Fig. 7.

Pol II occupancy decreases downstream of endogenous iSINEs. a To test for Pol II occupancy we performed ChIP assays for three endogenous genes carrying a single 1SINE in their 3′ UTR and five endogenous genes carrying a paired iSINE in their last UTR exon. Pol II ChIP was performed and the co-precipitated DNA was quantified by qPCR. We amplified three different regions: region A, about 10 kb upstream of the single or inverted SINE; region B, upstream of the iSINE or 1SINE in close proximity; and region C, downstream of the iSINE or 1SINE. Whereas for the 1SINEs (b) we observed both a decrease and increase in Pol II occupancy, the Pol II occupancy clearly drops for four out of five genes carrying an iSINE (c). The average and the standard error of the mean (SEM) calculated from six biological replicates are plotted. d The average and SEM of the three 1SINE- and five iSINE-containing genes. Asterisks indicate p values (region A to region C) calculated with Student’s t-test: *p < 0.05, **p < 0.005, ***p < 0.0005; n.s. not significant