Identification of RNA editing sites in HEK293 cells. Homo sapiens

The identification of RNA editing has proven to be a challenging task. Mapping and alignment artifacts hamper robust detection of RNA editing sites. RNA editing sites are characterized by RNA-DNA-differences (RDDs) that are mediated by two well known classes of RNA editing enzymes. The most prominent class of ADARs (Adeosine deaminases that act on RNA) catalyzes the hydrolytic deamination of adenosine to inosine which is recognized as guanosine by the translational and transcriptional machinery. RNA editing sites are identified by means of A->G substitution in RNS-seq assays. The less frequent C-to-U editing is mediated by the family of APOBECs (apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like) – APOBEC3 has been shown to edit single stranded DNA as a means of defending against foreign DNA. In this study, we have conducted knockdown experiments in HEK293 of editing enzymes to identify edited sites by means of comparing RNA-seq samples of total RNA. In one assay ADAR1 and ADAR2 have been knockdown by using known siRNAs from the literature. In the second assay a set of siRNAs has been applied to knockdown APOBEC3 (B, C, F).