sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity.
It has been possible to create tools to predict single guide RNA (sgRNA) activity in the CRISPR/Cas9 system derived from Streptococcus pyogenes due to the large amount of data that has been generated in sgRNA library screens. However, with the discovery of additional CRISPR systems from different bacteria, which show potent activity in eukaryotic cells, the approach of generating large data sets for each of these systems to predict their activity is not tractable. Here, we present a new guide RNA tool that can predict sgRNA activity across multiple CRISPR systems. In addition to predicting activity for Cas9 from S. pyogenes and Streptococcus thermophilus CRISPR1, we experimentally demonstrate that our algorithm can predict activity for Cas9 from Staphylococcus aureus and S. thermophilus CRISPR3. We also have made available a new version of our software, sgRNA Scorer 2.0, which will allow users to identify sgRNA sites for any PAM sequence of interest.
Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.
Raj
0000-0002-2216-313X
R
Chari
Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.|Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States.
Nan Cher
NC
Yeo
Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.|Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States.
Alejandro
A
Chavez
Department of Genetics, Harvard Medical School , Boston, Massachusetts 02115, United States.|Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States.
George M
GM
Church
D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D064113:CRISPR-Cas Systems / Q000235:genetics / Q000502:physiology*; D005818:Genetic Engineering / Q000379:methods*; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000235:genetics; D013211:Staphylococcus aureus / Q000235:genetics / Q000378:metabolism; D013297:Streptococcus pyogenes / Q000235:genetics / Q000378:metabolism
D001426:Bacterial Proteins; D000094704:RNA, Guide, CRISPR-Cas Systems
CRISPR; Cas9; genome engineering; sgRNA activity prediction; sgRNA scorer