Journal: Genome Research

Article Title: Reorganization of the host epigenome by a viral oncogene

doi: 10.1101/gr.132308.111

Figure Lengend Snippet: Small e1a causes global deacetylation and redistribution of H3K18ac. ( A ) Venn diagram showing the overlap between significant peaks of H3K18ac in mock- (dark blue) and dl 1500-infected cells (light blue). ( B ) Venn diagram showing the overlap between significant peaks of H3K9ac in mock- (dark orange) and dl 1500-infected cells (yellow). ( C ) Patterns of H3K18ac and H3K9ac in the intergenic region between COPS8 and COL6A3 genes in mock-, dl 1500-infected, and asynchronous IMR90 cells. ( D ) Quantitative PCR (% of input) for EP300 and CREBBP in mock- and dl 1500-infected cells for the COL6A3 intergenic region, and CCNE2 and POLD3 promoters are shown as bar plots. Patterns of H3K18ac in mock- and dl 1500-infected cells at CCNE2 and POLD3 loci are also shown. For each histone modification, the y -axis indicates the number of input-normalized ChIP-seq reads across the locus ( x -axis). (Light blue arrows) New peaks of acetylation in e1a-expressing cells. (Dark arrows) Direction of transcription. ( E , F ) Overview of distribution of H3K18ac and H3K9ac peaks in mock- and dl 1500-infected cells in relation to gene structure are shown as pie charts. ( G ) Distribution of significant peaks of H3K18ac with respect to TSS in mock- (dark blue) and dl 1500-infected (light blue) cells. ( H ) Distribution of significant peaks of H3K9ac with respect to TSS in mock- (dark orange) and dl 1500-infected (yellow) cells.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO 2 .

Techniques: Infection, Real-time Polymerase Chain Reaction, Modification, ChIP-sequencing, Expressing

Journal: Genome Research

Article Title: Reorganization of the host epigenome by a viral oncogene

doi: 10.1101/gr.132308.111

Figure Lengend Snippet: Analyses of RB-family protein genome-wide binding in contact-inhibited IMR90 fibroblasts. ( A ) Overview of RB1, RBL2, and RBL1 peak distributions in mock-infected cells in relation to gene structure are shown as pie charts. ( B ) Average binding profiles (significant counts) of the indicated RB-family members across the TSS regions of their respective target genes. ( C ) A 600-bp region around the peaks of RB1, RBL2, and RBL1 in mock-infected cells were analyzed for TF binding motifs using sitepro (Galaxy). Top three significant motifs for each family member are shown. All P -values are less than 1 × 10 −10 . ( D ) The distributions of the RB-family proteins across ±5 kb of TSS for genes with at least one RB-family member bound are shown as heat maps. The seven clusters are based on combinatorial binding patterns of the three proteins. ( E ) Relative gene expression changes of each of the seven clusters after e1a expression at 24 h p.i. are shown as box plots.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO 2 .

Techniques: Genome Wide, Binding Assay, Infection, Gene Expression, Expressing

Journal: International Journal of Epidemiology

Article Title: Association between perinatal methylation of the neuronal differentiation regulator HES1 and later childhood neurocognitive function and behaviour

doi: 10.1093/ije/dyv052

Figure Lengend Snippet: Methylation of CpG5 blocks ETS transcription factor binding to the HES1 promoter sequence. Results are typical of three analyses. (a) The unmethylated biotin-labelled probe showed a strong shift upon incubation with nuclear extract from the human neuroblastoma cell line IMR32; this shift was markedly reduced by co-incubating with 500-fold excess of the unlabelled specific competitor, but not with 500-fold excess of an unlabelled non-specific competitor. (b) Binding to the probe was markedly diminished by co-incubation with 100-fold excess of an unlabelled oligonucleotide containing the core consensus sequence for ETS (GGAA) but not with 100-fold excess of a mutated ETS core competitor (c) The unmethylated probe was incubated with 50-, 100- and 500-fold excesses of the unmethylated or methylated competitor; binding to the unmethylated probe was competed out with a 100-fold excess of the methylated competitor compared with a 500-fold excess of the unmethylated competitor.

Article Snippet: Electrophoretic mobility shift assays were carried out using 5 µg of IMR32 nuclear extract (sc-2148, Santa Cruz Biotechnology, USA).

Techniques: Methylation, Binding Assay, Sequencing, Incubation