About

Crispam is an allele-specific gRNA design tool that is based on the SNP-derived PAM targeting approach.
The SNP-derived PAM targeting approach allows highly specific targeting of an allele of interest.

Citation info: “CrisPam: SNP-derived PAM Analysis Tool for Allele-Specific Targeting of Genetic Variants Using CRISPR/Cas Systems”. Rabinowitz R., Almog S., Darnell R. and Offen D. (2020)

SNP-derived PAM

The CRISPR/Cas system can tolerate some mismatches between the crRNA and the target DNA. The bases at the 8th to 13th positions at the 3′ end of the spacer (regarding type II Cas proteins) are termed the seed sequence along with the first base at the 5′ end. Mismatches at the seed sequence are thought to be not tolerated and abolish DNA cleavage. Previous studies have shown that targeting an allele caused by a point mutation by incorporating the variant base within the gRNA is seemingly insufficient, resulting in a non-specific knockdown of both the target allele and the wildtype allele in some proportion [1,2].

An SNP-derived PAM approach overcomes this potential limitation of targeting the disease-causing allele while leaving the wildtype allele intact. This method dramatically increases the specificity of targeting the mutant allele alone by choosing a PAM sequence that is present exclusively within the mutant sequence. Meaning, the point mutation generates the PAM sequence (figure 1) [2,3].

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Figure 1: SNP-derived PAM.



When targeting a gene without a particular DNA cleavage location preference, almost any of the Cas enzymes are optional. However, when targeting a SNP in general, or if utilizing the SNP-derived PAM approach in particular, the selection of Cas is limited mostly due to the condition of PAM presence in proximity to the SNP or having a PAM generated by the SNP.
CrisPam is a pythonic code that obtains data of a given SNP, and tests whether it generates a unique PAM sequence in the DNA of the mutation allele only. The candidate PAMs, 26 PAM sequences of 23 Cas variants (Table 1), are tested for each given point mutation. The CrisPam Database is a list of SNPs that were found to be generating at least one PAM.

The CrisPam web tool offers researchers to use their own SNP data (by manually typing DNA sequences, automatically fetch sequence by rsID or genomic coordinates, or use the batch mode to analyse multiple sequences) to find the most suitable Cas variant for their allele-specific targeting experiments using the CRISPR system.

90% of the SNPs checked were found to be “PAM-generators”.

We have tested all human known pathogenic and likely-pathogenic SNPs (obtained from NCBI dbSNP) using CrisPam. The resulted database is available (See CrisPam DB page for more information).

Some SNPs are “multiple-PAM generators”; meaning they generate more than one PAM (e.g. figure 1). For such SNPs, considerations such as delivery vector capacity may also determine the most suitable Cas protein for the experiment. Some information regarding the variety of Cas protein is available in the following table:

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Table 1: The Cas Repository - 26 unique PAMs of 23 Cas enzymes

It is recommended to use CrisPam as the first step in experiment design. Further off-targets and efficiency predictions of the desired gRNA are required.

Code


References:

  • Capon SJ, Baillie GJ, Bower NI, da Silva JA, Paterson S, Hogan BM, et al. Utilising polymorphisms to achieve allele-specific genome editing in zebrafish. Biol Open . Company of Biologists; 2017
  • Christie KA, Courtney DG, DeDionisio LA, Shern CC, De Majumdar S, Mairs LC, et al. Towards personalised allele-specific CRISPR gene editing to treat autosomal dominant disorders. Sci Rep . Nature Publishing Group; 2017
  • Courtney DG, Moore JE, Atkinson SD, Maurizi E, Allen EHA, Pedrioli DML, et al. CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting. Gene Ther . 2016