The Chinese Hamster Ovary miRNome: new strategies for the de novo identification, annotation and profiling of conserved and novel miRNAs

Although Chinese hamster ovary cells are the predominant cell factory for complex biopharmaceuticals including monoclonal antibodies, no genomic sequence information is publicly available. Therefore, as microRNAs might represent valuable tools for cell factory engineering, we deep sequenced the small RNA fraction of 6 CHO cell lines representing biotechnologically relevant stages of cell line development. In the absence of the CHO genome sequence, we developed generalizable strategies for the identification of highly conserved as well as novel miRNA genes, yielding 387 mature CHO miRNA sequences. Further quantitative expression analysis indicated that miRNAs are markers of cell status and sequencing of 26 validated target mRNAs of the miR-17-92 cluster suggests that miRNA target regions are commonly conserved in CHO cells. Thus, miRNAs will also orchestrate the cellular behaviour of CHO cells, and the here published sequence information will establish them as markers for cell line development and for designing of cell factories.