Introduction to Whole Genome Methylation

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10.1038/s41418-020-00726-3

Whole-genome methylation sequencing found that PGC7 could induce promoter demethylation of genes related to development.

PGC7 promotes tumor oncogenic dedifferentiation through remodeling DNA methylation pattern for key developmental transcription factors

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10.1038/s42003-021-02342-4

Whole-genome methylation analysis in the first generation of offspring (F 1 ) showed that, although there was no significant difference in methylation level as had previously been observed in the parent plants, some residual imprints of DNA methylation differences were detected.

Potential evidence for transgenerational epigenetic memory in Arabidopsis thaliana following spaceflight

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10.14348/molcells.2021.0001

We detected significantly elevated expression of thioredoxin-interacting protein (TXNIP), a known TSG, in UHRF1-knockdown cells, and this gene is hypermethylated in cervical cancer tissue and cell lines, as indicated by whole-genome methylation analysis.

UHRF1 Induces Methylation of the TXNIP Promoter and Down-Regulates Gene Expression in Cervical Cancer

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10.1093/plcell/koab162

Here, utilizing the highly efficient multiplex CRISPR-Cas9 genome-editing system, we created single- and multiple-knockout mutants for all nine DNA methyltransferases in rice (Oryza sativa) and profiled their whole-genome methylation status at single-nucleotide resolution.

Multiplex CRISPR-Cas9 editing of DNA methyltransferases in rice uncovers a class of non-CG methylation specific for GC-rich regions.

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10.1016/j.envres.2021.111389

Six placenta samples were selected for whole-genome methylation analysis using Infinium Human Methylation 450K Beadchip, followed by pyrosequencing-based methylation analysis of three selected genes in 146 placentas.

Differential methylation of genes in the human placenta associated with bisphenol A exposure.

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10.1021/acsnano.0c07323

After 28-day continuous and intermittent subacute exposure to these SAS via diet, whole-genome methylation levels in mouse peripheral leukocytes and liver were significantly altered in a dose- and SAS type-dependent manner, with minimal toxicity detected by conventional toxicological assessments, especially at a human-relevant dose (HRD).

Genome-Wide DNA Methylation Alterations and Potential Risk Induced by Subacute and Subchronic Exposure to Food-Grade Nanosilica in Mice.

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10.1016/j.biomaterials.2021.120980

The underlying mechanism of this effect was evaluated via whole-genome methylation.

Endothelin-1 enhances the regenerative capability of human bone marrow-derived mesenchymal stem cells in a sciatic nerve injury mouse model.

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10.1016/j.bbih.2021.100247

Illumina®MethylationEPIC Beadchips (~850k CpG sites) were processed on the iScan System to examine whole-genome methylation differences.

DNA methylation and exposure to violence among African American young adult males

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10.1101/2021.03.12.435154

To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen.

DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

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10.1016/j.prp.2021.153449

ADAM12 (a disintegrin and metalloproteases 12), is a gene that was commonly hypermethylated in esophageal cancer using whole-genome methylation microarray in our previous study.

Methylation status of ADAM12 promoter are associated with its expression levels in colorectal cancer.

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10.1101/2020.12.22.423778

We completed a whole-genome methylation and variant analysis in a non-smoking Zoroastrian-Parsi individual, collecting two samples, 12 years apart (at 53 and 65 years respectively) (ZPMetG-Hv2a-1A (old, t0), ZPMetG-Hv2a-1B (recent, t0+12)) and analysing them using a GridION Nanopore sequencer at 13X genome coverage overall.

Dynamic methylome modification is associated with mutational signatures in aging and the etiology of disease

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10.3389/fmolb.2021.675198

Methods: Whole-genome methylation datasets integrated from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were profiled (n = 1,268).

A High Epigenetic Risk Score Shapes the Non-Inflamed Tumor Microenvironment in Breast Cancer

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Whole Genome Methylation
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What is/are Whole Genome Methylation?

Whole Genome Methylation - Whole-genome methylation sequencing found that PGC7 could induce promoter demethylation of genes related to development. [1] Whole-genome methylation analysis in the first generation of offspring (F 1 ) showed that, although there was no significant difference in methylation level as had previously been observed in the parent plants, some residual imprints of DNA methylation differences were detected. [2] We detected significantly elevated expression of thioredoxin-interacting protein (TXNIP), a known TSG, in UHRF1-knockdown cells, and this gene is hypermethylated in cervical cancer tissue and cell lines, as indicated by whole-genome methylation analysis. [3] Here, utilizing the highly efficient multiplex CRISPR-Cas9 genome-editing system, we created single- and multiple-knockout mutants for all nine DNA methyltransferases in rice (Oryza sativa) and profiled their whole-genome methylation status at single-nucleotide resolution. [4] Six placenta samples were selected for whole-genome methylation analysis using Infinium Human Methylation 450K Beadchip, followed by pyrosequencing-based methylation analysis of three selected genes in 146 placentas. [5] After 28-day continuous and intermittent subacute exposure to these SAS via diet, whole-genome methylation levels in mouse peripheral leukocytes and liver were significantly altered in a dose- and SAS type-dependent manner, with minimal toxicity detected by conventional toxicological assessments, especially at a human-relevant dose (HRD). [6] The underlying mechanism of this effect was evaluated via whole-genome methylation. [7] Illumina®MethylationEPIC Beadchips (~850k CpG sites) were processed on the iScan System to examine whole-genome methylation differences. [8] To address this paradox, we examined whole-genome methylation patterns in the brains and ovaries of young honey bee workers that had been subjected to divergent social contexts: the presence or absence of the queen. [9] ADAM12 (a disintegrin and metalloproteases 12), is a gene that was commonly hypermethylated in esophageal cancer using whole-genome methylation microarray in our previous study. [10] We completed a whole-genome methylation and variant analysis in a non-smoking Zoroastrian-Parsi individual, collecting two samples, 12 years apart (at 53 and 65 years respectively) (ZPMetG-Hv2a-1A (old, t0), ZPMetG-Hv2a-1B (recent, t0+12)) and analysing them using a GridION Nanopore sequencer at 13X genome coverage overall. [11] Methods: Whole-genome methylation datasets integrated from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were profiled (n = 1,268). [12]