Fig. 4: De novo TAD establishment is independent of transcription.
From: Three-dimensional folding dynamics of the Xenopus tropicalis genome
a, Western blot of RPB1 in WT embryos at the four developmental stages. b, Western blot of proteins in embryos with RPB1 knocked down by morpholinos and in embryos that were rescued. Note that the CTCF and Rad21 protein levels at delayed s10 were similar to s9 WT. Morpholino control (Ctrl); no morpholino (−); rpb1 morpholino (+); rpb1 rescue. See also Supplementary Table 4 for the rpb1 coding sequence for the rescue experiment. c, Schematic representation of the embryogenesis process arrested by RPB1 knockdown and transcription inhibition by α-amanitin. d, Example of a region showing the RPB1 knockdown effects on TAD structure at s9. e,f, Aggregated and normalized heatmaps for s9 and delayed s9 (e), and s10, s13 and delayed s10 (f) for the RPB1 knockdown experiment. g, Example of a region showing the RPB1 knockdown and rescue effects on TAD structure at s11. h, Western blot of proteins in embryos inhibited with α-amanitin. Note that the CTCF and Rad21 protein levels at s9 sustained were similar to s9 WT. Water as control (Ctrl); no α-amanitin (−); the amount of α-amanitin injected was 2 ng per embryo. All western blot experiments in this figure were repeated at least twice unless otherwise stated. i, Example of a region showing the effects of α-amanitin inhibition on TAD structure. j, Aggregated and normalized TAD analysis for embryos of WT s11 and α-amanitin-inhibited s9 sustained.
