TABLE 1.
Location of kLANA-enriched regions in the KSHV genome.
| Gene | kLANA peak coordinates on KSHV genome |
Distance of peak summit from TSS (bp) | Enrichment of kLANA, BRD2 and BRD4 at selected TSS |
Epigenetic marks at kLANA peaks |
||||||||||
| kLANA |
BRD2 |
BRD4 |
DNA methylation | H3K9ac/K14ac | H3K4me3 | H3K9me3 | H3K27me3 | |||||||
| Start | End | DMSO | I-BET151 | DMSO | I-BET151 | DMSO | I-BET151 | |||||||
| K6 | 25411 | 28222 | −513 | 2.60 | 1.62 | 1.55 | 0.69 | 1.07 | 0.14 | − | + | + | − | + |
| ORF32 | 50602 | 52462 | −566 | 2.45 | 1.90 | 0.63 | 0.60 | 0.59 | 0.18 | + | + | + | − | + |
| ORF40 | 60402 | 61784 | −1255 | 2.63 | 1.74 | 0.96 | 0.72 | 0.74 | 0.15 | + | + | + | − | + |
| ORF45 | 67647 | 69119 | −62 | 2.82 | 1.75 | 0.94 | 0.62 | 0.75 | 0.15 | + | + | + | − | + |
| K8.1 | 73069 | 75951 | 464 | 2.09 | 1.76 | 0.82 | 0.64 | 0.66 | 0.15 | + | + | + | − | + |
| vIRF-1 | 82679 | 83768 | 1458 | 3.00 | 1.80 | 0.63 | 0.34 | 0.64 | 0.13 | − | − | − | − | + |
| vIRF-1 | 85140 | 86191 | −647 | 3.17 | 1.76 | 1.18 | 0.61 | 1.10 | 0.16 | − | + | + | − | − |
| ORF58 | 94411 | 95945 | −84 | 2.20 | 1.41 | 0.63 | 0.35 | 0.52 | 0.13 | + | + | + | − | − |
| mir-K4 | 118948 | 121844 | −49 | 2.28 | 2.11 | 0.85 | 0.59 | 0.94 | 0.16 | − | + | + | − | + |
| ORF72 | 122138 | 123227 | −100 | 2.29 | 1.75 | 0.83 | 0.50 | 0.64 | 0.16 | + | + | + | − | + |
| ORF73 | 125536 | 128120 | −138 | 2.78 | 2.19 | 0.65 | 0.55 | 0.64 | 0.16 | − | + | + | − | − |
| ORF75 | 132565 | 134454 | −55 | 2.89 | 1.52 | 1.21 | 0.87 | 1.05 | 0.21 | + | + | + | − | − |
Peak coordinates represent the beginning and end of the kLANA peaks in the KSHV genome determined by the MACS peak caller. The numbers in these two columns refer to the nucleotide positions in the KSHV genome. Negative values for distances indicate a location of the kLANA peaks upstream of a TSS. The values for the enrichment for kLANA, BRD2, and BRD4 were calculated with respect to input. Read numbers for peak regions were extracted using the samtools ‘view’ command from both input and ChIP BAM files. The number of reads at these locations were normalized based on a linear scaling factor, which was derived from the total number of reads. Mean fold enrichment values for peak regions in ChIP samples were calculated with respect to matched input samples from the two biological replicates. In the columns ‘Epigenetic marks at kLANA peaks,’ plus and minus signs indicate an overlap or no overlap of the epigenetic mark with kLANA peaks, respectively, using data from Gunther and Grundhoff (2010), Hu et al. (2014).