siRNA-mediated loss of LncRNA-HIT affects H3K27ac at its site of nascent transcription.

(A) Relative location of LncRNA-HIT and its nearest neighbors, Hoxa11 and Hoxa13. (B) Visualization of the nascent LncRNA-HIT (green peaks) detected by ChIRP-seq using the USCS Genome Browser. Peaks identified by the even and odd LncRNA-HIT probe sets are indicated on the left axis using even and odd probe sets specific for the LncRNA-HIT lncRNA and displayed by the UCSC genome browser. The localization of the fourteen H3K27ac peaks (black peaks) proximal to the LncRNA-HIT associated peaks as determined by overlaying the H3K27ac limb bud ChIP-seq dataset, GSE3064 [62]. (C) qChIP Analysis of the fourteen H3K27ac regions proximal to the nascent LncRNA-HIT peaks revealed a loss in fragment enrichment in response to the LncRNA-HIT siRNA treatments in limb bud mesenchyme. Values represent the mean fold change H3K27ac fragment enrichment compared to parallel treatments using scrambled LncRNA-HIT siRNA controls for three independent assays. Error bars represent the standard deviation of the mean for the three independent assays.