library preparation and methylation sequencing  (Epigenomics ag)

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Article Title: Accounting for ALA Natural Mutations Enhances the Efficiency of Graphene Oxide Nanopriming in Bar-Modified Arabidopsis.

doi: 10.1002/advs.202500058

Figure Lengend Snippet: Figure 5. Genome-wide DNA methylation analysis in WT and GM seeds before and after GO treatments. a) Circos plots show the methylation levels across different chromosomes for WT and GM seeds before and after GO exposure. The colored sections on the outer ring represent different chromo- somes. The concentric rings from outer to inner illustrate untreated samples, 0.75 mg-C/L GO-treated samples, and 1.5 mg-C/L GO-treated samples. Whole-genome methylation levels were calculated as mean values within 100 kb windows for each chromosome. The color gradient from cyan to red indicates the methylation percentages, whereas the innermost ring represents gene density. b) Whole-genome methylation levels in CG, CHG, and CHH contexts for WT and GM seeds after various GO exposures (sample size n = 3). Data are presented as means ± SD, with gray and red dots depicting individual data points in the WT and GM groups. Three biological replicates were included for each treatment. Independent sample two-sided t-tests were performed: * indicates significant differences within the same genotype relative to the condition without GO, and # indicates significant differences between GM and WT under the same treatment. Significant differences are marked with p values. c) Differential methylation regions at promoter regions and gene bodies of key genes (Figure 1c) are represented by a color gradient showing Log2FC in methylation levels. Triangles and circles indicate CG and CHH methylation, respectively. No differential methylation was observed in the CHG context. Regions without differential methylation are blank. d) Dot plots of differential methylation for ALA metabolism-related genes compare promoter and gene body methylation across conditions. Blue and red dots denote different comparisons, as indicated in the legend. Dots with circles indicate methylation levels with |Log2FC| >10.

Article Snippet: Library construction was performed using an MGIEasy whole-genome bisulfite library preparation kit (MGI).

Techniques: Genome Wide, DNA Methylation Assay, Methylation

Journal: Scientific Reports

Article Title: DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis

doi: 10.1038/s41598-020-78151-2

Figure Lengend Snippet: Hypomethylated CpG sites were frequently detected in the whole genome of the Dnmt3b -deficient (KO) liver. ( A ) Distribution of methylation levels in the CG context on gene functional elements. Each region of each gene was equally divided into 50 bins; subsequently, the C-site levels of the corresponding bins of all regions were averaged. Promoter was defined as a region of 2 kb length located upstream of the TSS site. ( B ) The violin plot indicates the distribution of methylation levels of differentially-methylated regions (DMRs) in the CG context. ( C ) Distribution of the DMR length. The dotted line indicates a length of 200 bp, DMRs longer than those, which we determined as the target of analysis. ( D ) (top) CpG methylation level in Sox9 gene obtained from whole-genome bisulfite sequencing (WGBS). DMRs are indicated by red rectangles. (bottom, left) CpG methylation level at each CpG site in one of the Sox9 DMRs calculated by targeted bisulfite sequencing, conducted on the loci where primers could be designed, shown by black rectangles. Data are presented as the mean ± s.d. N = 3 for both genotypes. (Bottom, right) The overall methylation level in this DMR. Whiskers show the minimum and the maximum. The P value was determined using the two-tailed paired t test. Images in ( D ) were made on GraphPad Prism ver 7.00.

Article Snippet: WGBS library preparation, sequencing, mapping, and methylation analysis were performed by Novogene (Beijing, China).

Techniques: Methylation, Functional Assay, CpG Methylation Assay, Methylation Sequencing, Two Tailed Test

Journal: Scientific Reports

Article Title: DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis

doi: 10.1038/s41598-020-78151-2

Figure Lengend Snippet: Genes related to oxidative phosphorylation are downregulated in Dnmt3b -deficient (KO) liver. ( A ) Normalized enrichment score (NES) of significantly enriched KEGG gene sets through gene set enrichment analysis (GSEA) of four Dnmt3b -WT mice and four KO mice with no thioacetamide (TAA) treatment. Enrichment plot for the gene set KEGG_OXIDATIVE_PHOSPHORYLATION is shown in ( C ). ( B ) NES of significantly enriched KEGG gene sets through GSEA of four Dnmt3b -WT mice and four KO mice treated with TAA for 4 weeks. Enrichment plot for the gene set KEGG_OXIDATIVE_PHOSPHORYLATION is shown in ( D ). FWER P-value cutoff = 0.05 and FDR Q-value cutoff = 0.01 in both ( A ) and ( B ). ( E ) IGV screenshot of the Sirt4 gene demonstrating CpG methylation level obtained from WGBS and a differentially methylated regions (DMR) on the gene body, indicated by a red rectangle.

Article Snippet: WGBS library preparation, sequencing, mapping, and methylation analysis were performed by Novogene (Beijing, China).

Techniques: Phospho-proteomics, CpG Methylation Assay, Methylation