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Making point mutations using CRISPR/Cas9 and the dpy-10 co-CRISPR marker

To generate point mutations, we currently favor the use of single-strand oligo DNA (ssODN) repair templates (Zhao et al) in combination with the use of pha-1 rescue as a co-CRISPR marker. However, it is also possible to use dpy-10 as a co-CRISPR marker, as described by Arribere et al. In this approach, a guide RNA and ssODN repair template that convert wild-type dpy-10 into the dominant dpy-10(cn64) allele are co-injected with the sgRNA and repair template that generate the mutation of interest. The cn64 mutation causes a dominant Rol phenotype. P0 animals that produce Rol progeny are more likely to yield progeny that have also undergone your desired genome engineering.

Selection of the sgRNA target sequence

For oligonucleotide mediated repair, you will want the sgRNA target sequence to be close to the site you want to mutate (<30 bp) in order to minimize the size of the oligo that needs to be ordered.

Designing the repair template

Design an oligo nucleotide as follows:

  • Incorporate the desired mutation(s).
  • Incorporate mutations in the sgRNA target site to prevent recutting after repair. Ideally, mutate one of the Gs in the PAM sequence. If that is not feasible, incorporate silent mutations close to the 3'-end of the 20 bp recognition sequence.
  • Incorporate silent mutations that create a unique primer binding site, to enable detection of the desired change by PCR. In our hands, primers with several mismatches, even of the 3'-most nucleotide, still yield PCR product. Hence, we try to mutate 4-5 basepairs, including the 3'-most basepair if possible. Ideally, the changed sites are near the desired mutation, especially if the sgRNA recognition sequence is futher away from the desired mutation site. However, the mutations can be introduced anywhere, including overlapping the sgRNA target site. This would simultaneously prevent recutting after repair.
  • Use 35 bp homology arms flanking the first and last mutation.
  • Sense oligos with respect to the strand of the gene have been reported to work best.
CRISPR mutation example

Example of introducing a mutation. In this example, a Ser to Ala change is desired. A sgRNA target site is located nearby. The ssODN repair template contains the desired change, plus a number of silent changes that simultaneously alter the target site so it is no longer recognized after repair, and serve as a primer binding site that can be used to detect a successful genome edit event. Not indicated is a second primer needed for detection, which can be chosen anywhere in the next 300 - 2000 nucleotides.

Primers to design

mutation detection primers

Schematic overview of primers to be designed.

For the detection and sequencing of a successfully engineered point mutation, 4 primers need to be designed (see image above):

  1. Primer F1 anneals to the left of the mutated site, and is used in combination with primer R1 to amplify a small region to be sequenced to confirm the mutation. Primer F1 also serves as the sequencing primer, so should not be placed too far away from the mutated site (generally < 250 bp away should result in a good sequence quality near the mutated site).
  2. Primer F2 should overlap the mutation site, and should only anneal to the wild-type sequence.
  3. Primer F3 should overlap the mutation site, and should only anneal to the mutated sequence (the forward detection primer in the template design figure).
  4. Primer R1 is the reverse primer for all forward primers.

Primers F2 and F3 are used to determine the genotype of (candidate) edited animals:

  • Animals that are homozygous wild-type will only show an amplicon using F2/R1.
  • Animals that are homozygous mutant will only show an amplicon using F3/R1.
  • Heterozygous animals will yield a PCR product with both primer sets.

Injection

Inject the following mixture into 20-40 your adults (we currently do not use a fluorescent co-injection marker):

  • 50 ng/µl ssODN repair template carrying your desired mutation
  • 50 ng/µl sgRNA construct targeting your gene of interest
  • 50 ng/µl ssODN repair template to introduce the dpy-10(cn64) mutation.
  • 50 ng/µl sgRNA construct targeting dpy-10
  • 50 ng/µl Peft-3::Cas9 (Calarco lab, Addgene plasmid #46168)

Following the injection, place each P0 on an individual NGM plate.

The sequence of the dpy-10(cn64) ssODN:

5'-cacttgaacttcaatacggcaagatgagaatgactggaaaccgtaccgcATgCggtgcctatggtagcggagcttcacatggcttcagaccaacagcct

The sequence of the dpy-10 targeting sgRNA:

5'-GCTACCATAGGCACCACGAG

Detection of mutation by PCR

  1. Wait until the first F1 progeny are adult. Select plates that contain Rol animals (dpy-10(cn64)/+). Note that in addition to repair of dpy-10, loss of function mutations in dpy-10 will also be generated. Hence, you may observe dpy-10(0)/dpy-10(0) Dpy animals, as well as dpy-10(cn64)/dpy-10(0) DpyRol animals.
  2. Plates with a jackpot brood (>30% Rol progeny) have the highest chance of yielding animals with your desired edit. If such plates are present, continue only with those. If not, pick progeny from all plates with Rol animals.
  3. Pick 50 - 100 F1 animals to individual plates, and allow these to produce progeny overnight. We usually pick a mixture of wild type and Rol animals.
  4. Lyse the F1 animals, and use the F3/R1 primer pair to detect the mutation.
  5. Recover the mutant strain from the F2 progeny of F1 animals that show the desired mutation by PCR. If the successful edit happened in a Rol animal, the cn64 mutation can easily be lost again as the F1 animal was heterozygous (unless your desired edit was near the dpy-10 locus and occured on the same chromosome as the dpy-10(cn64) editing event). Use primer sets F2/R1 and F3/R1 to identify homozygous mutant animals (this may not be possible if the mutation is lethal).
  6. Use primer set F1/R1 to amplify the region containing the mutation and confirm by sequencing. Preferably this is done on a homozygous mutant animal. If this is not possible, the mutation can be characterized by sequencing a heterozygous animal, as each mutated site should result in a double peak.