Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data

Chinese hamster ovary (CHO) cells are currently the most important mammalian host for the manufacture of biopharmaceuticals. To enhance our understanding of cellular processes, pathways, and the genetic setup of CHO cell lines, we predicted PIWI interacting RNAs (piRNAs) from small RNA sequencing data. Although piRNAs are the least understood class of small non-coding RNAs that mediate RNA silencing, it is believed that they play a pivotal role in protecting genome integrity by repressing transposable elements. Since genomic integrity is the key to prolonged stability of recombinant CHO cell lines, we characterized piRNA sequences and expression in six CHO cell lines by computational analysis of an existing small RNA sequencing dataset using proTRAC and the published CHO genome as reference. Here we present the result of this analysis consisting of 25,626 piRNAs and 540 piRNA clusters. Moreover we provide first evidence for differential piRNA expression in adherent and suspension-adapted CHO-K1 and DUKXB11 host cell lines as well as their recombinant derivatives, indicating that piRNAs might be tools for cell line development and engineering.