Fig. 4

Antisense transcript promoters are already poised for transcription. a Antisense transcript induction upon ICP4 overexpression. EYFP-ICP4 or the EYFP-only control plasmid were transfected into HeLa cells and RNA was isolated and subjected to random hexamer-directed RT followed by qPCR with primer pairs as indicated. Experiments were performed with two measurements each from two biological replicates and normalized to the wild-type EYFP-ICP4 value using the D. melanogaster spike-in RNA. Error bars represent standard deviations. In control cells, the FOXO3 antisense transcript could not be reliably quantified since the amplicon was not present in all samples (Additional file 1: Figure S4). b ChIP-qPCR with ICP4-3xflag. ChIP was performed from ICP4-3xflag-transfected HeLa cells, and untransfected cells as control, followed by qPCR using different amplicons, indicated as green lines, around the transcription start sites of FOXO3 and EFNB1. Values are presented as percentage input, and averaged from two measurements each from two biological replicates. Error bars represent standard deviations. c Histone marks at promoter regions. Encode Broad histone marks are shown around the transcription start sites of the unidirectional POLR1B and the bidirectional FOXO3 genes. Transcripts of the sense transcripts and the inducible FOXO3 antisense transcript are indicated. d Histone mark metaplots. Metaplots were generated for four histone marks around the transcription start sites of inducible and constitutively transcribed antisense transcripts, together with 1000 unidirectional control genes