AFM Study of Gene Silencing by DNA Methylation and Its Interactions Involving Chromatin and Methyl CpG Binding Proteins (original) (raw)

DNA methylation: gene expression regulation

Folia Biologica et Oecologica, 2016

Epigenetic modifications are responsible for the modulation of gene expression without affecting the nucleotide sequence. The observed changes in transcriptional activity of genes in tumor tissue compared to normal tissue, are often the result of DNA methylation within the promoter sequences of these genes. This modification by attaching methyl groups to cytosines within CpG islands results in silencing of transcriptional activity of the gene, which in the case of tumor suppressor genes is manifested by abnormal cell cycle, proliferation and excessive destabilization of the repair processes. Further studies of epigenetic modifications will allow a better understanding of mechanisms of their action, including the interdependence between DNA methylation and activity of proteins crucial to the structure of chromatin and gene activity. Wider knowledge of epigenetic mechanisms involved in the process of malignant transformation and pharmacological regulation of the degree of DNA methylat...

Role of DNA methylation in stable gene repression

Journal of Biological …, 2007

A large fraction of the animal genome is maintained in a transcriptionally repressed state throughout development. By generating viable Dnmt1 - / - mouse cells we have been able to study the effect of DNA methylation on both gene expression and chromatin structure. Our results confirm ...

DNA methylation and cancer; A Review Article

Epigenetics is the study of the changes in gene expression that are heritable and do not involve a change in the DNA sequence. DNA methylation is one of the key epigenetic mechanisms that is clearly understood. DNA methylation is the process that add methyl group to the 5 th carbon atom of the cytosine base at CpG dinucleotides without changing the nucleotide sequence. Transcriptional silencing in X inactivation and genomic imprinting are two important epigenetic mechanisms where DNA methylation plays a major role. It is well known that DNA hypermethylation and hypomethylation are directly associated with tumor formation. Hypomethylation leads to the inappropriate and increased levels of gene expression in tumors. Trancriptional repression that is seen in cancers is also mostly due to hypermethylation. DNA methylation plays a major role in transcriptional silencing in X inactivation, genomic imprinting and tumor or cancer formation. Changes in the pattern of DNA methylation have been a consistent finding in cancer cells. DNA methylation plays an important role in the generation of mutations in human tumors. The high incidence of C-toT transitions found in the p53 tumor-suppressor gene. DNA methylation plays a crucial role in the regulation of gene expression and chromatin organization within normal eukaryotic cells. In cancer patterns of DNA methylation are altered with global hypomethylation and hypermethylation of a subset of CpG-dense gene-associated regions (CpG islands).

DNA methylation and epigenetic inheritance

Methods, 2002

Mammalian cell lines silence genes at low frequency by the methylation of promoter sequences. These silent genes can be reactivated at high frequency by the demethylating agent 5-azacytidine (5-aza-CR). The inactive and active epigenetic states of such genes are stably inherited. A method for silencing genes is now available. It involves treatment of permeabilized cells with 5-methyl deoxycytidine triphosphate (5-methyl dCTP) which is incorporated into DNA. The methylation of promoter sequences has been confirmed using the bisulfite genomic sequencing procedure. Methylated oligonucleotides homologous to promoter sequences might be used to specifically target and silence given genes, but results so far have not been conclusive. Treatments that silence or reactivate genes by changing DNA methylation can be referred to as epimutagens, as distinct from mutagens that act by changing DNA sequences. The epimutagen 5-aza-CR reactivates genes but has little mutagenic activity, whereas standard mutagens (such as ethyl methane sulfonate and ultraviolet light) have little reactivation activity. Nevertheless, much more information is required about the effects of DNA-damaging agents in changing DNA methylation and gene activity and also about the role of epimutations in tumor progression.

The impact of chromatin in human cancer: linking DNA methylation to gene silencing

Carcinogenesis, 2002

For decades, chromatin was considered to be an inert structure whose only role was the compacting and confining of DNA inside the eukaryotic nucleus. However, tremendous progress in this field over the last 10 years has dramatically elevated chromatin to a key position in the control of gene activity. Its role in mediating the transformation of a normal cell into a malignant state is particularly interesting. On one side of this story there is the discovery that aberrant methylation patterns in an increasing number of tumour suppressor and DNA repair genes determine carcinogenetic transformation; while on the other side, there is the existence of a series of methyl-DNA binding activities that recruit co-repressor complexes and modify the structure of the chromatin to produce a transcriptionally silenced state. Although this field has seen rapid progress in recent years, detailed mechanisms by which this machinery modifies chromatin structure to its appropriate state and the specific targeting of repressor complexes have yet to be resolved. In this review we present the models of how repressor complexes may modify chromatin structure and mediate silencing of tumour suppressor and DNA repair genes.

Evidence for gene silencing by endogenous DNA methylation

Proceedings of the National Academy of Sciences, 1998

Transformed cells can spontaneously silence genes by de novo methylation, and it is generally assumed that this is due to DNA methyltransferase activity. We have tested the alternative hypothesis that gene silencing could be due to the uptake of 5-methyl-dCMP into DNA, via the di- and triphosphonucleotides. 5-Methyl-dCMP would be present in cells from the ongoing repair of DNA. We have isolated a strain of Chinese hamster ovary (CHO) cells, designated HAM − , which spontaneously silences two tested genes at a very high frequency. We have shown that this strain incorporates 5-[ 3 H]methyldeoxycytidine into 5-methylcytosine and thymine in DNA. It also has low 5-methyl-dCMP deaminase activity. Another HAM + strain has high deaminase activity and a very low frequency of gene silencing. The starting strain, CHO K1, has a phenotype intermediate between HAM − and HAM + .

Gene Silencing and DNA Methylation

American Journal of Phytomedicine and Clinical Therapeutics, 2014

This review revealed a new mechanism for gene regulation through “gene silencing” at the transcriptional level (TGS) or at the post -transcriptional level (PTGS), which play a key role in many essential cellular processes. Today dsRNA is used as a powerful tool to experimentally elucidate the function of essentially any gene in a cell. The immense impact of the discovery of RNA interference (RNAi) on biomedical research and its novel medical applications in the future are reviewed in this article, with particular stress on therapeutic applications of radio -labeled antisense oligonucleotides (RASONs) for diagnosis and treatment of various cancers and neurodegenerative diseases by “gene silencing”. Antisense oligonucleotides (ASONs) can also modulate alternative splicing which 74% of all human genes undergo. Epigenetic changes affect chromatin structure and thus regulate processes such as transcription, X-chromosome inactivation, allele-specific expression of imprinted genes, and inactivation of tumor suppressor genes. Treatment with inhibitors of DNA methylation and histone deacetylation can reactivate epigenetically silenced genes and has been shown to restore normal gene function. In cancer cells, this results in expression of tumor suppressor genes and other regulatory functions, inducing growth arrest and apoptosis.

DNA methylation: A molecular lock

Current Biology, 1997

In mammals, the promoters of expressed genes are generally unmethylated, whereas those of genes that are not expressed are methylated. Two recent papers help to explain the mechanism by which methylation modulates gene expression.