Figure 1. ChIP and ChRIP approach. (a) ChIP. RNA Polymerase II (blue circles) transcribes gene (black open boxes = exons; black line = intron) into nascent RNA (yellow), while SF (light blue diamond) binds to RNA cotranscriptionally. Following formaldehyde crosslinking and chromatin shearing, fragments containing the SF are immunopurified using specific antibodies (green). The purified DNA is then analyzed by qPCR with primers covering regions along the gene. DNA fragments that were crosslinked to SF and RNA are enriched during immunoprecipitation, thus giving a higher qPCR signal; (b) ChRIP. Acetylated histone H4 (AcH4) as a marker of actively transcribed chromatin is crosslinked to RNA Polymerase II and nascent RNA. Following formaldehyde crosslinking and shearing, the AcH4 chromatin fragments are immunopurified, nascent RNA is extracted, and the presence or absence of introns (and thus cotranscriptional splicing) are verified by RT‐qPCR.

Figure 2. Analyzed qPCR data showing fold enrichment of SRp55‐GFP on four amplicons along induced c‐fos relative to (a) nonspecific IgG and (b) nonspecific IgG as well as the gene desert region. The error bars represent SEM values.