EXPERIMENT_TITLE: GSM5946397: Lamin AC WT cells, replicate 1; Homo sapiens; Human gammaherpesvirus 4; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: 5x10^6 cells per condition were collected for in situ Hi-C. Libraries of total ligation products were produced using Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer's protocol.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Approximately 90% of the world population is infected with EBV and carries the virus in a silent, asymptomatic state for life. In immunocompromised individuals, EBV infection can cause B-cell transformation and malignancies. One approach to control EBV infectivity is by changing the expression of viral genes. We are interested in how epigenetics contributes to regulating the gene expression patterns adopted by EBV during latency. The host's hijacking is a well know strategy adopted by viruses to modify the epigenome, the transcriptome and the proteome of the host with the aim to survive and remain silent in the host. We observed that in B cells, EBV infection mimics antigen-mediated activation, resulting in the induction of specific proteins named Lamin A/C. Lamins have multiple and central roles: they provide nuclear physical support, anchor the heterochromatin to the nuclear periphery and seem to play a role in several nuclear functions requiring the chromatin structure rearrangement. The interaction with lamins has already been studied in the context of EBV lytic reactivation, but their role in the control of the EBV latency states and as epigenetic regulators of different EBV genes expression profiles has not been investigated. The binding of the Lamin AC to important regulatory regions of EBV genome was assessed through ChIP-Seq, and gene expression (RNA-Seq) profiles were evaluated in wild type and Lamin AC KO cell lines. Differences in protein and RNA expressions in B cells activated by using both EBV and a simulation of the immune response were analyzed. Our data suggest two main conclusions: lamins might contribute to the epigenetic control of EBV genes expression during latency changing the interaction of the host structural proteins with key regulatory regions in the viral genome and a possible mechanism with who EBV modifies the nucleus and hijacks cellular mechanisms. Overall design: HiC experiment in LAMIN A/C WT and KO cells. The analysis was focused on the EBV genome only.
SAMPLE_TITLE: Lamin AC WT cells, replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "GM12878 cell line"}, {"TAG": "cell line", "VALUE": "GM12878"}, {"TAG": "genotype", "VALUE": "Lamin A/C WT"}, {"TAG": "replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Lamin AC WT cells, replicate 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Lamin AC WT cells, replicate 1
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