Engineered nucleases, including zinc-finger nucleases (ZFNs) and TAL-effector nucleases (TALENs), are promising tools for targeted genetic engineering 
. The ability to enrich cells with targeted mutations greatly facilitates the process of using engineered nucleases to construct such cells 
. We previously developed surrogate reporters that enable the efficient enrichment of cells containing nuclease-induced mutations via flow cytometry 
. This method is, however, limited by the availability of flow cytometers. Furthermore, sorted cells occasionally fail to form colonies after exposure to a strong laser and hydrostatic pressure. Thus, we attempted to develop methods to select mutant cells without the use of flow cytometers.
Magnetic separation has been used as an alternative method to isolate cells that express specific antigens 
. Magnetic separation does not require flow cytometers and is faster and easier to perform than flow cytometric sorting 
. To separate transgenic cells from wild-type cells immunomagnetically, H-2Kk
, a truncated mouse MHC class I molecule, is used as a selection marker 
is expressed only in some rare mouse strains such as AKR/J or CBA/J, but not in human or most other murine cells 
, rendering H-2Kk
a good marker to distinguish transgenic cells from control cells. To avoid any effects generated by the expression of H-2Kk
, a truncated H-2Kk
that lacks a cytoplasmic domain is used 
. Magnetic separation using H-2Kk
is effective in the enrichment of transiently transfected cells 
and lenti- or retro-virally transduced cells 
. Here we adopt this system to enrich mutant cells generated by engineered nucleases.
Selection of cells using resistance factors against antibiotics is widely used for the isolation of genetically-modified cells in prokaryotes 
and eukaryotes 
. Hygromycin B is an aminoglycoside antibiotic produced by the bacterium Stepretomyces hygroscopicus
, which kills both prokaryotes and eukaryotes by inhibiting protein synthesis through interference with aminoacyl-tRNA recognition and ribosomal translocation 
. Hygromycin B phosphotransferase, encoded by the hygromycin-resistance gene that was originally isolated from Escherichia coli
, phosphorylates hygromycin B, resulting in its inactivation 
. This gene has been successfully used as a selection marker for transformed prokaryotes 
and transgenic eukaryotes 
. The hygromycin resistance gene has also been adopted to prepare donor DNA that will be integrated into a host genome via engineered nuclease-enhanced homologous recombination, allowing selection of cells with targeted genetic modifications 
. However, the isolation of engineered nuclease-induced mutant cells using hygromycin selection based on transiently active episomal reporters has yet to be demonstrated.
Here we present two novel reporter systems that enable enrichment of nuclease-induced mutant cells using magnetic separation and hygromycin selection. These reporters express H-2Kk and the hygromycin resistance protein, respectively, only when insertions or deletions (indels) are generated at the target sequences in the reporter systems, enabling efficient enrichment of mutant cells without using a flow cytometer.