RNA-seq of MCF7 cell lines after EPIC1 siRNA knockdown

In an integrated analysis of long noncoding RNA (lncRNA) epigenetic alterations in 6475 tumor samples and 781 cancer cell lines, we characterized the epigenetic landscape for 1,006 epigenetically activated and 1,117 epigenetically silenced lncRNAs across 20 cancer types. Combining bioinformatics analyses and functional validation, we identified epigenetically induced lncRNA 1 (EPIC1) as a potential oncogene. EPIC1 is epigenetically activated in 15 cancer types and correlated with poor survival of breast cancer. In EPIC1 hypermethylated cancer cell lines, its expression can be induced by demethylating agent in a time- and dose-dependent manner. Knockdown of EPIC1 inhibits MYC targets expression, leads to cell cycle arrest, inhibits colony formation, and decreases cancer cell growth in vitro and in vivo. Mechanistically, EPIC1 directly interacts with MYC 148-220 aa region through its 5' end. Overexpression of EPIC1 increases MYC targets expression and promotes cell proliferation, which can be abolished by the MYC knockdown. Overall design: MCF-7 cells were transfected with 40 nM siRNAs targeting EPIC1 or a control gene luciferase. After transfection for 72 hours, total RNA was isolated and RNA libraries were prepared for sequencing.