RFLP pattern of the -gene-like -genes; cloning and hybridization of the sequences with high degree of homology to the fourth exon of the -gene

<p><b>Copyright information:</b></p><p>Taken from "Transgenerational changes in the genome stability and methylation in pathogen-infected plants"</p><p></p><p>Nucleic Acids Research 2007;35(5):1714-1725.</p><p>Published online 20 Feb 2007</p><p>PMCID:PMC1865051.</p><p>© 2007 The Author(s).</p> () RFLP analysis of -gene-like loci was performed after digestion with three different enzymes, HindIII, EcoRI, DraI. () PCR amplification from the plasmid carrying the -gene (3) or from SR1 plant genome (2), using primers annealing to the fourth exon of the -gene; (1) is the marker. () Cloning of the PCR fragment (line 2 from B) from SR1 plants. Digestion of the pGEM cloning vector with EcoRI shows the number of fragments of different sizes. The frame shows the band corresponding to the cloning vector; the bands of lower molecular weight represent the PCR fragments. () Hybridization of the colonies containing the PCR product (1—positive control, bacteria containing the vector; 2—negative control, empty bacteria; 3–10—clones with different degree of homology to the fourth exon. Clones 3–8 have the homology of >75%, whereas 9 and 10—only 60–65% (overexposed blot shown)

Global genome methylation was analyzed by ROPS assay after digestion with either HpaII or MspI

<p><b>Copyright information:</b></p><p>Taken from "Transgenerational changes in the genome stability and methylation in pathogen-infected plants"</p><p></p><p>Nucleic Acids Research 2007;35(5):1714-1725.</p><p>Published online 20 Feb 2007</p><p>PMCID:PMC1865051.</p><p>© 2007 The Author(s).</p> ‘Y’ axis shows radioactive incorporation (dpm/µg) in PC and PI lines. Each bar represents the average (with SD) from five individual assays, each representing the readings from five plants. Asterisks show the significance of the data, where one represents 95% and two represent at least 99% confidence interval

RFLP showed increased instability of the -gene loci, and similar stability of other loci

<p><b>Copyright information:</b></p><p>Taken from "Transgenerational changes in the genome stability and methylation in pathogen-infected plants"</p><p></p><p>Nucleic Acids Research 2007;35(5):1714-1725.</p><p>Published online 20 Feb 2007</p><p>PMCID:PMC1865051.</p><p>© 2007 The Author(s).</p> Examples of the polymorphisms in RFLP of -gene-like loci from PI plants are shown in A–C. () RFLP in the sample digested with HindIII. () RFLP in the sample digested with EcoRI. () RFLP in the sample digested with DraI. Occasional differences () were found in hybridization with 5.8S probe (PI plant). Additional examples of the RFLP are shown in Figures 6S–8S

Additional file 2: Figure S1. of Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice

H3K4me3 ChIP-on-chip analysis in the livers of A/J and WSB/EiJ mice fed a choline- and folate-deficient diet. Heat map illustrating significant differences in hepatic H3K4me3-enrichment of CpG islands between A/J (a) and WSB/EiJ (b) mice fed the CFD diet. Unsupervised hierarchical clustering analysis was performed using one-way ANOVA with p value cut-off at 0.05. The color bar identifies high-H3K4me3-enriched (red) and low-H3K4me3-enriched (green) genes. (c) Table showing number of differentially H3K4me3-enriched CpG islands in hepatic DNA in A/J and WSB/EiJ mice fed a control or CFD diet. Ratio IP/input DNA was calculated using ArrayTrack application. (TIFF 1501 kb