Outline of the experimental strategy.

<p>The nuclear transcriptome as well as RNAPII-associated genomic sequences of actively transcribing cells are analysed by nucRNA-Seq and RNAPII ChIP-Seq, respectively, as indicated. Top: schematic representation of transcription in the nucleus: four transcribing RNAPII complexes depicted as green shapes are associated with two chromatin fibres, DNA shown in red and blue, respectively; a third chromatin region, which is not being transcribed, is shown with DNA in black; histone complexes are yellow circles, nascent transcripts are shown as thin wavy lines, colours corresponding to chromatin. The nucRNA-Seq procedure is outlined on the left; purified nuclear RNA from the two transcribed regions is shown as wavy or straight lines colour-coded as above, DNA is depicted as thicker lines, random primers are black arrows, a putative genomic region with aligned Illumina paired-end (PE) tags signifies nucRNA-Seq data. The RNAPII ChIP-Seq procedure is outlined on the right; immunoprecipitated RNAPII-associated nucleosomes are depicted and colour-coded as above with cross-links as yellow crosses, anti-RNAPII antibodies are shown as red Y shapes, purified DNA is represented by thick lines, a putative genomic region with PE tags signifies RNAPII ChIP-Seq data.