Project description:Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale.
Project description:We have developed a generally adaptable, novel high-throughput chromosome conformation capture assay for use in trans (V3C-seq) that allows genome-wide identification of the direct associations of a lytic virus genome with discreet regions of the cellular chromosome. Upon infection, the parvovirus Minute Virus of Mice genome associated directly with sites of cellular DNA damage. These sites also exhibited damage in uninfected cells when cycling through S-phase. As infection proceeded, new sites of DNA damage were induced, and virus subsequently also associated with these.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs
Project description:Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs