Abstract C/EBPα has known to be a transcription factor that involved in Neutrophil differentiation for decades. However, exploring the Chromatin RNA Immunoprecipitation Sequencing (RIP), we discover that C/EBPα is a RNA binding protein mainly interacts with RNA introns. Structure study and RNA electrophoretic mobility shift assay (REMSA) show that C/EBPα interacts with RNA through two novel RNA binding domains distinct from its DNA binding domain. Mouse bone marrow transplantation and in vitro cytokine assay reveal that C/EBPα RNA binding is critical for Macrophage differentiation but not Neutrophil differentiation. Mechanically, RNA binding domains control specific gene transcription. In particular, PU.1 intron 4 RNA interacts with C/EBPα and recruit C/EBPα to its enhancer site, which facilitate PU.1 expression. Taken together, C/EBPα is demonstrated to be a RNA binding protein with unique function distinct from its DNA binding activity. Our finding transforms our knowledge of transcriptional regulation by transcription factor. One-Sentence Summary C/EBPα interacts with RNA through novel RNA binding domains and regulates PU.1 expression during Macrophage differentiation.

C/EBPα acts as an RNA binding protein essential for its chromatin recruitment and promotes Macrophage differentiation