[Zbrafish] NEW Solicitation for NIH-funded Resource to Target Zebrafish Genes with Zinc Fingers

Keith Joung via zbrafish%40net.bio.net (by keith.joung from zincfingers.org)
Thu Dec 30 12:43:39 EST 2010

Dear Colleagues,

Recent published reports have shown that ZFNs are effective tools for
making targeted mutations in zebrafish.  We have received resources
from the NIH to support the engineering of zinc finger nucleases
(ZFNs) for use by the zebrafish community.  As part of this NIH-
supported effort, engineered zinc finger arrays targeting specific
zebrafish genes will be generated and made available to the academic
community by depositing plasmids encoding these proteins with Addgene,
a non-profit plasmid distribution service (http://www.addgene.org/).
We are writing again to solicit recommendations for appropriate genes
to target in this effort.  Gene recommendations will only be accepted
via e-mail beginning at noon Eastern U.S. Time on Friday, January 21,
2011. Recommendations will be considered in the order in which they
are received and checked for appropriateness using the criteria
described below.  Up to 48 recommendations will be chosen for
targeting during this current round.  Another request later in 2011
will solicit additional gene recommendations.

For a gene to be considered appropriate for this effort, it will have
to meet the following criteria:

1.      Not be redundant with other gene disruption efforts.  We will
ask each recommender to verify that mutations in the gene of interest
do not already exist and that efforts to generate mutations in the
recommended gene are not underway elsewhere.

2.      Be potentially targetable by the CoDA and/or OPEN methods for
zinc finger engineering (Sander et al., Nat Methods 2011; Maeder et
al., Mol Cell 2008; Foley et al., PLoS ONE 2009).  We will use
bioinformatic tools to determine the probability of successfully
targeting a specific gene with ZFNs.  Exon sequences of a potential
target gene will be analyzed using the most up-to-date version of our
ZiFiT software which identifies ZFN sites that can potentially be
targeted using the CoDA and/or OPEN engineering methods.

3.      Be the first gene recommended by a given lab in calendar year
2011.  We intend to construct zinc finger arrays for no more than one
gene per lab per calendar year to ensure that recommendations for
targets come from as broad a range of sources as possible.  Although
up to five gene recommendations may be submitted by any given lab per
calendar year, only the first gene to meet the criteria above will be

If you have a gene you would like to recommend for targeting with
ZFNs, please complete the form available at http://zincfingers.org/form2/
and e-mail the form to zebrafishzfs from zincfingers.org on or after 12:00
Noon (Eastern US time) January 21, 2011.  Note that recommendations
from scientists at commercial entities will not be accepted.  A
separate recommendation form and e-mail must be sent for EACH gene

VERY IMPORTANT NOTE:  Each gene submitted should include BOTH its
Ensembl Gene ID (ENSDARG) and the gene name.  If the specific
transcript is important then the Ensembl Transcript ID (ENSDART)
should also be included (e.g.-- Example: ENSDARG00000024771 ,
ENSDART00000033574 , slc24a5).  In the event that Ensembl has
incorrectly annotated the gene of interest, the full genomic sequence
of your gene should be included with exons denoted by upper case and
introns in lower case. Genes not correctly submitted in one of these
formats will NOT be considered for targeting.

With best regards,

Keith Joung
Randall Peterson
Joanna Yeh
Jeffry Sander
Massachusetts General Hospital

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