Journal: Oncoscience

Article Title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer

doi:

Figure Lengend Snippet: A. ChIP-Seq binding profile of DAXX in PC3 cells at the NRP1 locus. Previously published (accessed through GEO database repository - NCBI) ChIP-Seq data for chromatin modification H3K4me3, H3K4me1, H3K27ac, H3K27me3, and factors RNA polymerase II and CTCF are shown. B. Annotation of 59,778 DAXX ChIP-Seq peaks relative to RefSeq transcript annotations. C. Heatmap depicting the ChIP-Seq read density within ±3 kb from DAXX peaks for DAXX and several chromatin marks. Regions were hierarchically clustered to segregate regions with different enrichment patterns. D. Enrichment of epigenetic ChIP-Seq experiments relative to promoter-distal DAXX ChIP-Seq peaks. E. Results of de novo motif enrichment on DAXX ChIP-Seq peaks using HOMER. F. Overlap between promoter-distal DAXX and putative enhancers (promoter-distal H3K27ac peaks). Significance of overlap p -value < 10 −100 (binomial test, relative to random genomic distribution). G. Overlap between DAXX and CTCF peaks. Significance of overlap p -value < 10 −100 (binomial test, relative to random genomic distribution).

Article Snippet: The human prostate cancer cell line PC3, which was obtained from Scott Crist (Purdue University), was maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine.

Techniques: ChIP-sequencing, Binding Assay, Modification

Journal: Oncoscience

Article Title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer

doi:

Figure Lengend Snippet: A. ChIP-Seq binding profile of DAXX, DNMT1, and epigenetic markers in PC3 cells at the ETV1 locus. DNMT1 binding is shown for both WT and DAXX K/D conditions B. Annotation of 2,237 DNMT1 ChIP-Seq peaks relative to RefSeq transcript annotations. C. Overlap between DAXX and DNMT1 peaks. Significance of overlap p -value < 10 −100 (binomial test, relative to random genomic distribution). D. Results of de novo motif enrichment on DAXX ChIP-Seq peaks using HOMER. E. Overlap between DNMT1 peaks found in PC3 WT cells and PC3 DAXX K/D cells.

Article Snippet: The human prostate cancer cell line PC3, which was obtained from Scott Crist (Purdue University), was maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine.

Techniques: ChIP-sequencing, Binding Assay

Journal: Oncoscience

Article Title: The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer

doi:

Figure Lengend Snippet: A. Total RNA was isolated from PC3 cells as described under Methods. High quality RNA was obtained, as evidenced by high RINs (RNA Integrity Numbers). The first two lanes represent WT samples, whereas lanes 3 and 4 represent DAXX K/D samples. B. Massively parallel RNA sequencing (RNA-Seq) was used to investigate in an unbiased fashion the expression of different genes, comparing the WT and DAXX K/D expression patterns in PC3 cells, using duplicate samples described in A .. RNA-Seq reads were aligned to the human genome using STAR. Gene expression was determined using HOMER. 2,716 genes were found to be induced and 2,329 repressed by DAXX K/D. Genes induced by DAXX K/D included those involved in autophagy. C. DNMT1 levels at DAXX ChIP-Seq peaks within 10kb of the TSS of genes upregulated by shDAXX are shown. Genes upregulated in DAXX K/D cells have lower DNMT1 levels than those in WT cells, indicating that DNMT1 is employed by DAXX in WT cells to repress these genes.

Article Snippet: The human prostate cancer cell line PC3, which was obtained from Scott Crist (Purdue University), was maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine.

Techniques: Isolation, RNA Sequencing, Expressing, Gene Expression, ChIP-sequencing