Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

Authors:
Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee, J Keith Joung
In:
Source: Nat Biotechnol
Publication Date: (2016)
Issue: 34(8):: 869-74
Platform:
4D-Nucleofector® X-Unit
Experiment
Human cell culture and transfection. U2OS cells (obtained from Toni Cathomen, Freiburg) and HEK293 cells were cultured at 37 °C with 5% CO2 in Advanced DMEM supplemented with 10% heat-inactivated FBS, 2 mM GlutaMax, and penicillin/streptomycin (all cell culture products were obtained from Life Technologies). Cell line identity was validated by STR profiling (ATCC), and mycoplasma testing was performed twice per month. 2 × 105 cells were transfected using the SE Cell Line Nucleofector Kit with 500 ng Cpf1- or SpCas9-encoding plasmid and 250 ng gRNA expression plasmid and the DN-100 program for U2OS cells, or with 300 ng Cpf1- or SpCas9-encoding plasmid and 150 ng gRNA expression plasmid using the CM-137 program for HEK293 cells, on a 4D-Nucleofector according to the manufacturer’s instructions (Lonza). For negative control transfections, Cpf1- or SpCas9-encoding plasmids were co-transfected with a U6-null plasmid that did not encode a crRNA. Genomic DNA extraction was performed approximately 72 h following nucleofection using an Agencourt DNAdvance Genomic DNA Isolation Kit (Beckman Coulter).
Abstract
The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively) have on-target efficiencies in human cells comparable with those of the widely used Streptococcus pyogenes Cas9 (SpCas9). We also report that four to six bases at the 3' end of the short CRISPR RNA (crRNA) used to program Cpf1 nucleases are insensitive to single base mismatches, but that many of the other bases in this region of the crRNA are highly sensitive to single or double substitutions. Using GUIDE-seq and targeted deep sequencing analyses performed with both Cpf1 nucleases, we were unable to detect off-target cleavage for more than half of 20 different crRNAs. Our results suggest that AsCpf1 and LbCpf1 are highly specific in human cells.