Journal: bioRxiv

Article Title: DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

doi: 10.1101/2022.03.24.485667

Figure Lengend Snippet: (A) The numbers of functional EPIC and MM285 array probes on different vertebrate and invertebrate species. (B) Distribution of the DNA methylation reading of functional probes in the rat genome. Rat DNA samples were derived from mixing fully methylated and fully unmethylated rat DNA using titration ratios from 0% to 100%. (C) Probe success rates of the mouse (left) and EPIC arrays (right) on human-mouse mixture titrated at a range of percentages of the mouse DNA (X-axis). Curves of different color represent probe sets that either work on both species (yellow) or just the designed species. (D) Principal component analysis showing the leading PC (PC1) on the X-axis and combined PC2-10 on the Y-axis. Samples are colored by tissue with symbol shape representing species. (E) Heatmap display of the DNA methylation level of species-specific probes and (F) tissue-specific probes. (G) Cross-validation of estimating human DNA fraction using human-mouse variant probes (X-axis) and using human-mouse non-syntenic probes from both mouse and EPIC arrays. Each triangle represents a human-mouse titration sample. Each round dot represents a PDX sample. Color of the triangle corresponds to the known titration fraction of human DNA.

Article Snippet: The first method uses 19 human-mouse syntenic Infinium-I probes with single-nucleotide variations at the extension bases between human and mouse.

Techniques: Functional Assay, DNA Methylation Assay, Derivative Assay, Methylation, Titration, Biomarker Discovery, Variant Assay

Journal: bioRxiv

Article Title: DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse

doi: 10.1101/2022.03.24.485667

Figure Lengend Snippet: (A) 4-way Venn diagram showing the predicted probe functionality in human, mouse, rat and hamster genomes. Validation of the mean signal intensity of probes from different sequence-based utility categories for human, hamster, rat, and mouse DNA. Probes are classified by whether they are functional in human, hamster, and rat. Probes are always functional in mouse by design. Strong signal is only observed when the probe category is predicted to work in the corresponding species. (B) A Heatmap showing the significance (p-value) distinguishing different factors (rows). Wilcoxon rank sum test was used to evaluate the significance of the difference. For tissue, we performed a one-vs-rest pairwise comparison. Percentage of variance explained is shown on top of the heatmap. PC1 is entirely linked to species, while the other PCs are by tissue or a combination of tissue and species. (C) Heatmap showing the pairwise Spearman’s correlation coefficients of 8 human (rows) and 8 mouse tissues (columns). (D) A scatter plot showing the magnitude of tissue-associated variation (X-axis) and species-associated variation (Y-axis) in DNA methylation for each human-mouse syntenic probe (dot). (E and F) LOESS curves fitted between the signal ratios (Y-axis) and the known proportions of human blood DNA mixed in mouse fat (light gold) or spleen (red) DNA samples (X-axis). The signal ratios were calculated using (E) the 19 syntenic probes with SNVs at the extension bases between human and mouse and (F) the non-syntenic probes in the mouse (n=259,626) and human (n=733,164) arrays. (G and H) Standard curves derived using the mean of the two LOESS fitted values from the fat and spleen DNA for the two methods based on (G) the syntenic human-mouse variant probes and (H) the non-syntenic probes in the mouse and human arrays.

Article Snippet: The first method uses 19 human-mouse syntenic Infinium-I probes with single-nucleotide variations at the extension bases between human and mouse.

Techniques: Biomarker Discovery, Sequencing, Functional Assay, Comparison, DNA Methylation Assay, Derivative Assay, Variant Assay

Journal: The Journal of Cell Biology

Article Title: A noncatalytic function of the ligation complex during nonhomologous end joining

doi: 10.1083/jcb.201203128

Figure Lengend Snippet: Requirement of LIG4 for DSB-stimulated DNA-PKcs autophosphorylation in cells and contribution of Cer-XLF. (A and B) Nalm6 control and N114P2 LIG4 -null pre-B cells were treated for 1 h with increasing doses of Calicheamicin γ1 (Cali) as indicated (A) or with 160 pM Cali followed by incubation in fresh medium under normal growth conditions for the specified time (B). Whole-cell extracts were heat denatured, separated on SDS-PAGE gels, and electrotransferred onto membranes that were blotted with antibodies as indicated. Protein samples were separated on 8% acrylamide SDS-PAGE gels for standard separation or 15% for γ-H2AX isolation. (C) Western blotting on the whole-cell extracts of BuC control and BuS Cer-XLF - mutant fibroblasts after treatment with increasing doses of Cali as indicated for 1 h. NT, not treated; PhS59, phosphorylation of SAF-A on S59.

Article Snippet: Mouse monoclonal antibody against SAF-A PhS59 as previously published ( ) was manufactured by Biotem by using phosphopeptide EPGNGS(Ph)LDLGGDC as an antigen.

Techniques: Control, Incubation, SDS Page, Isolation, Western Blot, Mutagenesis, Phospho-proteomics