Supplementary Figure 6: Firre-hnRNPU interaction is biologically relevant, and hnRNPU has a previously shown role in Xist localization.
From: Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
(a) Endogenous Firre was captured by desthiobiotin-modified DNA oligos in mESCs. The efficiency of capture was measured by qRT-PCR by comparing the RNA levels in the eluate and what is left on the beads post-elution after normalizing to 10% of the total input. The specificity of capture was measured by comparing the eluates from the targeting and scramble oligos. The endogenous RNA pull-down was repeated in mESCs, in which Firre was knocked down to test the specificity of the oligo for the RNA. (b) The endogenous pull-down was repeated in HEK293s to test for the human FIRRE. Additionally, specificity of the oligo was tested by measuring the elutions for the enrichment or depletion of an unrelated lincRNA, linc-Arid4a. (c) Western blot of HEK293 lysates before and after transfection with siRNAs targeting hnRNPU and scramble siRNAs. (d) RNA FISH of Xist in HEK293s after siRNA-mediated depletion of hnRNPU.
