Fig. 4

Platr10 lncRNA is required for the formation of intrachromosomal looping in the Oct4 locus. A Location of 3C primers used to detect the interaction between the Oct4 promoter and enhancer. Enh, enhancers; pOct4, Oct4 promoter; 5’-Ct, the 5’ upstream control region of Oct4; 3’-Ct, The 3’ downstream control region of Oct4; E1-E5, exons; Bm, BamH1; Bg, Bgl2. Arrows: intrachromosomal interactions. B Knockdown of Platr10 abolishes the intrachromosomal interaction loop. shCT, negative control shRNA; shPlatr10, shRNA that targets Platr10 lncRNA; iPSC, induced pluripotent stem cell; FIB, fibroblasts. Primer sets that detect the presence of looping are marked in red. The 3C interaction was quantitated by qPCR and was standardized over the 3C control Ercc3 gene. For comparison, the relative 3C interaction was calculated by setting the 5’ or 3’ control as 1. **p < 0.01 as compared with the shPlatr10 treatment and FIB controls. C Profiling Platr10-binding proteins. The Platr10-binding protein factors were mapped by RNA pulldown MS sequencing using biotin-labeled Platr10 sense lncRNA in E14 cells. The Platr10 antisense RNA was used as the control. The binding signal was calculated as the protein enrichment ratio (the PEAKS score, −10logP) after adjusting over that of the antisense control. The protein interaction network was constructed using the String database web tool (https://string-db.org/)