Accession	GSE52421
Status	2014/10/27
Title	Genome-wide ChIP sequence analysis of KSHV-infected primary effusion lymphoma (PEL) cell line BCBL-1 and human umbilical vein endothelial TIVE-LTC cells
Organism	Homo sapiens;Human gammaherpesvirus 8
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	Kaposi’s sarcoma-associated herpesvirus (KSHV) is a g-herpesvirus which persists as circular extrachromasomal DNA in the nucleus during latent infection. During latency a limited number of viral proteins are expressed, including LANA (latency-associated nuclear antigen). LANA is a multi-functional protein known to interact with transcriptional regulators and chromatin remodelers, and to regulate the LANA and RTA promoters. We hypothesized that LANA may contribute to the establishment of latency through controlling chromatinization and histone modification of KSHV episomes. We performed ChIP-seq analysis and correlated H3K4me3, H3K27me3, polII, and LANA occupancy of the KSHV genome at nucleotide resolution. Epigenetic marks were analyzed in BCBL-1 lymphoid cells and in telomerase-immortalized vein endothelial TIVE-LTC cells. We found that the transcription active mark H3K4me3, but not silencing mark H3K27me3, was enriched at KSHV regions where LANA is bound. Co-occupancy of LANA and H3K4 was also detected on 167 host genes, of which 89 are actively transcribed. By comparing LANA occupancy with the profiling of 43 transcription factors from ENCODE, a subset of transcription factors was enriched at regions where LANA is bound, including znf143, CTCF, and Stat1. These results indicate that LANA also plays a role in modulating expression of host genes. Co-immunoprecipitation of LANA with the H3K4 methyltransferase hSET1 suggests that LANA recruits hSET1 to specific loci on the viral genome, leading to H3K4 methylation and ensuring transcription of latency-associated genes. Host gene expression may be regulated by the same mechanism.
Samples	GSM ID Sample info Characteristics Description GSM1265864 Pol_II ChIPSeq TIVE cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:Pol II (Santa Cruz Biotechnology, sc-899); cell line:TIVE-LTC - GSM1265865 H3K4me3 ChIPSeq TIVE_SureSelect cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:H3K4me3 (Abcam, ab8580); cell line:TIVE-LTC The SureSelect Library Prep system (Agilent Technologies) was used to enrich KSHV DNA. Adapters were ligated to ChIP-seq DNA, and 150 bp to 300 bp fragments gel-selected and amplified with 10 PCR cycles. The PCR products were purified with Agencourt AMPure XP beads, denatured, and hybridized with custom KSHV RNA baits at 65 C for 48 h. RNA-DNA hybrids were recovered with Dynal MyOne Streptavidin T1 magnetic beads, and the DNA eluted, purified, and reamplified for 22 PCR cycles. Finally the purified PCR products were quantified and sequenced. GSM1265866 H3K27me3 ChIPSeq TIVE_SureSelect cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:H3K27me3 (Upstate, 07-449); cell line:TIVE-LTC - GSM1265867 Pol_II ChIPSeq TIVE_SureSelect cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:Pol II (Santa Cruz Biotechnology, sc-899); cell line:TIVE-LTC - GSM1265868 Rat IgG ChIPSeq BCBL-1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:control rat IgG ((Santa Cruz Biotechnology, sc-2026); cell line:BCBL-1 - GSM1265869 LANA ChIPSeq BCBL-1 BR1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:rat LANA (ABI Inc., LN53); cell line:BCBL-1 - GSM1265870 LANA ChIPSeq BCBL-1 BR2 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:rat LANA (ABI Inc., LN53); cell line:BCBL-1 - GSM1265871 LANA ChIPSeq TIVE BR1 cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:rat LANA (ABI Inc., LN53); cell line:TIVE-LTC - GSM1265872 LANA ChIPSeq TIVE BR2 cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:rat LANA (ABI Inc., LN53); cell line:TIVE-LTC - GSM1265856 Rabbit IgG ChIPSeq BCBL-1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:control rabbit IgG (Santa Cruz Biotechnology, sc-2027); cell line:BCBL-1 - GSM1265857 H3K4me3 ChIPSeq BCBL-1 BR1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:H3K4me3 (Abcam, ab8580); cell line:BCBL-1 - GSM1265873 LANA ChIPSeq TIVE_SureSelect cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:rat LANA (ABI Inc., LN53); cell line:TIVE-LTC - GSM1265858 H3K4me3 ChIPSeq BCBL-1 BR2 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:H3K4me3 (Abcam, ab8580); cell line:BCBL-1 - GSM1265859 H3K27me3 ChIPSeq BCBL-1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:H3K27me3 (Upstate, 07-449); cell line:BCBL-1 - GSM1265860 Pol_II ChIPSeq BCBL-1 cell type:Primary effusion lymphoma (PEL) cell line; chip antibody:Pol II (Santa Cruz Biotechnology, sc-899); cell line:BCBL-1 - GSM1265861 H3K4me3 ChIPSeq TIVE BR1 cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:H3K4me3 (Abcam, ab8580); cell line:TIVE-LTC - GSM1265862 H3K4me3 ChIPSeq TIVE BR2 cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:H3K4me3 (Abcam, ab8580); cell line:TIVE-LTC - GSM1265863 H3K27me3 ChIPSeq TIVE cell type:Long-Term-Infected Telomerase-Immortalized Vein Endothelial Cells; chip antibody:H3K27me3 (Upstate, 07-449); cell line:TIVE-LTC -
Platform	GPL10999  : Illumina Genome Analyzer IIx (Homo sapiens)
Literature	25033463
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