Genomic insulator elements and uses thereof
Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.
1. A viral vector comprising: a cassette comprising a nucleic acid sequence encoding a therapeutic agent driven by a promoter regulated by an enhancer,
wherein the cassette is bracketed by genomic insulator elements,
wherein each of the genomic insulator elements comprises a CTCF binding site core sequence selected from the group consisting of:
(SEQ ID NO.: 2)
CCACCAGGGGGAGC,
(SEQ ID NO.: 3)
TCAGTAGAGGGCGC,
(SEQ ID NO.: 4)
CCACTAGGGGGCAG,
(SEQ ID NO.: 5)
CAGCAGAGGGCGCT,
and
(SEQ ID NO.: 6)
CAGTAGAGGGCGCT.
2. The viral vector of claim 1 , wherein the viral vector is a retroviral vector or a lentiviral vector.
3. The viral vector of claim 1 , wherein the CTCF binding site core sequence is CCACCAGGGGGAGC (SEQ ID NO: 2).
4. The viral vector of claim 1 , wherein the CTCF binding site core sequence is TCAGTAGAGGGCGC (SEQ ID NO: 3).
5. The viral vector of claim 1 , wherein the CTCF binding site core sequence is CCACTAGGGGGCAG (SEQ ID NO: 4).
6. The viral vector of claim 1 , wherein the CTCF binding site core sequence is CAGCAGAGGGCGCT (SEQ ID NO: 5).
7. The viral vector of claim 1 , wherein the CTCF binding site core sequence is CAGTAGAGGGCGCT (SEQ ID NO.: 6).
8. The viral vector of claim 1 , wherein each of the genomic insulator elements comprises 150 to 250 nucleotides.
9. The viral vector of claim 1 , wherein each of the genomic insulator elements comprises 119 to 284 nucleotides.
10. A method for administering the therapeutic agent, the method comprising administering the viral vector of claim 1 to a subject in need thereof.
11. The method of claim 10 , wherein the viral vector is a retroviral vector or a lentiviral vector.
12. The method of claim 10 , wherein the CTCF binding site core sequence is CCACCAGGGGGAGC (SEQ ID NO: 2).
13. The method of claim 10 , wherein the CTCF binding site core sequence is TCAGTAGAGGGCGC (SEQ ID NO: 3).
14. The method of claim 10 , wherein the CTCF binding site core sequence is CCACTAGGGGGCAG (SEQ ID NO: 4).
15. The method of claim 10 , wherein the CTCF binding site core sequence is CAGCAGAGGGCGCT (SEQ ID NO: 5).
16. The method of claim 10 , wherein the CTCF binding site core sequence is CAGTAGAGGGCGCT (SEQ ID NO: 6).
17. The method of claim 10 , wherein each of the genomic insulator elements comprises 150 to 250 nucleotides.
18. The method of claim 10 , wherein each of the genomic insulator elements comprises 119 to 284 nucleotides.
19. A viral vector comprising a cassette comprising a nucleic acid sequence encoding a therapeutic agent driven by a promoter regulated by an enhancer, wherein the cassette is bracketed by genomic insulator elements, and wherein each of the genomic insulator elements comprises a CTCF binding site core sequence of SEQ
(SEQ ID NO.: 1)
CACCAGGTGGCGCT.
20. The viral vector of claim 19 , wherein the viral vector is a retroviral vector or a lentiviral vector.
21. The viral vector of claim 19 , wherein each of the genomic insulator elements comprises 150 to 250 nucleotides.
22. The viral vector of claim 19 , wherein each of the genomic insulator elements comprises 119 to 284 nucleotides.
23. A method for administering the therapeutic agent, the method comprising administering the viral vector of claim 19 to a subject in need thereof.
24. The method of claim 23 , wherein the viral vector is a retroviral vector or lentiviral vector.
25. The method of claim 23 , wherein each of the genomic insulator elements comprises 150 to 250 nucleotides.
26. The method of claim 23 , wherein each of the genomic insulator elements comprises 119 to 284 nucleotides.