Fig. 6

Snhg3 is regulated by pluripotency factors and its associated protein network. a Genome browser plot of histone methylation related to transcriptional activation (H3K4me3) and repression (H3K27me3) in the gene body region of Snhg3 in mouse embryonic stem cells (mESCs). The gray peaks indicate potential H3K4me3-binding sites in Snhg3. The purple box highlights the proximal promoter regions (− 0.5 kb to + 1.5 kb of transcriptional start site) of Snhg3. b ChIP-qPCR analysis of Nanog, Oct4, or Sox2 occupancy in the Snhg3 promoter region in mESCs. IgG was used as a negative control. c qRT-PCR analysis of the expression levels of Nanog, Oct4, and Snhg3 after knocking down Nanog or Oct4 in mESCs. d Cellular fractionation was performed in mESCs, and mRNA levels of Snhg3 were measured by qRT-PCR. Xist and Gapdh served as nuclear and cytoplasmic markers, respectively. The percentage of subcellular fractions of each gene is shown. e RNA immunoprecipitation assay was performed by using anti-Nanog, anti-Oct4, or anti-Sox2 antibodies to precipitate Snhg3 in mESCs. IgG was used as a negative control. f Flowchart of RNA pull-down and mass spectrometry (MS) for Snhg3-associated proteins. g Pie charts of Gene Ontology (GO) term analysis of the 126 total Snhg3-associated proteins identified by MS. h Model for lncRNA Snhg3 function in mESCs. Snhg3 is bound and activated by pluripotency factors Nanog and Oct4 in mESCs and can form a protein complex with Nanog and Oct4, which in term safeguards self-renewal and pluripotency in mESCs. Data are presented as mean ± SD; n = 3, two-way ANOVA. **p < 0.01, ***p < 0.001 for all panels