYPE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 214.2-215
Author(s):  
C. Perez-Sanchez ◽  
A. M. Patiño-Trives ◽  
M. A. Aguirre ◽  
P. S. Laura ◽  
M. Luque-Tévar ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Association Studies ◽  
Methylation Profile ◽  
Aberrant Methylation ◽  
Functional Classification ◽  
Research Support ◽  
Genome Wide

Background:Recent studies underlined the crucial role of DNA methylation in several autoimmune diseases by altering gene expression profiles, thus influencing disease severity. Yet, aberrant methylation patterns in monocytes, key players in the pathogenesis of APS patients, has not been evaluated.Objectives:To analyze the genome-wide DNA methylation profile of monocytes from APS patients and its relationship with the cardiovascular (CV) pathology. 2. To evaluate the role of antiphospholipid antibodies (aPL) in the regulation of this process.Methods:Thirty-three APS patients and 15 healthy donors (HD) were included in the study. Monocytes were isolated from peripheral blood by positive immunomagnetic selection. The Illumina Infinium Methylation EPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs (TSS1500, TSS200, 5UTR, 3UTR, first exon, intergenic, gene body). Beta values (β) estimating methylation levels were obtained at each CpG site, and differentially methylated genes (DMG) between APS and HD were identified. Functional classification of that genes was carried out by gene ontology analysis (PANTHER database). Gene expression of selected DMG genes was evaluated by RT-PCR. CV-risk parameters, including carotid intima-media thickness (CIMT) and microvascular endothelial function were further assessed, and correlation/association studies were developed with clinical and analytical variables. The effects of aPLs were also evaluated byin vitrostudies.Results:Genome-wide DNA methylation analysis identified 813 DMG, including 279 hypomethylated and 534 hypermethylated. Functional classification of these genes revealed signatures associated with biological processes and pathways related to their clinical profile, including immune response, adhesion, oxidative stress and vascular signaling. Correlation and association studies showed that the methylation levels of genes related to immune response were associated with the CV-risk score, aGAPSS (CCR2, TXLNB, GLIPR), type of thrombosis (SIGLEC11, COLEC11, LRRC16A, AHSA1, TRIL) and aPL titers (CLEC4G, RGS4, HLA-DPA1, GBP6, RAET1E, HLA-G, HLA-DPA1, HLA-H, TXLNB). Besides, methylation levels of DMG related to vascular signaling and adhesion processes were associated with the presence of thrombotic recurrences (VEGFA, MAPK14, ITGA8, EPCAM, PCDHA6, DLG1) as well as with traditional CV-risk factor such as hypertension and dyslipidemia (ITGA11, DSCAM, CLEC4F, CDH4, LTBP2, PCDHB14). In addition, methylation levels of DMG genes related to oxidative stress (GP2, PGD, ADH1) were associated with microvascular endothelial dysfunction. An altered mRNA expression of some of those genes with aberrant methylation and related to increased CV-risk and thrombotic recurrences in APS was also identified. Both, abnormal methylation and transcription levels of several genes were further associated with a pathological increase of the CIMT. Finally, in vitro studies supported the role of aPLs as key players in the altered methylation and transcriptomic profiles of APS patients.Conclusion:APS patients showed an impaired methylation profile in monocytes of genes associated with clinical features of the disease, including aPL titers, CV risk, thrombotic recurrences, endothelial dysfunction and early atherosclerosis. These results offered a map to the monocytes methylome and shed light on the pathophysiology of APS, paving the way for the development of new, more effective biomarkers and therapeutics.Acknowledgments:Funded by ISCIII (PI18/0837 and RIER RD16/0012/0015) co-funded with FEDER.Disclosure of Interests:Carlos Perez-Sanchez: None declared, Alejandra M. Patiño-Trives: None declared, Maria A Aguirre: None declared, Pérez Sánchez Laura: None declared, María Luque-Tévar: None declared, Iván Arias de la Rosa: None declared, Carmen Torres-Granados: None declared, Maria del Carmen Abalos-Aguilera: None declared, Pedro Seguí Azpilcueta: None declared, Javier Rodríguez: None declared, Esteban Ballester: None declared, Nuria Barbarroja Puerto Grant/research support from: ROCHE and Pfizer., Speakers bureau: ROCHE and Celgene., Eduardo Collantes Estevez Grant/research support from: ROCHE and Pfizer, Speakers bureau: ROCHE, Lilly, Bristol and Celgene, Chary Lopez-Pedrera Grant/research support from: ROCHE and Pfizer.

On Future Directions in Pathology

1982 ◽  
Vol 40 ◽  
pp. 274-277
Author(s):  
Benjamin F. Trump ◽  
Irene K. Berezesky ◽  
Raymond T. Jones
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Clinical Pathology ◽  
Future Directions ◽  
Diagnostic Pathology ◽  
The Past ◽  
Transmission Electron ◽  
Organ Systems ◽  
The Many

The role of electron microscopy and associated techniques is assured in diagnostic pathology. At the present time, most of the progress has been made on tissues examined by transmission electron microscopy (TEM) and correlated with light microscopy (LM) and by cytochemistry using both plastic and paraffin-embedded materials. As mentioned elsewhere in this symposium, this has revolutionized many fields of pathology including diagnostic, anatomic and clinical pathology. It began with the kidney; however, it has now been extended to most other organ systems and to tumor diagnosis in general. The results of the past few years tend to indicate the future directions and needs of this expanding field. Now, in addition to routine EM, pathologists have access to the many newly developed methods and instruments mentioned below which should aid considerably not only in diagnostic pathology but in investigative pathology as well.

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