SAMPLE PREPARATION FOR DOWNSTREAM ANALYSIS OF EPIGENETIC MODIFICATIONS (DNA METHYLATION AND HISTONE MODIFICATIONS) IN THE REGULATION OF GENE EXPRESSION

The natural products obtained from plants, bacteria, fungi and marine have been used in the treatment of human diseases throughout the centuries. These compounds of them also interfere with the expression of genes by influencing epigenetic mechanisms. Recent researches showed significant outcomes suggesting that epigenetic silencing of the main regulatory genesis a sign of cancer onset and its progression. Epigenetic mechanisms that regulate expression of genes without mutation in the DNA are carried through DNA methylation, histone modification, chromatin remodeling and RNA interference. DNA methylation observed in the promoter regions of genes and prevents binding of the transcription factors by suppressing gene expression or by altering the nucleosome package of DNA, and may also directly inhibit transcription. Plant based products, such as curcumin, flavonoids, genistein, have been shown to exhibit cytostatic and apoptotic activities by influencing DNA methylation-based gene expression regulation in tumor cells. Additionally, natural products such as sulforaphane, retinoic acid, cucurbitacin B, casein Q, parthenolide, folate, cobalamin, pyridoxine and methionine also are used as anti-cancer agents based on DNA methylation. On the other hand, microRNAs (miRNAs) play a particular role in the epigenetic regulation of gene expression in post-transcription and post-translation processes. Quercetin, tryptolide, and honokiol are the natural compounds used in miRNA based agents. Histone modifications, which also affect the chromatin structure, play an important role in the initiation and progression of carcinogenesis as well as regulation of gene expression. As expected particular inhibitors of histone acetyltransferases (HATs) and histone deacetylase (HDAC) enzymes which are responsible of histone modifications have been developed for epigenetic intervention in cancer treatment. Numerous natural compounds are known to affect histone-modifying enzymes; such as romidepsin, epigallocatechingallate (EGCG), daidzein, sulphorafane, glucoraphanin, parthenolide, triptolide, sinapinic acid. Natural epigenetic modulators developed for epigenetic mechanisms enable the destruction of apoptotic, necrotic or autophagic pathways of tumor cells. Beside epigenetic mechanisms, these products exert their effects through influencing the cell cycle, DNA repair, and epigenetic mechanisms which modulate gene expression. More extensive in vitro and in vivo studies are required to investigate the effect of natural product-based epigenetic agents which seems to be very promising for future cancer treatment approaches.

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Characterization of histone modifications associated with DNA damage repair genes upon exposure to gamma rays in Arabidopsis seedlings

Journal of Radiation Research ◽

10.1093/jrr/rrw077 ◽

2016 ◽

Vol 57 (6) ◽

pp. 646-654 ◽

Cited By ~ 9

Author(s):

Suvendu Mondal ◽

Young Sam Go ◽

Seung Sik Lee ◽

Byung Yeoup Chung ◽

Jin-Hong Kim

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Gamma Irradiation ◽

Histone Modifications ◽

Gamma Rays ◽

Regulation Of Gene Expression ◽

Chromatin Modification ◽

Histone H3 ◽

Marker Genes ◽

Transcription Start Sites

Abstract Dynamic histone modifications play an important role in controlling gene expression in response to various environmental cues. This mechanism of regulation of gene expression is important for sessile organisms, like land plants. We have previously reported consistent upregulation of various marker genes in response to gamma rays at various post-irradiation times. In the present study, we performed various chromatin modification analyses at selected loci using the standard chromatin immunoprecipitation procedure, and demonstrate that upregulation of these genes is associated with histone H3 lysine 4 tri-methylation (H3K4me3) at the gene body or transcription start sites of these loci. Further, at specific AtAgo2 loci, both H3K4me3 and histone H3 lysine 9 acetylation (H3K9ac) are important in controlling gene expression in response to gamma irradiation. There was no change in DNA methylation in these selected loci. We conclude that specific histone modification such as H3K4me3 and H3K9ac may be more important in activating gene expression in these selected loci in response to gamma irradiation than a change in DNA methylation.

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MicroRNAs, epigenetics and disease

Essays in Biochemistry ◽

10.1042/bse0480165 ◽

2010 ◽

Vol 48 ◽

pp. 165-185 ◽

Cited By ~ 24

Author(s):

Asli Silahtaroglu ◽

Jan Stenvang

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Histone Modifications ◽

Target Genes ◽

Regulation Of Gene Expression ◽

Specific Gene ◽

Rna Molecules ◽

Normal Differentiation ◽

Affect Gene Expression ◽

Epigenetic Processes

Epigenetics is defined as the heritable chances that affect gene expression without changing the DNA sequence. Epigenetic regulation of gene expression can be through different mechanisms such as DNA methylation, histone modifications and nucleosome positioning. MicroRNAs are short RNA molecules which do not code for a protein but have a role in post-transcriptional silencing of multiple target genes by binding to their 3′ UTRs (untranslated regions). Both epigenetic mechanisms, such as DNA methylation and histone modifications, and the microRNAs are crucial for normal differentiation, development and maintenance of tissue-specific gene expression. These mechanisms also explain how cells with the same DNA content can differentiate into cells with different functions. Changes in epigenetic processes can lead to changes in gene function, cancer formation and progression, as well as other diseases. In the present chapter we will mainly focus on microRNAs and methylation and their implications in human disease, mainly in cancer.

