RT Journal Article
SR Electronic
T1 casmini-tool: a comprehensive database for efficient and specific guide RNA design using dCasMINI
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.09.17.558168
DO 10.1101/2023.09.17.558168
A1 Spencer Lopp
A1 Robin W. Yeo
A1 Nishant Jha
A1 Xiao Yang
A1 Gabriella Alvarez
A1 Courtney Klappenbach
A1 Daniel O. Hart
A1 Lei S. Qi
A1 Timothy P. Daley
YR 2023
UL http://biorxiv.org/content/early/2023/09/18/2023.09.17.558168.abstract
AB The dCasMINI protein is a hyper-compact, nuclease-inactivated CRISPR-Cas system engineered for transcriptional modulation and epigenetic editing [Xu et al., 2021]. The small size of dCas-Mini (529 amino acids), less than half the size of comparable Cas9 molecules, makes it ideal for AAV-based therapies which are frequently limited by AAV’s small cargo capacity. Unlike Cas9 or Cas12a, there is no available computational tools for designing CasMINI guides. To facilitate and accelerate the development of dCasMINI-based applications, we synthesized knowledge regarding CasMINI guide design and built a website to assist researchers in designing optimal guides for dCasMINI-based experiments for transcriptional inhibition (CRISPRi) and activation (CRISPRa), which covers 99.7% of genes for CRISPRi and 99.9% of genes for CRISPRa. We experimentally characterized the importance of each nucleotide position on the guide RNA for determining its activity. Based on this information,, our tool offers more sensitively mapping off-targets and provides information about alignment mismatches in the spacer seed region, which we have experimentally determined to be critical for true binding events. The tool is freely available at casmini-tool.com.Competing Interest StatementL.S.Q. is the founder of Epicrispr Biotechnologies, and also serves as a scientific advisor for Laboratory of Genomics Research and Kytopen. S.L., R.W.Y., X.Y., D.O.H., L.S.Q., and T.P.D. hold provisional patents relating to this work, are employees of and acknowledge outside interest in Epicrispr Biotechnologies.