eIF2A regulates cell migration without overtly affecting translation

The RNA-binding protein eIF2A has been implicated in a variety of cellular processes including tumorigenesis. This role has been attributed to its function as alternative translation initiation factor. However, the mechanisms by which eIF2A regulates translation and its contribution to oncogenic transformation are unclear. Here, we shed light on these aspects using a melanoma cell model consisting of the non-tumoral melanocytic cell line MelST and its metastatic counterpart obtained by RasV12 overexpression (MelSTR). Depletion of eIF2A from MelST and MelSTR cells revealed acquired dependencies upon Ras transformation for migration. Surprisingly, analysis of the transcriptome (RNA-Seq) and translatome (ribosome profiling) upon eIF2A depletion showed minor to no changes in translation. RIP-Seq and RT-qPCR furthermore indicate that eIF2A binds mRNA targets in a translation-independent manner. Interestingly, protein interactome analyses point towards a function of eIF2A in cytoskeletal remodeling and indeed we can show that eIF2A localizes to the centrosome and affects its composition and orientation, linking eIF2A with migration. In addition, eIF2A promotes migration in a manner that depends on its RNA-binding activity. Together, these results indicate that eIF2A does not function as a translation factor in melanoma cells, but through a novel function which is based on its RNA-binding activity and its connections to the centrosome. To identify direct eIF2A mRNA targets and the binding regions in melanoma SKMEL-147 cell lines, iCLIP was performed in triplicates. Anti-eIF2A antibody (abcam #ab169528) was used to immunoprecipitate eIF2A. As a negative control, non UV crosslinked samples were included.