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zfclogo.jpg 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

  • 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.

  • 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.

  • 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.