The influence of CpG (5′-d(CpG)-3′ dinucleotides) methylation on ultrasonic DNA fragmentation

Гарафутдинов, Р.Р.; Galimova, A. A.; Сахабутдинова, А. Р.

doi:10.1080/07391102.2018.1533888

Cited by 4 publications

(4 citation statements)

References 41 publications

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“…28 DNA methylation is extensively studied to regulate gene expression via various mechanisms. 29 DNMTs conclude a group of nuclear enzymes capable of catalyzing the methylation of CpG dinucleotides, which can lead to an epigenetic methylome distinguished between normal cells and cancer cells. 30 Similarly, as previously reported, lncRNA PVT1 could induce the methylation of CpG Island in the miR-146a promoter in three PCa cell lines (LNCaP, PC-3, and DU145), thereby promoting the development of the PCa tumorigenesis.…”

Section: Discussionmentioning

confidence: 99%

RETRACTED: MCM3AP-AS1 KD Inhibits Proliferation, Invasion, and Migration of PCa Cells via DNMT1/DNMT3 (A/B) Methylation-Mediated Upregulation of NPY1R

Li¹,

Lv²,

Liu³

2020

Molecular Therapy - Nucleic Acids

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Prostate cancer (PCa) is a heterogeneous tumor that commonly occurs among males worldwide. This study explored the potential role that long non-coding RNA MCM3AP antisense RNA 1 (MCM3AP-AS1) plays in PCa progression, and investigated its mechanism. MCM3AP-AS1 and neuropeptide Y receptor Y1 (NPY1R) expression was determined in PCa cells. The regulatory role of MCM3AP-AS1 in PCa cells was defined using scratch test, Transwell assay, 5-ethynyl-2 0 -deoxyuridine (EdU) assay, and flow cytometry. Methylation-specific PCR (MSP) was used to test the methylation level of NPY1R. Subsequently, the interaction among MCM3AP-AS1, DNA methyltransferase (DNMT)1/DNMT3 (A/B), and NPY1R was investigated using RNA immunoprecipitation, RNA pull-down, and chromatin immunoprecipitation. Finally, we observed xenograft tumor in nude mice. MCM3AP-AS1 was highly, whereas NPY1R was poorly, expressed in PCa. Lentivirus-mediated overexpression of MCM3AP-AS1 promoted proliferation, invasion, and migration while suppressing apoptosis of PCa cells, whereas opposite trends were detected after inhibition of the mitogenactivated protein kinase (MAPK) pathway. MCM3AP-AS1 promoted methylation of NPY1R promoter via recruitment of DNMT1/DNMT3 (A/B), thereby downregulating NPY1R expression to activate the MAPK pathway. Furthermore, overexpressed MCM3AP-AS1 was observed to facilitate PCa development in vivo, which could be reversed by overexpressed NPY1R. Altogether, MCM3AP-AS1 silencing inhibits PCa progression by disrupting methylation of the NPY1R promoter to inactivate the MAPK pathway.

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Section: Discussionmentioning

confidence: 99%

RETRACTED: MCM3AP-AS1 KD Inhibits Proliferation, Invasion, and Migration of PCa Cells via DNMT1/DNMT3 (A/B) Methylation-Mediated Upregulation of NPY1R

Li¹,

Lv²,

Liu³

2020

Molecular Therapy - Nucleic Acids

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“…We analyzed raw WGS data and found that cytosine methylation strongly affects the cleavage rate of CpG dinucleotides in the human genome. This fact agrees with recent observations of another group 3 . In all studied datasets from 1000 Genomes project the cleavage rate of methylated CpG dinucleotides was higher than the cleavage rate of other dinucleotides including unmethylated CpGs 1,2 .…”

Section: Discussionsupporting

confidence: 94%

“…We assume that this result can be explained by methylation of cytosines 2 . Recently it was shown that in the honeybee genome methylated CpG dinucleotides break more frequently than unmethylated ones 3 .…”

Section: In the Course Of Sample Preparation For Next Generation Sequmentioning

confidence: 99%

A Method for Identification of the Methylation Level of CpG Islands From NGS Data

Урошлев

Abdullaev

Umarova

et al. 2020

Sci Rep

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In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.

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“…Note 2. Sonication is a widely used method for DNA shearing, however, there is evidence it preferentially targets methylated DNA and can be used as a hypomethylating agent [39, 40]. NEBNext UltraShear is a novel enzymatic shearing module developed to circumvent the use of ultra-sonication and aid with high-throughput sample fragmentation, being performed in a PCR strip tube or plate format and followed directly by library preparation steps.…”

Section: Notesmentioning

confidence: 99%

Whole Genome Methylation Sequencing via Enzymatic Conversion (EM-seq): Protocol, Data Processing and Analysis

Olova,

Andrews

2023

Preprint

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Whole genome bisulfite sequencing (WGBS) has been the gold standard technique for base resolution analysis of DNA methylation for the last 15 years. It has been, however, associated with technical biases, which lead to overall overestimation of global and regional methylation values, and significant artifacts in extreme cytosine-rich DNA sequence contexts. Enzymatic conversion of cytosine is the newest approach, set to replace entirely the use of the damaging bisulfite conversion of DNA. The EM-seq technique utilises TET2, T4-BGT and APOBEC in a two-step conversion process, where the modified cytosines are first protected by oxidation and glucosylation, followed by deamination of all unmodified cytosines to uracil. As a result, EM-seq is degradation-free and bias-free, requires low DNA input, and produces high library yields with longer reads, little batch variation, less duplication, uniform genomic coverage, accurate methylation over a larger number of captured CpGs, and no sequence-specific artifacts.

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The influence of CpG (5′-d(CpG)-3′ dinucleotides) methylation on ultrasonic DNA fragmentation

Cited by 4 publications

References 41 publications

RETRACTED: MCM3AP-AS1 KD Inhibits Proliferation, Invasion, and Migration of PCa Cells via DNMT1/DNMT3 (A/B) Methylation-Mediated Upregulation of NPY1R

RETRACTED: MCM3AP-AS1 KD Inhibits Proliferation, Invasion, and Migration of PCa Cells via DNMT1/DNMT3 (A/B) Methylation-Mediated Upregulation of NPY1R

A Method for Identification of the Methylation Level of CpG Islands From NGS Data

Whole Genome Methylation Sequencing via Enzymatic Conversion (EM-seq): Protocol, Data Processing and Analysis

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