Accession	GSE19905
Status	2010/6/7
Title	Global analysis of DNA methylation patterns on the latent KSHV episome in PEL and de novo infected endothelial cells
Organism	Human gammaherpesvirus 8
Experiment type	Methylation profiling by genome tiling array
Summary	Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of epigenetic modifications during latent infection with Kaposi's sarcoma associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). Using high resolution tiling microarrays in conjunction with immunprecipitation of methylated DNA (MeDIP) and modified histones (ChIP), we have determined global patterns of epigenetic modifications across the KSHV genome in several tumor-derived cell lines as well as de novo infected endothelial cells, revealing highly distinct landscapes of epigenetic modifications associated with latent KSHV infection. We find that KSHV genomes are subject to profound methylation at CpG dinucleotides, leading to the establishment of characteristic global DNA methylation patterns. However, such patterns evolved slowly and thus are unlikely to govern latency early during the infection process. In contrast, we observed that latent histone modification patterns were rapidly established upon a de novo infection. Our analysis furthermore demonstrates that such patterns are not characterized by the absence of activating histone modifications, since both H3K9/K14-ac and H3K4-me3 marks were prominently detected at several loci, including the promoter of the lytic cycle transactivator Rta. While these regions were furthermore largely devoid of the constitutive heterochromatin marker H3K9-me3, we observed rapid and widespread deposition of H3K27-me3 across latent KSHV genomes, a bivalent modification which is able to repress transcription despite of the simultaneous presence of activating marks. Our findings suggest that the epigenetic patterns identified here induce a poised state of repression during viral latency, which can be rapidly reversed once the lytic cycle is induced. This dataset contains our MeDIP data; the ChIP-on-chip data are deposited in a separate dataset.
Samples	GSM ID Sample info Characteristics Description GSM498056 SLK_BacM_pos_control_MeDIP cell line: SLK;sample type: positive control;cell type: endothelial cells MeDIP positive control sample: prior to MeDIP, in vitro methylated KSHV bacmid Bac36 DNA was spiked into genomic SLK DNA and adjusted via real time PCR to mimic KSHV copy numbers as seen in BCBL1 and SLKP cells. GSM498057 BCBL1_MeDIP cell line: BCBL1;sample type: biological sample;cell type: B cells Analysis of DNA methylation patterns in the PEL-derived cell line BCBL1 GSM498058 SLKP_MeDIP cell line: SLKP;sample type: biological sample;cell type: endothelial cells Analysis of DNA methylation patterns in long-term infected SLKP cells GSM498059 AP3_MeDIP cell line: AP3;sample type: biological sample;cell type: B cells Analysis of DNA methylation patterns in the PEL-derived cell line AP3 GSM498060 SLK5dpi_MeDIP cell line: SLK;sample type: biological sample;cell type: endothelial cells Analysis of DNA methylation patterns in de novo infected SLK cells at 5 days post-infection GSM498061 HBL6_MeDIP cell line: HBL6;sample type: biological sample;cell type: B cells Analysis of DNA methylation patterns in the PEL-derived cell line HBL6 GSM498062 SLK_Bac_neg_control_MeDIP cell line: SLK;sample type: negative control;cell type: endothelial cells MeDIP negative control sample: prior to MeDIP, unmethylated KSHV bacmid Bac36 DNA was spiked into genomic SLK DNA and adjusted via real time PCR to mimic KSHV copy numbers as seen in BCBL1 and SLKP cells. This dataset was used to perform MeDIP specific background correction for all other datasets and is thus not represented by its own 'MeDIP to input' ratio. GSM498063 SLK_Input cell line: SLK;sample type: spot performance control;cell type: endothelial cells The Cy3 channel of this sample was used as a negative control to permanently flag spots which exhibit cross-hybridization with cellular DNA; there is no ratio data for this sample.
Platform	GPL9942  : HPI-AG KSHV 15k v. 3.0
Literature	20532208