[Zbrafish] FINAL Update on Second Solicitation of the NIH-sponsored zebrafish ZFN project

Keith Joung via zbrafish%40net.bio.net (by keith.joung from zincfingers.org)
Sun Mar 11 18:10:39 EST 2012


Dear all,

We write to provide a final update on the status of our second effort
to target 48 zebrafish genes requested by the community.  We have now
successfully generated targeting constructs for 29 of the 48 genes, as
outlined below, and are preparing to release another solicitation for
additional genes to be targeted.

In our last update from October of last year, we initially identified
zinc finger array pairs made by OPEN or CoDA that can be used to
modify 13 different endogenous zebrafish genes.  We also reported that
we knew with certainty that we were unable to obtain zinc finger array
pairs for 10 zebrafish genes.

We have several updates to report:

(1) We discovered a clerical error after our last update e-mail and
realized that we had misidentified 8 of the 13 gene targets we
originally reported success for.  The five correctly-identified genes
remain in the Group I list below and are preceded by an asterisk (*).

(2) For the eight genes for which we originally reported success but
actually did NOT obtain zinc finger array pairs, we have constructed
TALE nucleases (TALENs) targeted to sites chosen in consultation with
the original requestors.  As shown by our group and others, TALENs can
also be used to introduce targeted alterations in zebrafish.  The
names of these eight genes are shown in the Group III list below.

(3) We identified additional CoDA and/or OPEN ZF pairs for sites in
sixteen more genes (including four genes previously reported in Group
II, now preceded by a pound sign (#) in the Group I list below).

(4) We confirmed that we were unable to obtain CoDA ZF pairs for sites
in 9 additional genes (these are listed in Group II and preceded by a
double asterisk (**)).

We thank you for your patience with this process.  Note that all of
the plasmids encoding the 21 pairs of ZFs from Group I are available
now from Addgene:  http://www.addgene.org/zfc/arrays/.  The eight
pairs of TALENs from Group III will also be available from Addgene in
the coming weeks here:  http://www.addgene.org/talengineering/TALENzebrafish/.

We plan to make another solicitation for target genes in the coming
month.

With best regards,

Keith Joung
Randy Peterson
Joanna Yeh
Jeffry Sander
Maureen Regan



Group I genes (ZF array pairs successfully obtained): (21 genes)

*gene_name "LOC566040"transcript_name "LOC566040"
*gene_name "esrrga"transcript_name "esrrga"
*gene_name "HACE1"
*gene_name "atp2c1"transcript_name "atp2c1"
*gene_name "dio2"transcript_name "dio2"
gene_name "im:7163548"transcript_name "im:7163548"
gene_name "fam82a2"transcript_name "fam82a2"
gene_name "morc3b"transcript_name "NP_001003579.1"
gene_name "psen2"transcript_name "psen2"
gene_name "zgc:162148"transcript_name "MICU1_DANRE"
gene_name "unc119b"transcript_name "unc119b"
#gene_name "cx52.9"transcript_name "cx52.9"
gene_name "flt1"transcript_name "A4QNT7_DANRE"
#gene_name "yap1"transcript_name "yap1"
gene_name "pde3b"transcript_name "pde3b"
gene_name "col6a2"transcript_name "col6a2"
#gene_name "SDC3"
gene_name "zgc:111821"transcript_name "zgc:111821"
gene_name "zgc:65890"transcript_name "zgc:65890"
gene_name "panx2"transcript_name "B1P2E8_DANRE"
#gene_name "si:ch211-221n23.1"transcript_name "ZN238_DANRE"

Group II genes (failed to obtain ZF array pairs) (19 genes):

gene_name "hnf4a"transcript_name "NP_919349.1"
gene_name "wt1b"transcript_name "wt1b"
gene_name "jup"transcript_name "jup"
gene_name "myca"transcript_name "myca"
gene_name "igf2bp1"transcript_name "igf2bp1"
gene_name "jazf1a"
**gene_name "emp2"transcript_name "emp2"
**gene_name "mych"transcript_name "mych"
**gene_name "sqstm1"transcript_name "NP_998338.1"
**gene_name "ahrrb"transcript_name "ahrrb"
**gene_name A9JTD0_DANREtranscript_name A9JTD0_DANRE
**gene_name "f9"transcript_name "NM_182868.1"
**gene_name "coq6"transcript_name "NP_001038869.1"
**gene_name "csf3r"transcript_name "csf3r"
**gene_name "trpv1"transcript_name "B6RTA2_DANRE"
**gene_name "cadm2a"transcript_name "cadm2a"
**gene_name "dab1a"transcript_name "A2BEF7_DANRE"
**gene_name "LOC565975"transcript_name "LOC565975"
**gene_name "vasa"transcript_name "vasa"

Group III genes (for which we have made TALENs) (8 genes):

gene_name "ptp4a3"transcript_name "ptp4a3"
gene_name "mchr1b"transcript_name "mchr1b"
gene_name "arsa"transcript_name "arsa"
gene_name "park2"transcript_name "park2"
gene_name "v2rl1"transcript_name "Q4VDB3_DANRE"
gene_name "gabra5"transcript_name "gabra5"
gene_name "drd4a"transcript_name "drd4a"
gene_name "gdf2"transcript_name "gdf2"



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