GRAS1 non-coding RNA protects against DNA damage and cell death by binding NKAP

Abstract

ABSTRACTNon-coding RNA (ncRNA) gene products are involved in diverse biological processes, but the biological mechanisms by which ncRNAs may regulate cell survival remain poorly understood. We found that the Growth Regulator Antisense (GRAS1) RNA transcript is a positive regulator of growth. Decreased levels of GRAS1 long non-coding RNA (lncRNA) caused DNA damage, cell death, and upregulated expression of genes associated with p53 signaling pathways. Extensive DNA damage occurred after GRAS1 knockdown, with multiple double strand breaks occurring in each cell. The number of cells arrested with low DNA content in sub-G1 phase increased significantly after GRAS1 knockdown. We used RNA antisense purification and mass spectrometry (RAP-MS) to identify the NF-κB activating protein (NKAP) as a direct protein interaction partner of GRAS1 lncRNA. NKAP protein levels decreased after GRAS1 knockdown, while mRNA levels were not affected. The decrease in NKAP protein after GRAS1 knockdown was blocked by proteasome inhibition. GRAS1 knockdown led to lipid peroxidation and overexpression of NKAP prevented the cell death effects of GRAS1 knockdown. NKAP overexpression protected against DNA damage in GRAS1 knockdown cells. We concluded that GRAS1 lncRNA binds and stabilizes NKAP to promote cell survival and protect against DNA damage and cell death.