Fig. 5

IL1RAPL1 expression changes in SETDB1 KO clones. a Map showing the location of IL1RAPL1 exons (vertical bars) and the regions assessed for the 5′ and 3′ qRT-PCRs. The thick black bar on the right corresponds to the region of chromatin change. b Graph showing expression of the 5′ and 3′ ends (x-axis) of the IL1RAPL1 gene relative to GAPDH (y-axis) in RPE1 cells as determined by qRT-PCR. Data corresponds to the mean of at least three biological replicates, each performed as three technical replicates. Error bars show standard error of the mean. c Graphs showing qRT-PCR results for RPE1 and SETDB1 mutants (x-axis) relative to GAPDH expression (y-axis). Data for the 5′ qRT-PCR (left) and 3′ qRT-PCR (right) are indicated above. Both qRT-PCR graphs show the mean and standard error for at least three biological replicates, each amplified as three technical replicates. d Schematic genomic map of the IL1RAPL1 locus with the chromatin change interval marked by the dashed box. Orange blocks beneath the gene model correspond to the locations of BAC clones used in FISH experiments. e Example images of scored categories of direct-labeled RNA FISH to IL1RAPL1 (green) and XIST (red), merged with DAPI (blue). White arrow heads indicate Xa and white arrows indicate Xi. The white horizontal scale bars correspond to 5 μm. f Graph showing the percentage of cells (y-axis) with IL1RAPL1 RNA FISH signals at the Xa in RPE1 and SETDB1 KO clones with the five different BAC clones (x-axis), and g Xi. Scoring data for each clone are given in Additional file 9. All error bars for RNA FISH show standard deviation