Engineering and optimization of improved systems, methods and enzyme compositions for sequence manipulation
View Patent ↗The invention provides for engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are compositions and methods related to components of a CRISPR complex particularly comprising a Cas ortholog enzyme.
1. A method of altering expression of at least one gene product comprising introducing into a eukaryotic cell containing and expressing a DNA molecule having a target sequence and encoding the gene product an engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) system comprising one or more vectors comprising:
a) a first regulatory element operable in a eukaryotic cell operably linked to at least one nucleotide sequence encoding a CRISPR-Cas system guide RNA that hybridizes with the target sequence, and
b) a second regulatory element operable in a eukaryotic cell operably linked to a nucleotide sequence encoding a Staphylococcus aureus Cas9 protein,
wherein components (a) and (b) are located on same or different vectors of the system,
whereby the guide RNA targets the target sequence and the Cas9 protein cleaves the DNA molecule, whereby expression of the at least one gene product is altered; and, wherein the Cas9 protein and the guide RNA do not naturally occur together.
2. The method of claim 1 , wherein the expression of two or more gene products is altered.
3. The method of claim 1 , wherein the CRISP R-Cas system further comprises one or more nuclear localization signal(s) (NLS(s)).
4. The method of claim 1 , wherein the CRISP R-Cas system comprises a trans-activating cr (tracr) sequence.
5. The method of claim 1 , wherein the guide RNA comprises a guide sequence and a tracr sequence.
6. The method of claim 1 , wherein the Cas9 protein is codon optimized for expression in the eukaryotic cell.
7. The method of claim 1 , wherein the eukaryotic cell is a mammalian or human cell.
8. The method of claim 1 , wherein the Cas9 protein comprises one or more mutations in one or more of the RuvC I, RuvC II, RuvC III or HNH domains and/or is truncated to at least 500 amino acids in comparison to the wild type Cas9 protein.
9. The method of claim 1 , wherein the expression of one or more gene products is increased.
10. The method of claim 1 , wherein the expression of one or more gene products is decreased.
11. The method of claim 1 , wherein the one or more vectors are viral vectors.
12. The method of claim 11 , wherein the viral vectors are selected from the group consisting of retroviral, lentiviral, adenoviral, adeno-associated and herpes simplex viral vectors.
13. A CRISPR-Cas system-mediated genome targeting method comprising introducing into a eukaryotic cell containing and expressing a DNA molecule having a target sequence and encoding at least one gene product an engineered, non-naturally occurring CRISPR-Cas system comprising one or more vectors comprising:
a) a first regulatory element operable in a eukaryotic cell operably linked to at least one nucleotide sequence encoding a CRISPR-Cas system guide RNA that hybridizes with the target sequence, and
b) a second regulatory element operable in a eukaryotic cell operably linked to a nucleotide sequence encoding a Staphylococcus aureus Cas9 protein,
wherein components (a) and (b) are located on same or different vectors of the system,
whereby expression of the at least one gene product is altered through the CRISPR-Cas system acting as to the DNA molecule comprising the guide RNA directing sequence-specific binding of the CRISPR-Cas system, whereby there is genome editing; and, wherein the Cas9 protein and the guide RNA do not naturally occur together.
14. The method of claim 13 , wherein the expression of two or more gene products is altered.
15. The method of claim 13 , wherein the CRISPR-Cas system further comprises one or more NLS(s).
16. The method of claim 13 , wherein the CRISPR-Cas system comprises a tracr sequence.
17. The method of claim 13 , wherein the Cas9 protein is codon optimized for expression in the eukaryotic cell.
18. The method of claim 13 , wherein the eukaryotic cell is a mammalian or human cell.
19. The method of claim 13 , wherein the expression of one or more gene products is increased.
20. The method of claim 13 , wherein the expression of one or more gene products is decreased.
21. The method of claim 13 , wherein the Cas9 protein comprises one or more mutations in one or more of the RuvC I, RuvC II, RuvC III or HNH domains and/or is truncated to at least 500 amino acids in comparison to the wild type Cas9 protein.
22. The method of claim 13 , wherein the one or more vectors are viral vectors.
23. The method of claim 22 , wherein the one or more viral vectors are selected from the group consisting of retroviral, lentiviral, adenoviral, adeno-associated and herpes simplex viral vectors.
24. An engineered, programmable, non-naturally occurring Type II CRISPR-Cas system comprising a Staphylococcus aureus Cas9 protein and at least one guide RNA that targets and hybridizes to a target sequence of a DNA molecule in a eukaryotic cell, wherein the DNA molecule encodes and the eukaryotic cell expresses at least one gene product and the Cas9 protein cleaves the DNA molecule, whereby expression of the at least one gent product is altered; and, wherein the Cas9 protein and the guide RNA do not naturally occur together.
25. The CRISPR-Cas system of claim 24 , wherein the Cas9 protein comprises one or more mutations in one or more of the RuvC I, RuvC II, RuvC III or HNH domains and/or is truncated to at least 500 amino acids in comparison to the wild type Cas9 protein.
26. The CRISPR-Cas system of claim 24 , wherein the CRISPR-Cas system further comprises one or more NLS(s).
27. The CRISPR-Cas system of claim 24 , wherein the Cas9 protein is codon optimized for expression in the eukaryotic cell.
28. The CRISPR-Cas system of claim 24 , wherein the eukaryotic cell is a mammalian or human cell.
29. The CRISPR-Cas system of claim 24 , wherein the expression of one or more gene products is increased.
30. The CRISPR-Cas system of claim 24 , wherein the expression of one or more gene products is decreased.