Journal: Cancers

Article Title: SMYD3 Promotes Cell Cycle Progression by Inducing Cyclin D3 Transcription and Stabilizing the Cyclin D1 Protein in Medulloblastoma

doi: 10.3390/cancers14071673

Figure Lengend Snippet: Chromatin immunoprecipitation (ChIP) analysis of transcriptomic and genome-wide SMYD3 binding profiles in MB. ( A ) Heat map showing the distribution and peak intensity of SMYD3 genomic occupancy from 5 kb downstream to 5 kb upstream. ( B ) Schematic representation of peaks into promoter peaks, upstream peaks, intron peaks, exon peaks, and intergenic peaks; pie diagram showing the distribution of peaks. ( C ) Graph depicting the ChIP peak at the global TSS (green) vs. Input peak (orange). ( D ) Pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showing SMYD3 enrichment scores. ( E ) List of genes and their representative pathways whose promoters were bound by SMYD3, as predicted by KEGG pathway analysis.

Article Snippet: The anti-SMYD3 antibody ChIP-enriched DNA was sent for ChIP seq analysis (Arraystar Inc., Rockville, MD, USA).

Techniques: Chromatin Immunoprecipitation, Genome Wide, Binding Assay

Journal: Cancers

Article Title: SMYD3 Promotes Cell Cycle Progression by Inducing Cyclin D3 Transcription and Stabilizing the Cyclin D1 Protein in Medulloblastoma

doi: 10.3390/cancers14071673

Figure Lengend Snippet: SMYD3 binds to the Cyclin D3 promoter. ( A ) Representation of the cyclin D3 (CCND3) gene promoter sequence; (red circles) the EPD software detected four SMYD3 consensus binding sites (−1166, −890, −247, −121 bps) on the cyclin D3 gene promoter. (Blue box) Region −311 to +367 was identified by SMYD3_ChIP-seq analysis. ( B ) Agarose gel showing the PCR amplification of RI (ChIP identified sequence), RII (SMYD3 binding sites within RI), and RIII regions (negative control). ( C ) Scheme depicting the RI, RII, and RIII regions cloned into the pXPG reporter vector. ( D ) Sequence peaks showing the SMYD3 binding sites on the cloned CCND3 promoter regions within the pXPG plasmid. ( E , F ) Effect of SMYD3 on Cyclin D3 (RI region) promoter activity by luciferase reporter assay in D458 (top) and MB002 (bottom) cells. D458 and MB002 cells were transfected with shRNA or overexpression vectors targeting SMYD3 for 48 h or treated with BCI-121 (80 μM) for 24 h. The statistical significance * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: The anti-SMYD3 antibody ChIP-enriched DNA was sent for ChIP seq analysis (Arraystar Inc., Rockville, MD, USA).

Techniques: Sequencing, Software, Binding Assay, ChIP-sequencing, Agarose Gel Electrophoresis, Amplification, Negative Control, Clone Assay, Plasmid Preparation, Activity Assay, Luciferase, Reporter Assay, Transfection, shRNA, Over Expression

Journal: Asian-Australasian Journal of Animal Sciences

Article Title: A demonstration of the H3 trimethylation ChIP-seq analysis of galline follicular mesenchymal cells and male germ cells

doi: 10.5713/ajas.17.0744

Figure Lengend Snippet: H3 trimethylation loci. The total number of peaks significantly identified were categorized according to their regional chromosomes (A). Each color bar presented in the legend was described as following: , peaks shared among all samples with either K4 or K27 trimethylation (All_shared_K4_and_K27); , peaks presented only among samples with K4 trimethylation (All_shared_K4_but_not_K27); , peaks presented only among samples with K27 trimethylation (All_shared_K27_but_not_K4); , peaks presented only in Lat_K4 (Unique_Lat_K4); , peaks presented only in Med_K4 (Unique_Med_K4); , peaks presented only in PS_K4 (Unique_PS_K4); , peaks presented only in RS_K4 (Unique_RS_K4); , peaks presented only in PS_K27 (Unique_PS_K27); , peaks presented only in RS_K27 (Unique_RS_K27), and , other peaks not in the previously mentioned groups. Distribution of precipitated DNA fragments acquired from sample ChIP-seq data according to chicken gene transcription start site was also demonstrated (B). Aggregation of fragments within 0–1 kilobases ( ) and 1–3 kilobases ( ) are presented.

Article Snippet: In conclusion, the current study provided an example for H3 trimethylation ChIP-seq analysis of chicken ( Gallus gallus ) cells.

Techniques: ChIP-sequencing

Journal: Asian-Australasian Journal of Animal Sciences

Article Title: A demonstration of the H3 trimethylation ChIP-seq analysis of galline follicular mesenchymal cells and male germ cells

doi: 10.5713/ajas.17.0744

Figure Lengend Snippet: Chromatin histone 3 (H3) trimethylation state and transcription of cellular retinoic acid binding protein 1 ( CRABP1 ), growth differentiation factor 10 ( GDF10 ), and gremlin 1 ( GREM1 ) genes. The heatmaps of CRABP1, GDF10 , and GREM1 genes were acquired from the integrative genomics viewer (IGV) interface. The chicken full genome sequences was used to identify the chromatin loci of these genes with transcription direction indicated by the arrow heads presented in the genome along with the associated promoters in the area (galGal5 and Promoter regions at the bottom of the figure). The figure show 3 types of data—ChIP-seq, RNA-seq, and Peak files acquired from each sample cell type. In brief, ChIP-seq data show the density of DNA fragments aligned to a chromatin region (aggregated DNA fragments) in blue heatmap. The RNA-seq data show the density of transcript fragments aligned to the gene regions representing level of gene expressions by red heatmap. Finally, the peak file of each cell sample indicated the chromatin region with significant peaks identifed by peak calling analysis.

Article Snippet: In conclusion, the current study provided an example for H3 trimethylation ChIP-seq analysis of chicken ( Gallus gallus ) cells.

Techniques: Binding Assay, ChIP-sequencing, RNA Sequencing

Journal: Asian-Australasian Journal of Animal Sciences

Article Title: A demonstration of the H3 trimethylation ChIP-seq analysis of galline follicular mesenchymal cells and male germ cells

doi: 10.5713/ajas.17.0744

Figure Lengend Snippet: UpSet plot of intersected peaks among cell types. The intersected peaks shared among cell types (Lat_K4, Med_K4, PS_K4, RS_K4, PS_K27, and RS_K27) were presented by UpSet plot. The connected lines among cell types shown in the lower panel of the plot represented the group of intersected peaks among them. The upper panel bar graph of the plot presented the number of peaks found in each group. The shared peak number among all samples with either K4 or K27 trimethylation and only K4 trimethylation are in red ( ) and orange ( ) color, accordingly. The horizontal leftmost bar graph (olive green color, ) show to total number of peaks presented in each cell type.

Article Snippet: In conclusion, the current study provided an example for H3 trimethylation ChIP-seq analysis of chicken ( Gallus gallus ) cells.

Techniques: