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Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M , JAG2 , and FLRT1 . Together, our results imply three-dimensional genome a ....
Credit: Genome 10K Project Study Take-Aways Unprecedented novel discoveries have implications for characterizing biodiversity for all life, conservation, and human health and disease. o This finding provides novel avenues of research to increase immune defenses, particularly relevant for emerging infectious diseases, such as the current COVID-19 pandemic. The flagship paper presented whole genome sequence analyses of 16 vertebrate species to illustrate high quality, near error free, near complete, low cost reference genome assemblies. o Though near 400 species have been sequenced at some level, the quality today reflects a quantum leap in precision sequence details and discovery. FORT LAUDERDALE/DAVIE, Fla. - Two decades ago, the full genome sequence of humankind was released. It was funded by international government and philanthropic sources at a cost of billions of dollars. ....
E-Mail The Vertebrate Genomes Project (VGP) today announces their flagship study and associated publications focused on genome assembly quality and standardization for the field of genomics. This study includes 16 diploid high-quality, near error-free, and near complete vertebrate reference genome assemblies for species across all taxa with backbones (i.e., mammals, amphibians, birds, reptiles, and fishes) from five years of piloting the first phase of the VGP project. Nature, with companion papers simultaneously published in other scientific journals, the VGP details numerous technological improvements based on these 16 genome assemblies. In the flagship study, the VGP demonstrates the feasibility of setting and achieving high-quality reference genome quality metrics using their state-of-the-art automated approach of combining long-read and long-range chromosome scaffolding approaches with novel algorithms that put the pieces of the genome assembly puzzle together. ....
Press release content from PR Newswire. The AP news staff was not involved in its creation. Active Motif Partners with Arima Genomics to Launch End-to-End Hi-C Service February 9, 2021 GMT SAN DIEGO and CARLSBAD, Calif., Feb. 9, 2021 /PRNewswire/ Epigenetics-based research tools and services company, Active Motif, Inc., announced today that it has launched an end-to-end Hi-C service in partnership with Arima Genomics, Inc. to investigate the three-dimensional folding patterns of the genome, providing researchers with greater access to this powerful technology and advancing their research. The launch of this Hi-C service extends Active Motif’s 15 years of experience and expertise offering Epigenetic Services, such as ChIP-Seq and ATAC-Seq services, and now allows researchers to gain a deeper understanding of the biological mechanisms at play in their clinical samples or experimental systems. Active Motif continues to offer the most comprehensive offering of epig ....