Compositions, systems, and methods for genome editing

1. A composition for modifying a genetic locus in a eukaryotic cell, comprising:

(a) a eukaryotic cell containing a genetic locus to be modified; and

(b) a Cas12a nuclease, or a polynucleotide encoding the Cas12a nuclease; and

(c) an engineered Cas12a crRNA that includes a spacer sequence corresponding to a specific sequence in the genetic locus, or a polynucleotide encoding the Cas12a crRNA; and

(d) a Cas12a tracrRNA, or a polynucleotide encoding the Cas12a tracrRNA, wherein the Cas12a tracrRNA is present in a molar amount that is at least 10-fold greater than the molar amount of the Cas12a nuclease and the engineered Cas12a crRNA.

2. The composition of claim 1 , wherein the Cas12a tracrRNA:

(a) is identified from the same genomic region as the Cas12a nuclease by at least the following steps:

(i) identifying in the genomic region flanking the DNA encoding the Cas12a nuclease at least one nucleotide sequence that comprises a CRISPR array including direct repeats; and

(ii) identifying as a putative Cas12a tracrRNA at least one nucleotide sequence in either the sense or antisense direction in the genomic region flanking the DNA encoding the Cas12a nuclease, wherein the putative Cas12a tracrRNA has a nucleotide sequence that has at least 50% complementarity with the nucleotide sequence of the direct repeat;

or

(b) has a nucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NOs:1, 3, 6, 139-146, and 149-169.

3. The composition of claim 1 , wherein the genetic locus in a eukaryotic cell is:

(a) in genomic nuclear DNA of a non-human animal, a human, a plant, or a fungus, or in DNA of a eukaryotic organelle;

(b) in a eukaryotic DNA molecule in vitro;

(c) in a eukaryotic cell, cell line, tissue, callus, or multicellular organism.

4. The composition of claim 1 , wherein the eukaryotic cell is:

(a) a cell of a non-human animal, a human, a plant, or a fungus; or

(b) a cell of a cell line or a cell of a multicellular organism, and wherein the genetic locus to be modified comprises a locus of interest in the genome of the eukaryotic cell; or

(c) a eukaryotic cell in vitro, ex vivo, or in vivo.

5. The composition of claim 1 , wherein the Cas12a tracrRNA is provided:

(a) as DNA encoding a first RNA molecule comprising the Cas12a tracrRNA and comprising a restriction endonuclease cleavage site that is suitable for insertion of a sequence coding for a functional RNA moiety; or

(b) as a functional RNA molecule comprising the Cas12a tracrRNA and a functional RNA moiety, or as a polynucleotide encoding the functional RNA molecule; or

(c) by a DNA expression system comprising (i) DNA sequence for a first promoter; and (ii) operably linked and heterologous to the first promoter, DNA encoding a first RNA molecule comprising a Cas12a tracrRNA and comprising a restriction endonuclease cleavage site that is suitable for insertion of a sequence coding for a functional RNA moiety; and (iii) optionally, a terminator 3′ to and operably linked to the DNA encoding the first RNA molecule; or

(d) by a DNA expression system comprising: (i) DNA sequence for a first promoter; and (ii) operably linked and heterologous to the first promoter, a DNA encoding a functional RNA molecule comprising a Cas12a tracrRNA and a functional RNA moiety; and (iii) optionally, a terminator 3′ to and operably linked to the DNA encoding a functional RNA molecule; or

(e) as a Cas12a tracrRNA synthesized in vitro; or

(f) as a Cas12a tracrRNA obtained from a naturally occurring source.

6. The composition of claim 1 , wherein the Cas12a tracrRNA is provided as a functional RNA molecule comprising the Cas12a tracrRNA and a functional RNA moiety, or as a polynucleotide encoding the functional RNA molecule, wherein the functional RNA moiety comprises an RNA sequence for annealing to a donor polynucleotide, and wherein the composition further comprises the donor polynucleotide.