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bioRxiv · 10.1101/2021.10.20.465166

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

Zhang, Y.·Bassal, M.·Friedrich, D.·Ummarino, S.·Verbiest, T.·Zhang, J.·Tenen, D.·Haribabu, A.·Tenen, D. G.
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Abstract

C/EBP 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/EBP is a RNA binding protein mainly interacts with RNA introns. Structure study and RNA electrophoretic mobility shift assay (REMSA) show that C/EBP 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/EBP 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/EBP and recruit C/EBP to its enhancer site, which facilitate PU.1 expression. Taken together, C/EBP 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 SummaryC/EBP interacts with RNA through novel RNA binding domains and regulates PU.1 expression during Macrophage differentiation.

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Zhang, Y., Bassal, M., Friedrich, D., Ummarino, S., Verbiest, T., Zhang, J., Tenen, D., Haribabu, A., Tenen, D. G.. 2021-10-20. C/EBPα acts as an RNA binding protein essential for its chromatin recruitment and promotes Macrophage differentiation. https://doi.org/10.1101/2021.10.20.465166

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