Bioinformatic tools for DNA methylation and histone modification: A survey

Chenarani, Nasibeh; Emamjomeh, Abbasali; Allahverdi, Abdollah; Mirmostafa, SeyedAli; Afsharinia, Mohammad Hossein; Zahiri, Javad

doi:10.1016/j.ygeno.2021.03.004

Cited by 17 publications

(10 citation statements)

References 115 publications

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“…According to previous studies, alterations in the 5mC distribution patterns can differentiate cancer cells from normal cells. There are known to be three major routes for CpG methylation that can contribute to the oncogenic phenotype 57,58 . The first is the loss of DNA cytosine methylation or general hypomethylation of the cancer genome, which leads to genome instability and increases in aneuploidy, which are both classic hallmarks of cancer.…”

Section: Epigenetic Changes In Lung Cancermentioning

confidence: 99%

Epigenetic regulation in lung cancer

Ramazi,

Dadzadi,

Sahafnejad

et al. 2023

MedComm

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Lung cancer is indeed a major cause of cancer‐related deaths worldwide. The development of tumors involves a complex interplay of genetic, epigenetic, and environmental factors. Epigenetic mechanisms, including DNA methylation (DNAm), histone modifications, and microRNA expression, play a crucial role in this process. Changes in DNAm patterns can lead to the silencing of important genes involved in cellular functions, contributing to the development and progression of lung cancer. MicroRNAs and exosomes have also emerged as reliable biomarkers for lung cancer. They can provide valuable information about early diagnosis and treatment assessment. In particular, abnormal hypermethylation of gene promoters and its effects on tumorigenesis, as well as its roles in the Wnt signaling pathway, have been extensively studied. Epigenetic drugs have shown promise in the treatment of lung cancer. These drugs target the aberrant epigenetic modifications that are involved in the development and progression of the disease. Several factors have been identified as drug targets in non‐small cell lung cancer. Recently, combination therapy has been discussed as a successful strategy for overcoming drug resistance. Overall, understanding the role of epigenetic mechanisms and their targeting through drugs is an important area of research in lung cancer treatment.

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Section: Epigenetic Changes In Lung Cancermentioning

confidence: 99%

Epigenetic regulation in lung cancer

Ramazi,

Dadzadi,

Sahafnejad

et al. 2023

MedComm

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“…Chromatin immunoprecipitation (ChIP) test is the most traditional strategy in studying DNA-protein interactions ( Kuo and Allis, 1999 ). In this procedure, chromatin proteins are temporarily cross-linked to DNA, and the harvested chromatin is sheared into several short DNA-protein parts ( Chenarani et al, 2021 ). Selected sections containing proteins of interest are subsequently immunoprecipitated by incorporating antibodies specific to these proteins.…”

Section: Histones and Histone Modificationsmentioning

confidence: 99%

“…The protein-bound DNA fragments are then purified and sequenced by numerous analytical methods ( Decaprio and Kohl, 2020 ). The result is a rundown of short DNA fragments attached by specific proteins ( Chenarani et al, 2021 ). However, the technique requires optimization of reaction conditions, and its application is limited by the sparse reads or low cell throughput.…”

Section: Histones and Histone Modificationsmentioning

confidence: 99%

Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease

et al. 2021

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Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.

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“…Some of the epigenetic influences may positively affect the health of humans, for example, exercise, microbiome, and alternative medicine, or lead to changes in epigenetic regulatory features in the DNA methylation and miRNAs expression including environmental toxicants and drugs of abuse. Other factors may affect human health positively or negatively, depending on the nature of the impact, such as financial status, psychological state, diet, social interactions, seasonal changes, therapeutic drugs, and disease [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

An Update of Epigenetic Drugs for the Treatment of Cancers and Brain Diseases: A Comprehensive Review

Sahafnejad

Ramazi

Allahverdi

2023

Genes

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Epigenetics has long been recognized as a significant field in biology and is defined as the investigation of any alteration in gene expression patterns that is not attributed to changes in the DNA sequences. Epigenetic marks, including histone modifications, non-coding RNAs, and DNA methylation, play crucial roles in gene regulation. Numerous studies in humans have been carried out on single-nucleotide resolution of DNA methylation, the CpG island, new histone modifications, and genome-wide nucleosome positioning. These studies indicate that epigenetic mutations and aberrant placement of these epigenetic marks play a critical role in causing the disease. Consequently, significant development has occurred in biomedical research in identifying epigenetic mechanisms, their interactions, and changes in health and disease conditions. The purpose of this review article is to provide comprehensive information about the different types of diseases caused by alterations in epigenetic factors such as DNA methylation and histone acetylation or methylation. Recent studies reported that epigenetics could influence the evolution of human cancer via aberrant methylation of gene promoter regions, which is associated with reduced gene function. Furthermore, DNA methyltransferases (DNMTs) in the DNA methylation process as well as histone acetyltransferases (HATs)/histone deacetylases (HDACs) and histone methyltransferases (HMTs)/demethylases (HDMs) in histone modifications play important roles both in the catalysis and inhibition of target gene transcription and in many other DNA processes such as repair, replication, and recombination. Dysfunction in these enzymes leads to epigenetic disorders and, as a result, various diseases such as cancers and brain diseases. Consequently, the knowledge of how to modify aberrant DNA methylation as well as aberrant histone acetylation or methylation via inhibitors by using epigenetic drugs can be a suitable therapeutic approach for a number of diseases. Using the synergistic effects of DNA methylation and histone modification inhibitors, it is hoped that many epigenetic defects will be treated in the future. Numerous studies have demonstrated a link between epigenetic marks and their effects on brain and cancer diseases. Designing appropriate drugs could provide novel strategies for the management of these diseases in the near future.

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Bioinformatic tools for DNA methylation and histone modification: A survey

Cited by 17 publications

References 115 publications

Epigenetic regulation in lung cancer

Epigenetic regulation in lung cancer

Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease

An Update of Epigenetic Drugs for the Treatment of Cancers and Brain Diseases: A Comprehensive Review

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