SLNCR-E2F1 oncogenic complexes promote melanoma formation

The long non-coding RNA SLNCR and the transcription factor E2F1 both have oncogenic activities in melanoma. Here we show that melanoma metastasis depends upon the formation of an oncogenic SLNCR–E2F1 complex. Unbiased computational analyses of patient samples revealed worse overall survival only in melanoma patients overexpressing both SLNCR and E2F1. Blocking SLNCR–E2F1 complex formation without reducing the levels of either SLNCR or E2F1 reversed melanoma invasion ex vivo and melanoma extravasation in mice. We discovered that E2F1 bound to sequences in SLNCR that are the RNA analogs of the E2F consensus DNA-binding element, suggesting that RNA and DNA binding engages the same domain in E2F1. Binding competition assays demonstrated that E2F1 preferentially bound to RNA compared to its cognate DNA element and that RNA efficiently competed with the consensus DNA-binding element for E2F1 binding. Molecular dynamics simulations indicated increased thermodynamic stability of E2F1–DNA interactions as compared to E2F1–RNA interactions. However, molecular dynamics simulations also indicated greater number of RNA-amino acid contacts within the E2F1 DNA binding domain (E2F1DBD) than DNA. This suggests better kinetic binding properties of RNA to the E2F1DBD as compared to DNA and may explain how RNA efficiently competed with DNA for E2F1DBD binding. E2F1 often binds to DNA as a heterodimer with DP1. Molecular dynamics simulations suggested that RNA binding to E2F1 may prevent E2F1–DP1 heterodimerization by masking key amino acids required for DP1 binding. These data reveal the SLNCR-driven oncogenic activities of E2F1 and identify the SLNCR–E2F1 complex as a target for future melanoma therapy. Overall design: To identify the genes regulated by SLNCR in A375 cells and characterize the transcription factors enriched in the differentially expressed genes we transfected a SLNCR overexpression plasmid or control vector into A375 cells n = 3 biological replicates for each condition and performed RNA-Seq.