Zinc Finger Consortium: Zinc Finger Arrays
Engineered Zinc Finger Arrays for Endogenous Zebrafish Gene Targets
Recent published reports have shown that engineered zinc finger nucleases (ZFNs) are effective tools for making targeted mutations in zebrafish. With support from the NIH and guidance from the academic community, the labs of Keith Joung, Randall Peterson, and Joanna Yeh are engineering zinc finger arrays targeted to various zebrafish genes. The table below lists zebrafish genes and associated pairs of zinc finger arrays that can be used to generate ZFNs targeted to a site within that gene.
To construct ZFN expression vectors, DNA encoding zinc finger arrays should be cloned into plasmids also available through Addgene--the specific vector to use depends on the length of the spacer sequence between the half-sites (see Nuclease Expression Vectors for more details).
IMPORTANT NOTE: All zinc finger arrays listed show transcriptional activation activity of three-fold or greater in a well-characterized bacterial two-hybrid reporter system but have NOT yet been tested for activity as ZFNs in zebrafish.
| Target Gene Name | Zinc Finger Arrays | Engineering Method | Full Target Site (5' to 3') | |
|---|---|---|---|---|
| Left half-site |
Right half-site |
|||
| CACNA1F | OZ507 and OZ508 | OPEN | OPEN | gCGTGACCTCgctgatAAGAAGAGg |
| xylt1 | OZ509 and OZ510 | OPEN | OPEN | cACCCTCTACaggacaGTAGCGGGTg |
| zgc:153086 | OZ511 and OZ512 | OPEN | OPEN | gAGCATCACCtcgctGGAGGTGAGc |
| PTRF/Cavin1 | OZ513 and OZ514 | OPEN | OPEN | gACAGCCGTCtgcatctGGAGGTGCCc |
| pitrm1 | OZ515 and OZ516 | OPEN | OPEN | cACCTGCAGCagattGAAGAAGAGg |
| cftr | OZ517 and OZ518 | OPEN | OPEN | gTGCAACCGCagctttTAGGACGGAt |
| fox1 (a2bp1l) | OZ519 and OZ520 | OPEN | OPEN | aGACTCCGTCccgtcgtGCTGAGGGCc |
| hnf1a | OZ521 and OZ522 | OPEN | OPEN | aACCTTCCCCagagaGAGGTAGTGg |
| VDAC2 | OZ523 and OZ524 | OPEN | OPEN | gCTCCCAACCactttGCTGGTGTCa |
| dopamine beta hydroxylase (dbh) | OZ525 and OZ526 | OPEN | OPEN | tCCCATCCTAtcgttGCATGAGCTc |
| mdka (midkine-related growth factor) | OZ527 and OZ528 | OPEN | OPEN | cACCCTCCTCgtggtGCTGGTGGCc |
| apoeb (apolipoprotein Eb) | OZ529 and OZ530 | OPEN | OPEN | gCCCCTCAGCccagatgGGAGGAGATg |
| dpf2 | OZ531 and OZ532 | OPEN | OPEN | cTGCTACTTCtggatGGAGAAACGa |
| pitx2 | OZ533 and OZ534 | OPEN | OPEN | cCGCTTCAGCggtctGTGGACTCGa |
| zebrafish similar to grp151 (or gpcr-2037) | OZ535 and OZ536 | OPEN | OPEN | aGCCATCATCaggttcaGGATGAGCCc |
| Kif6 | OZ537 and OZ538 | OPEN | OPEN | aAGCTTCCTCttcattgGCTGACTGCa |
| ldr (low density lipoprotein receptor) | OZ539 and OZ540 | OPEN | OPEN | tTGCATCCACggcagTCGGCAGTGc |
| Encephalopsin (Opn3) | OZ541 and OZ542 | OPEN | OPEN | aTCCATCCCAaacacatGTGGCAGAAt |
| NFATc1 | OZ543 and OZ544 | OPEN | OPEN | aCCTCGCCTCagtgtGACGGAGGAc |
| Swachmann-Bodian-Diamond Syndrome Gene (sbds) | OZ545 and OZ546 | OPEN | OPEN | tGTTGCCGTCgtgagGATGAAGAAa |
| CACNA1D (2of2) or cav1.3b | OZ547 and OZ548 | OPEN | OPEN | gAGCTCCGTCtcgctgGCGGCCGAAg |
