Additional file 1 of Epigenetic modifier alpha-ketoglutarate modulates aberrant gene body methylation and hydroxymethylation marks in diabetic heart
Creators: name: Dhat, Rohini
name: Mongad, Dattatray
name: Raji, Sivarupa
name: Arkat, Silpa
name: Mahapatra, Nitish R.
name: Singhal, Nishant
name: Sitasawad, Sandhya L.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. KEGG pathway list for DMRs showing hypo-5mC in gene body regions of cardiac tissue of STZ vs control. Table S2. KEGG pathway list for DMRs showing hyper-5mC in gene body regions of cardiac tissue of STZ vs control. Table S3. KEGG pathway list for DhMRs showing hyper-5hmC in gene body regions of cardiac tissue of STZ vs control. Table S4. Physiological, cardiac, and serum parameters of experimental animals. Table S5. Primer and oligos sequences. Fig. S1. GO enrichment analysis. Significantly enriched GO terms in (A) MEDIP-seq and (B) hMEDIP-seq analysis. Red, green, and blue bars represent the biological process, cellular component, and molecular function respectively. The x-axis represents -log10(p-value), the y-axis represents GO terms and the number to the right of the column indicates the number of enriched genes. Fig. S2. Enrichment of DMRs and DhMRs within gene body regions visualized by IGV. Locations of the differentially methylated and hydroxymethylated peaks within gene body regions were visualized by IGV genome browser. Hypermethylated/ hyperhydroxymethylated peaks are denoted by black color and hypomethylated/ hypohydroxymethylated peaks are denoted by red color. Refseq gene is shown in the first track, hMEDIP peaks in the middle track, and MEDIP peaks are in the lower track. Fig. S3. H&amp;E staining micrographs. H&amp;E-stained cardiac sections from three different rat LV tissues from each group; arrows indicate lymphocyte infiltration, and arrowheads indicate degeneration of myocardial fibers. Fig. S4. Densitometry analysis of western blot data. Densitometry analysis of western blot data is shown in Fig. 5B for (A) DNMT1, (B) DNMT3A, (C) DNMT3B, (D) MeCP2, (E) MBD2, and (F) TET1. Band intensities are normalized to Vinculin and represented as mean ± SD for three different animals. Statistical significance was determined by one-way ANOVA with Tukey’s multiple comparisons post-test where, *p &lt; 0.05, **p &lt; 0.001, ****p &lt; 0.0001vs control, and ###p &lt; 0.0002 vs STZ by one-way ANOVA. Fig. S5. Quantitative analysis of global 5mC/5hmC levels in in vitro experiments. (A, B) Densitometry analysis of 5mC- and 5hmC-specific dot blot analysis of gDNA isolated from NG- and HG-treated H9c2 cells in the presence of AKG treatment (A) 5mC levels and (B) 5hmC levels. (C, D) Densitometry analysis of 5mC- and 5hmC-specific dot blot analysis of gDNA isolated from NG- and HG-treated DNMT3b kockdown-H9c2 cells (C) 5mC levels and (D) dot blot intensities are normalized to methylene blue staining. (E,F) Immunofluorescence intensities of 5mC antibody staining in presence of NG or HG in (E) AKG-supplemented and (F) DNMT3b knockdown H9c2 cells fluorescence intensities were normalised to the DAPI staining. Results are represented as mean ± SD for three individual experiments and statistical significance was determined by one-way ANOVA with Tukey’s multiple comparisons post-test where, **p &lt; 0.001, ***p &lt; 0.0002, ****p &lt; 0.0001vs control, and ##p &lt; 0.001, ###p &lt; 0.0002, ####p &lt; 0.0001 vs STZ.