Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA-counterpart in terminal hematopoiesis

Abstract

Each day, about 10^12 erythrocytes and platelets are released into the blood stream. This substantial output from hematopoietic stem cells is tightly regulated by transcription factors and epigenetic modifications. Whether and how non-coding RNAs such as circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not well understood. We recently reported a circRNA expression map of hematopoietic cells, revealing that erythrocytes and platelets contain the highest levels and numbers of circRNAs. Here, we provide the first detailed and comprehensive analysis of circRNA expression during red blood cell and megakaryocyte differentiation. CircRNA expression significantly increased during erythroid precursor differentiation into red blood cells and in differentiating megakaryocytes, in particular upon enucleation. To determine if circRNAs can modulate hematopoietic differentiation, we compared the expression levels of circRNAs and mRNAs with that of ribosomal foot printing read. This multi-omics approach revealed that only 20 out of 748 (2.6%) circRNAs associated with translation regulation of their mRNA counterparts. Furthermore, irrespective of the thousands of identified putative open reading frames in circRNAs, deep ribosome-footprinting sequencing and mass spectrometry analysis provided little evidence for translation of endogenously expressed circRNAs in erythroblasts, megakaryocytes and platelets. In conclusion, circRNAs in platelets and red blood cells are highly abundant and alter their expression profile during differentiation, yet their contribution to regulate cellular processes remains enigmatic.