Journal: PLoS ONE

Article Title: Hiwi Mediated Tumorigenesis Is Associated with DNA Hypermethylation

doi: 10.1371/journal.pone.0033711

Figure Lengend Snippet: (A) Gene expression profiles of sh-Hiwi MFH cells treated with 1 uM or 5 uM 5-azacytidine cluster with gene expression profiles of doxycycline-induced sh-Hiwi MFH cells, using the whole gene set from both treatments. (B) Meth27 Illumina array of methylation of 27000 CpG site changes in sh-Hiwi MFH cells uninduced (x-axis) or induced with doxycycline for 7 days (y-axis). Graph shows all CpG islands and reveals no global shift in CpG methylation.

Article Snippet: These data suggest that CpG methylation status of genes (at least the 14,495 on the Illumina Meth27 array) are not affected; and thus that the overall change in global DNA methylation observed may be accounted by either DNA-methylation of repetitive elements (non-gene regions) or non-CpG gene methylation.

Techniques: Expressing, Methylation, CpG Methylation Assay

Journal: bioRxiv

Article Title: Methylation Array Signals are Predictive of Chronological Age Without Bisulfite Conversion

doi: 10.1101/2023.12.20.572465

Figure Lengend Snippet: Hippocampal DNA was isolated from dissected hippocampi of mice of various ages. In parallel, DNA was processed with standard bisulfite conversion (converted) or a mock conversion process lacking solely the bisulfite reagent (unconverted). Models were trained on both converted (A) and unconverted (B) data. This process was repeated for 100 iterations of generating new train/test splits and retraining to obtain distributions of prediction accuracy (C) and error (D) .

Article Snippet: The first dataset was processed as indicated by Illumina [ ], generating apparent methylation data from bisulfite-converted DNA samples (converted), while the second was generated using the same workflow but without addition of sodium bisulfite (unconverted).

Techniques: Isolation

Journal: bioRxiv

Article Title: Methylation Array Signals are Predictive of Chronological Age Without Bisulfite Conversion

doi: 10.1101/2023.12.20.572465

Figure Lengend Snippet: The loci selected by the previously described 100 clocks trained on converted and unconverted DNA were interrogated. A minority of sites (49 clock/556 primary selection) were common to only one clock in each data type. A majority in the converted (5,014/13,138) and unconverted (2,186/17,146) were unique. A) Three example loci that were age-predictive in both data types ( B - D) distributions of the correlation between methylation from converted (blue) or “methylation” from unconverted (orange) and age. Distributions are shown for sites unique to unconverted clocks (B) , common to both (C) , or unique to converted (D)

Article Snippet: The first dataset was processed as indicated by Illumina [ ], generating apparent methylation data from bisulfite-converted DNA samples (converted), while the second was generated using the same workflow but without addition of sodium bisulfite (unconverted).

Techniques: Selection, Methylation

Journal: Epigenomics

Article Title: Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models

doi: 10.2217/epi-2016-0138

Figure Lengend Snippet: Diagram of chromosome 21 (Hsa21), which is trisomic in Down syndrome. Effector genes on the triplicated Hsa21 act on downstream target genes, mostly on other chromosomes, both by acute transcriptional effects and via epigenetic effects, including alterations in DNA methylation that can propagate to daughter cells in growing and self-renewing tissues, to produce biological phenotypes. DS-DM: Differential CpG methylation.

Article Snippet: Microarray-based DNA methylation profiling (Illumina 27K) in peripheral blood leukocytes (PBL) from individuals with DS and age-matched controls revealed gains and losses of DNA methylation, strongly affecting approximately 100 genes, as a consistent epigenetic response to Ts21 in these cells [ ].

Techniques: DNA Methylation Assay, CpG Methylation Assay