dCas allele sequestration (das-CRISPR): A Versatile New Method to Achieve Monoallelic Gene Editing in Mouse Embryos and in cell culture.

Abstract

CRISPR-Cas9 technology is a powerful tool extensively used for genome editing in mouse and many other species. Streptococcus pyogenes Cas9 efficiently cuts both alleles in mouse zygotes leaving many edited embryos without a functional protein that might be needed to sustain development, to survive postnatally or to reproduce, thus complicating its overwhelmingly advantageous use in making gene modifications. About 25% of mouse genes are essential for embryonic development and another 7% are necessary for fertility, thus for these genes it is desirable to maintain a functional allele to establish viable lines from CRISPR-Cas9 edited mouse embryos. However, exclusive monoallelic editing is challenging to achieve with current CRISPR methods. Controlling the activity of Cas9 in genome editing is an ongoing research field focused on developing new methods to curtail its damage caused by excess of on-target and off-target editing. In this study we describe a novel and a simple method, we termed das-CRISPR, for dCas allele sequestration in combination with CRISPR system, that allows monoallelic editing of targeted allele in mouse and in cultured cell lines. This method incorporates the use of a nuclease deficient deadCas9 (dCas9) present at higher levels than an active Cas9, both complexed with the same single guide RNA (sgRNA) sequence. We showed the delivery of the two proteins as ribonucleoprotein complexes (RNP) into mouse zygotes leads to the generation of viable and fertile mice carrying lethal mutations in an essential gene. We found that greater amounts of dCas9 RNPs bind and protect a target site while the lower amount of functional Cas9 RNPs accessed the unoccupied target site resulting in higher frequency of monoallelic gene editing, compared to using just Cas9 alone. We also showed this method can mitigate and control the activity of Cas9 in mouse NIH3T3 cells in culture to achieve monoallelic editing. This method is a versatile approach to controlling excessive Cas9 activity on-target and off-target both in vitro and in vivo.