Quantitative proteomics identified lncRNA HOTAIR regulated nucleoproteins in HeLa cells

Abstract

Hox transcript antisense intergenic RNA (HOTAIR), which was called oncogenic long non-coding RNA (lncRNA) over expressed in the vast majority of cancer types, regulated various biological processes such as cell growth, apoptosis, proliferation and metastasis. It can regulate hundreds of genes via recruiting complexes: polycomb repressive complex 2 (PRC2) and lysine specific demethylase 1 (LSD1). At that, majority processes happened in nucleic. However, there are no reports to comprehensively research the regulated protein of HOTAIR in nucleic, which is important for explore the mechanism of HOTAIR functions. In this study, we employed a quantitative proteomics analysis of HOTAIR regulated nucleoproteins in cancer cells. Bioinformatical analysis, such as PANTHER, STRING, DAVID were used to understand the function and relationship of these nucleoproteins. In total, we found that 224 nucleoproteins were differential expressed after inhibition HOTAIR, implying that they could be potential targets of HOTAIR. Western blotting analysis, which was used to validation of the quantitative proteomics data, was consistent with stable isotope labelling by amino acids in cell culture (SILAC) experiments. Bioinformatic analysis shown that major changes in nucleoproteins involved in diverse protein class, including the nucleic acid binding and cytoskeletal proteins. Further functional studies of proliferating cell nuclear antigen (PCNA) revealed that various phenotypic effects observed after HOTAIR inhibition, at least in part, through the regulation of PCNA expression. By correlating the proteomic data with these functional studies, the current results provide novel insights into the mechanism underlying HOTAIR functions in cancer cells.