Fig. 5
Knockdown of chromatin modifiers activates a 2C-like gene expression program. a RNA-seq expression level of the 2C-related gene Zscan4c in the indicated knockdowns (left), and a boxplot showing the level of MERVL TEs in the same knockdown RNA-seq data. Bar chart values indicate the mean of the two biological replicates (shHdac5 or shRnf2), or a biological singlicate (shBrd7), relative to shLuc control knockdown. The boxplot shows the Log2 normalized read count mapping to the total set of MERVL TEs, from the same RNA-seq data. b Example genome view showing the RNA-seq pileup data and activation of MERVL-int and MT2_Mm TE expression in Brd7, Hdac5, and Rnf2 shRNA knockdowns. c Boxplot of RNA-seq expression for genes upregulated in the indicated knockdowns. For the sets of genes significantly upregulated in the indicated CM knockdown, their expression was measured in the indicated embryonic stages and in ESCs (RNA-seq data was taken from60). P values are from a Mann–Whitney U test. The x-axis indicates the overall level of expression of the knockdown-specific genes, in those cell types. d Upregulation of a 2C-related gene signature by the indicated CM knockdowns. A 2C-related gene signature was generated by taking the fold-change of all 2C genes versus ESCs and taking the top 200 fold-change upregulated genes. The expression of those top 200 2C genes was then measured in the indicated knockdowns, relative to shLuc control. e MA-scatter plots showing the expression of all genes and TEs in the shRnf2, shHdac5, and shBrd7 knockdowns. Labels and red spots indicate the expression of the shRNA target gene, the MERVL-int TE, and selected 2C-related genes (Zscan4a/b/c/d/e/f-cluster, Duxf3, Hsp90aa1, Hsp90ab1, and Gata2). Note that the effect is not related to deregulation of Trim28 or Kdm1a, two known MERVL regulators. For the boxplots in this figure, the midline indicates the median, boxes indicate the upper and lower quartiles and the whiskers indicate 1.5*interquartile range
