This study systematically shows, in various human cell lines, that cytosine base editors (CBEs), which are supposed to enzimatically convert cytosines to thymines in specific target sites of the genome, also cause many unintended changes at the level of the RNA.
Base editors are based on a dead Cas9 enzyme that can still recognize the target site by a guide RNA (gRNA), but can no longer introduce DNA double-strand breaks there.
The changes are caused by an enzyme (in this publication: rAPOBEC1) that is coupled to the dead Cas9 enzyme. The authors show that, at the RNA level, cytosines are inadvertently converted into uraciles, which leads to proteins being formed differently. These unwanted C-to-U changes at the RNA level occur regardless of unintended changes at the DNA level.
The off-target changes in the RNA described here occur independently of the respective guide RNA, but through an additional activity of the base editor. Mutations in the base editor are intended to reduce unwanted RNA activity and maintain activity only at the DNA level. These types of off-target effects are also found at the RNA level in adenosine base editors (ABEs) that convert from A (adenosine) to G (guanosine).