Extended Data Fig. 6: Knockdown of ERV RNA rescues super-enhancer transcription in TRIM28-degraded cells.
From: Hijacking of transcriptional condensates by endogenous retroviruses
a. Scheme of knockdown experiments with simultaneous TRIM28 degradation. b. qRT-PCR analysis from three independent biological replicates. Data presented as mean values ± SD. Experiment was performed twice, and the data shown are from one representative experiment. P values are from two-tailed t tests. ****: P < 10−4, ***: P < 10−3, **: P < 10−2, *: P < 0.05. c. Scheme of IAP knockdown experiments. d. qRT-PCR data displayed as fold change normalized to the 0 h control from three independent biological replicates. Data are presented as mean values ± SD. Each dot represents the mean of the three biological replicates of an individual experiment. P values are from two-tailed t-tests. ****: P < 10−4, ***: P < 10−3, **: P < 10−2, *: P < 0.05. e. Scheme of the experiment in which shRNAs are induced for 24 h and then treated either with DMSO (yellow), dTAG-13 (orange) or with dTAG-13 and Dox (maroon) for additional 24 h. f. qRT-PCR data as fold change normalized to the Dox (24 h) treatment control from three independent biological replicates. Data are presented as mean values ± SD. Experiment was performed twice, and data from one representative experiment is shown. P values are from two-tailed t-tests. ****: P < 10−4, ***: P < 10−3, **: P < 10−2, *: P < 0.05. g. RNA levels detected with total RNA-seq. Values from three biological replicates are normalized to levels detected at 0 h. Red arrowheads highlight the ERV taxa against whose sequences the shRNAs were designed. h. Representative images of IAP RNA FISH in cells described in panels (e–f). Scale bar: 2.5 μm. i. Analyses of cells used in Fig. 4d. (left) RNAPII IF intensities at the miR290-295 FISH foci (nDMSO = 100, ndTAG-13 = 52, nDox+dTAG-13 = 60). (right) RNAPII mean fluorescence intensity at random nuclear positions (nDMSO = 97, ndTAG-13 = 88, nDox+dTAG-13 = 60). Data presented as mean values ± SD from one staining experiment. P values are from two-sided Mann-Whitney tests. NS: not significant. j. Images of individual z-slices (same z) of the RNA-FISH and IF signal. Nuclear periphery determined by DAPI staining is highlighted as a white contour. Also shown are averaged signals of either RNA FISH or RNAPII IF centered on the miR290-295 FISH foci or randomly selected positions. Scale bars: 2.5 μm. The experiment is an independent biological replicate of the experiments shown in Fig. 4d.
