Collateral DNA damage produced by genome-editing drones: exception or rule?

Abstract

In the recent issue of Nature Biotechnology, Frock et al. (2015) developed an elegant technique to capture translocation partners that can be utilized to determine off-target regions of genome-editing endonucleases as well as endogenous mutators at nucleotide resolution.

Figure 1.. Translocations Discovered by LAM-PCR HTGTS

(A) Top: CRISPR/Cas9 wild-type (left) and D10A nickase (right) generates DSBs and DNA nicks, respectively, leading to on-target and potentially off-target DSBs; aberrant fusions of the DNA ends can cause chromosomal translocations. Bottom: scheme of LAM-PCR HTGTS technology to detect novel translocation partners. Cartoon illustrates the arrangement of chromosomes into three distinct territories within the nucleus. The highlighted square indicates the enlarged view of the on-target (red) and off-target (green) DSBs that are in proximity to each other, thus promoting translocations. Following DNA extraction and shearing, a biotinylated primer specific to the bait DSB is extended, amplifying the hybrid fragment on-target-off-target (bait-prey). The product is subsequently purified with streptavidin and ligated to an adaptor, allowing PCR amplification followed by the identification of the off-targets by next-generation sequencing. (B) Circos plot illustrating the different type of translocations discovered by the HTGTS method, including off-targets DSB “hotspots,” widespread DSBs reflecting non-specific and endogenous DSBs, and inter-homologous fusions involving DSBs generated on both homologous chromosomes. CRISPR/Cas9 (D10A nickase) suppresses translocation hotspots and reduces widespread DSBs in contrast to wild-type CAS9, although inter-homologous fusions at the bait chromosome still persist. (C) Combination of a known DNA break instigator (CRISPR/Cas9; leading to translocation pattern depicted by red lines, bottom) together with an uncharacterized genomic mutator (e.g., TALEN or AID, top) reveal novel translocation partner induced by the latter (blue lines, bottom).