FIGURE 4: The silencing defect at ‘knobs' in set2Δ is not associated with the Mst2 pathway. (A) Scheme depicting expression sites of the non-coding RNA TERRA and the positions of several loci within the ‘knob' regions on chromosomes I and II. Chromosomal positions refer to annotations in www.pombase.org but differ from the absolute positions due to missing sequences at the chromosomal termini. (B) RT-qPCR analysis in WT and set2Δ strains comparing transcript levels at pericentromeric and subtelomeric HC (shaded in grey) to loci in the ‘knob' region. Transcript levels from 12 independent experiments are shown relative to act1⁺. (C, D) ChIP-qPCR analysis of H3K9me2 and H3K36me enrichments in WT cells at loci analyzed in (B). Shown are ChIP data from 2-3 individual experiments analyzed as described in Figure 1D. (E) RT-qPCR analysis in mst2Δ and set2Δ single and double mutants; data from independent experiments analyzed as described in Figure 1C (WT n = 12; mst2Δ, mst2Δ set2Δ: n = 6; set2Δ: n = 9). (F) ChIP-qPCR analysis of TERRA and different loci located within the ‘knob' region; data from independent experiments analyzed as described in Figure 1D (n = 3).