| histamine receptor H3 (hrh3) | OZ549 and OZ550 | OPEN | OPEN | gCGCCACGGAcaataaaGAGGACTGCa |
| GUSB | OZ551 and OZ552 | OPEN | OPEN | gGTCATCTGCcattcGAGGCGGACa |
| REST corepressor 2 | OZ553 and OZ554 | OPEN | OPEN | gCTCACCATCtgttggaTGCGATGGAa |
| cdkn1a (p21) | OZ555 and OZ556 | OPEN | OPEN | aCGTTCACTCggtaaTGGGCCGACt |
| Atg7 | OZ557 and OZ558 | OPEN | OPEN | tTACTTCTGCaatgatGTGGTGGCTc |
| vipr1 | OZ559 and OZ560 | OPEN | OPEN | gGCCATCAGCtcgcattGGAGAAGTAg |
| NRF2b (nfe212b) | OZ561 and OZ562 | OPEN | OPEN | tGTCTCCGGCagaggGAGGAGGAGa |
| esrrga | OZ563 and OZ564 | CODA | CODA | tAGCTACCGCTGGCGTCTGAGGAGc |
| HACE1 | OZ565 and OZ566 | CODA | CODA | gCTCATCTCCACCGAGCTGGAGAAg |
| atp2c1 | OZ567 and OZ568 | CODA | CODA | tTACCTCCACGATCTTGCTGATGGAg |
| dio2 | OZ569 and OZ570 | CODA | OPEN | aAGCTGCTCCAAACTCTAAGGTGGTg |
| im:7163548 | OZ571 and OZ572 | CODA | CODA | tGTCTTCATCTCCTTCAGATGCTGTCc |
| fam82a2 | OZ573 and OZ574 | CODA | CODA | gCACCGCTGCAGTAAGAGCTGAGGAAt |
| morc3b (NP_001003579.1) | OZ575 and OZ576 | CODA | OPEN | cAACCTCAGCATAAAGCTGGAGGAg |
| psen2 | OZ577 and OZ578 | CODA | OPEN | cGGCATCTCCAGAGCCCGAGGCGGACc |
| zgc:162148 (MICU1_DANRE) | OZ579 and OZ580 | CODA | CODA | gTCCAGCAGCGGTGAGGATGAAGACg |
| unc119b | OZ581 and OZ582 | CODA | CODA | tTGCTGCCGCGGATGCTGTGGCGGTTa |
| cx52.9 | OZ583 and OZ584 | OPEN | OPEN | cTTCATCTTCCGCATGCTGGTGCTg |
| flt1 (A4QNT7_DANRE) | OZ585 and OZ586 | CODA | CODA | cTGCACCTTCACAAAAGGCCGCTGGCt |
| LOC566040 | OZ587 and OZ588 | OPEN | OPEN | cAGCACCAGCCAGCCCAGAGTTGGGGt |
| yap1 | OZ589 and OZ590 | CODA | OPEN | gCCCAGCTGCAGGGAGGCAGGTGAGg |
| pdeb3 | OZ591 and OZ592 | OPEN | CODA | gGTCCGCCTCAGGTAGAGGGTGAGg |
| col6a2 | OZ593 and OZ594 | CODA | CODA | aGTCCTCCGATGGCCCAGGTGATGTTc |
| SDC3 | OZ595 and OZ596 | CODA | CODA | aGTCCGCCTCCACCCGAGGTAGAG |
| zgc:111821 | OZ597 and OZ598 | CODA | CODA | tGGCAGCAGCTTTTCGAAGAATAGg |
| zgc:65890 | OZ599 and OZ600 | OPEN | CODA | aATCTTCCACAGTGATGAGGACGTGc |
| panx2 (B1P2E8_DANRE) | OZ601 and OZ602 | CODA | OPEN | tGCCCTCTGCCGCCCTGTGGTAGCAg |
| si:ch211-221n23.1 (ZN238_DANRE) | OZ603 and OZ604 | OPEN | OPEN | cCGCAACTGCTGACCTGCTGCAGAGc |
Scientists using these zinc finger arrays in a publication should notify [email protected] and acknowledge NIH grant number R01 GM088040 in the publication.
References
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Rapid 'open-source' engineering of customized zinc-finger nucleases for highly efficient gene modification. Maeder ML et al. Mol Cell.. 2008. Jul 25. 31(2):294-301. PubMed PMID 18657511.
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Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Maeder ML et al. Nat Protoc.. 2009. Sept 17. 4(10):1471-1501. PubMed PMID 19798082.
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Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Foley JE et al. Nat Protoc.. 2009. Dec 3. 4(12):1855-1867. PubMed PMID 20010934.