Fig. 1

LncRNA RP11-196G18.23 binds to ERF promoter and interacts with DNMT3A. A Flowchart of DE-lncRNAs analysis and candidate lncRNAs screening. DE-lncRNAs were analyzed according to log2Ratio > 0.5 and probability > 0.8. LongTarget was used to predict the interactive lncRNAs on ERF promoter. B RP11-196G18.23 was predicted to bind to the ERF promoter shown in the UCSC genome browser. The orange peaks show the binding region of RP11-196G18.23 in the ERF promoter. The number above ‘0’ indicates the maximal number of overlapping triplexes at an address in the region. The shadowed light green bar marks the lncRNA binding sites in the promoter regions. C Regression analysis between ERF and RP11-196G18.23 expression based on the data from GEO database (GSE53983). The gray region indicated the 95% confidence interval. D Copy number of RP11-196G18.23 overexpression in HUDEP-2 and CD34⁺ HSPCs. E, F ChIRP analysis of RP11-196G18.23 interaction with ERF in RP11-196G18.23 OE HUDEP-2 cells. The retrieved ERF DNA (E) and RNA (F) was quantified by qPCR. LacZ, negative control probe. Odd and even, the RP11-196G18.23 probes. ERF p1 and p2, two fragments on ERF promoter. GAPDH, negative control for qPCR. G RIP analysis of interaction of RP11-196G18.23 with DNMT3A in HUDEP-2 cells. IgG, the control for the specificity of the anti-DNMT3A antibody. GAPDH, the negative control. H RNA pull-down analysis of specific association of DNMT1 or DNMT3A with lncRNA RP11-196G18.23 in RP11-196G18.23 OE HUDEP-2 cells. Non-template control (NTC), negative control. AS, antisense sequence of RP11-196G18.23. I Western blot analysis of the protein retrieved from RP11-196G18.23-ChIRP. J ChIP analysis of association of DNMT3A with the ERF promoter (p1 and p2 region) was performed using HUDEP-2 cells without (Ctrl) or with RP11-196G18.23 OE. MYOD1, negative control for qPCR. Data are shown as the means ± SEM from at least two independent experiments (*p < 0.05; ***p < 0.001)