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Out of sight, out of mind? Germ cells and the potential impacts of epigenomic drugs

F1000Research ◽

10.12688/f1000research.15935.1 ◽

2018 ◽

Vol 7 ◽

pp. 1967 ◽

Cited By ~ 5

Author(s):

Ellen G. Jarred ◽

Heidi Bildsoe ◽

Patrick S. Western

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Histone Modifications ◽

Germ Cells ◽

Epigenetic Modifications ◽

Reproductive Age ◽

Specific Gene ◽

And Function ◽

Substantial Interest ◽

Target Effects

Epigenetic modifications, including DNA methylation and histone modifications, determine the way DNA is packaged within the nucleus and regulate cell-specific gene expression. The heritability of these modifications provides a memory of cell identity and function. Common dysregulation of epigenetic modifications in cancer has driven substantial interest in the development of epigenetic modifying drugs. Although these drugs have the potential to be highly beneficial for patients, they act systemically and may have “off-target” effects in other cells such as the patients’ sperm or eggs. This review discusses the potential for epigenomic drugs to impact on the germline epigenome and subsequent offspring and aims to foster further examination into the possible effects of these drugs on gametes. Ultimately, the information gained by further research may improve the clinical guidelines for the use of such drugs in patients of reproductive age.

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Epigenetics and sarcoidosis

European Respiratory Review ◽

10.1183/16000617.0076-2021 ◽

2021 ◽

Vol 30 (160) ◽

pp. 210076

Author(s):

Iain R. Konigsberg ◽

Lisa A. Maier ◽

Ivana V. Yang

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Lung Disease ◽

Histone Modifications ◽

Genetic Variants ◽

Lung Diseases ◽

Hypersensitivity Pneumonitis ◽

Epigenetic Modifications ◽

Regulatory Mechanisms ◽

Beryllium Disease

Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.

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DNA methylation and regulation of gene expression: Guardian of our health

The Nucleus ◽

10.1007/s13237-021-00367-y ◽

2021 ◽

Author(s):

Gaurab Aditya Dhar ◽

Shagnik Saha ◽

Parama Mitra ◽

Ronita Nag Chaudhuri

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Regulation Of Gene Expression

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Acute Exercise Increases the Expression of KIR2DS4 by Promoter Demethylation in NK Cells

International Journal of Sports Medicine ◽

10.1055/a-0741-7001 ◽

2018 ◽

Vol 40 (01) ◽

pp. 62-70 ◽

Cited By ~ 6

Author(s):

Alexander Schenk ◽

Walter Pulverer ◽

Christine Koliamitra ◽

Claus Bauer ◽

Suzana Ilic ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Nk Cells ◽

Promoter Methylation ◽

Acute Exercise ◽

Nk Cell ◽

Epigenetic Modifications ◽

Control Group ◽

Chronic Exercise ◽

Positive Effects

AbstractPositive effects of exercise on cancer prevention and progression have been proposed to be mediated by stimulating natural killer (NK) cells. Because NK cell receptors are regulated by epigenetic modifications, we investigated whether acute aerobic exercise and training change promoter DNA methylation and gene expression of the activating KIR2DS4 and the inhibiting KIR3DL1 gene. Sixteen healthy women (50–60 years) performed a graded exercise test (GXT) and were randomized into either a passive control group or an intervention group performing a four-week endurance exercise intervention. Blood samples (pre-, post-GXT and post-training) were used for isolation of DNA/RNA of NK cells to assess DNA promoter methylation by targeted deep-amplicon sequencing and gene expression by qRT-PCR. Potential changes in NK cell subsets were determined by flow cytometry. Acute and chronic exercise did not provoke significant alterations of NK cell proportions. Promoter methylation decreased and gene expression increased for KIR2DS4 after acute exercise. A high gene expression correlated with a low methylation of CpGs that were altered by acute exercise. Chronic exercise resulted in a minor decrease of DNA methylation and did not alter gene expression. Acute exercise provokes epigenetic modifications, affecting the balance between the activating KIR2DS4 and the inhibiting KIR3DL1, with potential benefits on NK cell function.

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TET2 coactivates gene expression through demethylation of enhancers

Science Advances ◽

10.1126/sciadv.aau6986 ◽

2018 ◽

Vol 4 (11) ◽

pp. eaau6986 ◽

Cited By ~ 35

Author(s):

Lu Wang ◽

Patrick A. Ozark ◽

Edwin R. Smith ◽

Zibo Zhao ◽

Stacy A. Marshall ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Regulation Of Gene Expression ◽

Estrogen Receptor Α ◽

Dna Demethylation ◽

Estrogen Response ◽

Dna Base ◽

Modified Dna ◽

Global Increase ◽

Methylation Patterns

The tet methylcytosine dioxygenase 2 (TET2) enzyme catalyzes the conversion of the modified DNA base 5-methylcytosine to 5-hydroxymethylcytosine. TET2 is frequently mutated or dysregulated in multiple human cancers, and loss of TET2 is associated with changes in DNA methylation patterns. Here, using newly developed TET2-specific antibodies and the estrogen response as a model system for studying the regulation of gene expression, we demonstrate that endogenous TET2 occupies active enhancers and facilitates the proper recruitment of estrogen receptor α (ERα). Knockout of TET2 by CRISPR-CAS9 leads to a global increase of DNA methylation at enhancers, resulting in attenuation of the estrogen response. We further identified a positive feedback loop between TET2 and ERα, which further requires MLL3 COMPASS at these enhancers. Together, this study reveals an epigenetic axis coordinating a transcriptional program through enhancer activation via DNA demethylation.

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Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00253.2016 ◽

2016 ◽

Vol 311 (6) ◽

pp. L1245-L1258 ◽

Cited By ~ 19

Author(s):

Isaac K. Sundar ◽

Irfan Rahman

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Dna Methylation ◽

Cigarette Smoke ◽

Histone Modifications ◽

Expression Patterns ◽

Chromatin Modification ◽

Gene Expression Patterns ◽

Validation Data ◽

Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

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