Long Noncoding RNA CCDC26 Interacts With Vimentin, HNRNPC, CBX1, and CBX5 Proteins in Multiple Intracellular Compartments of Myeloid Leukemia Cells

Long noncoding RNAs (lncRNAs) are involved in various biological events. Previously we reported that lncRNA CCDC26 controls myeloid leukemia cell proliferation and mortality by regulating the proto-oncogene KIT. However, the mechanism of lncRNA CCDC26 effects on carcinogenesis and cell differentiation remains unclarified. To investigate the mechanism of lncRNA CCDC26 activity, we analyzed its protein partners using the S1 aptamer/cross-linking-immunoprecipitation (S1-CLIP) experiment. We identified a cytoskeleton protein (vimentin), chromatin proteins (chromobox 1/5 transcription factors [CBX1 and CBX5]) and a nuclear splicing-related protein heterogeneous nuclear ribonucleoprotein C (HNRNPC) as its interaction partners. As lncRNA CCDC26 is ubiquitously present in the cell (in cytoplasm, nucleoplasm, and chromatin cellular fractions); these results evidence that lncRNA CCDC26 is a unique multifunctional lncRNA that functions by interacting with several proteins in multiple intracellular compartments. We further identified the sequence through which it interacts with proteins by using a series of truncated-lncRNA CCDC26 fragments and RNA immunoprecipitation (RIP) experiments. Furthermore, using RIP, we identified the vimentin domain required for the lncRNA CCDC26 binding. Notably, CCDC26 knockdown reduced CBX1/CBX5 binding at certain gene promoters, correlating with increased gene expression. These findings suggest that CCDC26 may regulate transcription by interacting with CBX1 and CBX5.