Application of 5-Methylcytosine DNA Glycosylase to the Quantitative Analysis of DNA Methylation

Choi, Woo Lee; Mok, Young Geun; Huh, Jin Hoe

doi:10.3390/ijms22031072

Cited by 6 publications

(5 citation statements)

References 35 publications

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“…This way, approaches such as DeMEter (DME) coupled with quantitative PCR (DME-qPCR) have been developed to quantify DNA methylation in plants. This has been demonstrated in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) [147]. On the other hand, 5 mC is involved in regulation of gene expression, repair, replication, transcription, recombination and transposon suppression in plants.…”

Section: Epigenomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

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Section: Epigenomicsmentioning

confidence: 99%

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

et al. 2021

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“…Methylation of CpG islands located in gene promoters often leads to transcriptional silencing ( 66 ). DNA methylation contributes to various diseases, particularly human cancers ( 67 ). The DNA methylation level of SOX9 gradually increases in normal cervical tissues, CIN I, CIN II-III, and CC tissues.…”

Section: Cervical Cancermentioning

confidence: 99%

SOX9: Advances in Gynecological Malignancies

Chen

Wen

et al. 2021

Front. Oncol.

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Transcription factors of the SOX family were first discovered in mammals in 1990. The sex-determining region Y box 9 belongs to the SOX transcription factor family. It plays an important role in inducing tissue and cell morphogenesis, survival, and many developmental processes. Furthermore, it has been shown to be an oncogene in many tumors. Gynecological malignancies are tumors that occur in the female reproductive system and seriously threaten the lives of patients. Common gynecological malignancies include ovarian cancer, cervical cancer, and endometrial cancer. So far, the molecular mechanisms related to the incidence and development of gynecological malignancies remain unclear. This makes it particularly important to discover their common causative molecule and thus provide an effective therapeutic target. In recent years, studies have found that multiple mechanisms are involved in regulating the expression of the sex-determining region Y box 9, leading to the occurrence and development of gynecological malignancies. In this review, we discuss the prognostic value of SOX9 expression and the potential of targeting SOX9 for gynecological malignancy treatment. We also discuss progress regarding the role of SOX9 in gynecological malignancy pathogenesis through its mediation of important mechanisms, including tumor initiation and proliferation, apoptosis, migration, invasion, chemoresistance, and stem cell maintenance.

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“…Other members of this superfamily are involved in the removal of oxidized, alkylated and deaminated nucleobases from the genome (Zharkov, 2008;Fedorova et al, 2010). DME/ROS1 enzymes attract attention as potential tools for targeted regulation of gene activity: for example, the possibility of targeted DNA demethylation in human cells by A. thaliana DME (AtDME) was used to analyze the level of mC in genomic DNA (Choi W.L. et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L.

et al. 2022

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One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulation of development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologues of DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied. Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1), which contains all main structural domains required for catalytic activity. Using homologous modeling, we have constructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix– hairpin–helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA, and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand. The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower efficiency, showing minimal activity in the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted in a global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein and other homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the status of epigenetic methylation and to control gene activity.

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Application of 5-Methylcytosine DNA Glycosylase to the Quantitative Analysis of DNA Methylation

Cited by 6 publications

References 35 publications

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

SOX9: Advances in Gynecological Malignancies

Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L.

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