Project description:For Large White (LW) and Meishan (MS) skeletal muscle, we performed H3K27ac BL HiCHIP to establish enhancer-promoter interaction maps. We also performed GRID-seq which uses a bivalent linker to ligate RNA to DNA in situ.
Project description:H3K27ac HiChIP analysis was performed in an adult T-cell leukemia/lymphoma cell line (TL-Om1) to analyze active chromatin-chromatin interactions in TL-Om1 cells.
Project description:H3K27ac HiChIP analysis was performed in GI-MEN DOX-ASCL1 cells to analyze active chromatin-chromatin interactions in GI-MEN DOX-ASCL1 cells.
Project description:We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, H3K27ac HiChIP, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. In addition, MRPA results suggest nuclear receptor motifs are required for the activity of some p300 late enhancers. With Hi-C and H3K27ac HiChIP data of E12.5, P0 and adult CMs, we identified chromatin structure changes such as chromatin loops, compartment switch, and new TAD boundaries are associated with dynamic p300 binding. This study provides data source of CM-selective p300 enhancers, chromatin 3D structure and gene expression during CM development and maturation.
Project description:We report no global changes in H3K27Ac upon expression of ZNF384 fusions but 47 loci with increased H3K27Ac. Therefore we performed HiChIP H3K27Ac to determine if those loci are enhancers. We did not observe any differential looping.
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).