EXPERIMENT_TITLE: GSM5426091: HEK293T-EBNA2-1-176-HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For HEK293T Hi-C, cells were crosslinked,digested and ligated. Then protein were degraded by protein K, precipitated by isopropanol. Hi-C libraries were prepared using in-situ Hi-C protocol. Dynabeads MyOne Streptavidin C1 beads was washed once with 1×Tween Washing Buffer. The beads were added to Hi-C DNA and incubated at RT for 15 min with rotation. The beads were washed by adding 200μl of 1×TWB. Heat the tubes on a Thermomixer at 55°C for 2 min with mixing. The beads were reclaimed using a magnet, supernatant was discarded. Repeat washing. End-repair and dA tailing following the in situ Hi-C protocol, adapters were added to DNA fragments. PCR amplification was performed with thirteen to nineteen cycles using Illumina primers.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Epstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by manipulating epigenetics, but the details are unclear. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation. Through the recently developed ATAC-see technology, we observed that EBNA2 reorganized chromatin topology to form accessible chromatin domains (ACDs) of the host genome by phase separation. The N-terminal region of EBNA2, which is necessary for phase separation, is sufficient to induce ACDs. The C-terminal domain of EBNA2 promotes the acetylation of accessible chromatin regions by recruiting histone acetylase p300 to ACDs. According to these observations, we proposed a model of EBNA2 reorganizing chromatin topology for its acetylation through phase separation to explain the mechanism of EBNA2 hijacking the host genome by controlling its epigenetics. Our findings help to understand the molecular mechanism of the EBV-associated diseases and develop therapeutics for these diseases. Overall design: Examination of 2 different histone modifications in Human  nasopharyngeal carcinoma cells.
SAMPLE_TITLE: HEK293T-EBNA2-1-176-HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HEK293T cells"}, {"TAG": "cell line", "VALUE": "HEK293T"}, {"TAG": "cell type", "VALUE": "embryonic kidney cell"}, {"TAG": "treatment", "VALUE": "Transient transfection with EBNA2(1-176) plasmid"}]
Pool_Member_@attributes_sample_title: HEK293T-EBNA2-1-176-HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HEK293T-EBNA2-1-176-HiC
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