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Identikit Project

mc21 at columbia.edu mc21 at columbia.edu
Mon Nov 15 06:20:50 EST 2004


Dear Members of the C. elegans Community,

	One of the biggest problems facing the characterization of gene
expression patterns in C. elegans is the difficulty of identifying all 
the cells
expressing a given gene.  I would like to enlist your support for a
collaborative effort to create a C. elegans Identikit, a set of strains 
that
will allow the ready identification of gene expression patterns.  The 
Identikit
will be based on reconstituted GFP (recGFP), which was described in 
recent paper
from my lab (Zhang et al., Combinatorial marking of cells and 
organelles with
reconstituted fluorescent proteins Cell 119: 137-144, 2004).  recGFP is 
a two
component system that produces a fluorescent product only when both 
components
are made in the same cell.  The Identikit will consist of strains in 
which one
of the components is expressed from characterized promoters.  
Constructs with
promoters to be tested are linked to the other recGFP component and 
transformed
into him animals.  The resulting transformant males can then be mated to
Identikit animals, and fluorescence should tell where the promoter is 
expressed.
We currently have three different color variants and can obtain either
cytoplasmic or nuclear labeling.  Thus, we should be able to label 
several
different cells in each strain.

	My lab is planning to construct the Identikit in collaboration with Don
Moerman (who is determining gene expression patterns for many 
promoters). I have
submitted a proposal for funding from NIH and Don is seeking funds from 
Genome
Canada.  Initially, we will demonstrate that multiple rec fluorescent 
proteins
can allow cells expression in the same animal and begin the 
construction of the
Identikit.  We will concentrate on generating strains that allow the
identification of the cells of the nervous system.  Ultimately, we want 
to have
strains that will identify all cells in the animal. A list of the 
promoters,
whose expression patterns we have or are confirming, is given below.  
We will be
setting up a web site to describe our progress on the construction of 
the
Identikit (when this site is up, we will have a link through WormBase), 
and we
will make the strains freely available (probably through the C. elegans 
Stock
Center) as they are developed.

	Don and I envision this effort as one involving the entire C. elegans
community.  I am writing not only to tell you about the project, but 
also to ask
for your support.  This support can take several forms.  First, I would
appreciate any letters of support, which I will include as supplemental
information for the grant application.  Please send such letters to me 
by email
(mc21 at columbia.edu).  Second, we would like to hear about any promoter 
fusions
that expressed intact GFP in a small numbers of cells, even if you do 
not know
the identity of the expressing cells.  For our purposes, the best 
strains are
those that express GFP early, strongly, and in very few and dispersed 
cell
types, but we are interested in hearing about any expressions that you 
feel
might be useful.  We would like to have the strains and will confirm or
determine the expression patterns.  We hope to obtain a large number of
promoters that can be used for the Identikit.  Below I've listed the 
promoters
we are examining at the moment and the cells they are expressed in.  In 
some
cases other promoters may have more restricted or stronger expression, 
so these
do not represent a final set.  Again, please email me your suggestions. 
  Third,
we would like to take advantage of your expertise. If you are 
particularly
knowledgeable about a part of the animal's anatomy and would like to be 
part of
this effort, please let us know.  For example, Scott Emmons has offered 
to help
us identify cells expressing recGFP in males.  Finally, we welcome any 
other
suggestions you care to make.

All the best,

Marty Chalfie


  ----------------------------------------------------------------
| GENE	  | CELLS	  | GENE    | CELLS                      |
  ----------------------------------------------------------------
| cat-2	  | ADE, PDE, CEP | mec-17* | ALM, PLM, AVM, PVM         |
| flp-1*  | AVK		  | odr-2b* | SMB, RME, ALN, PLN, RIG    |
| gcy-5*  | ASER	  | ser-2   | OLL, PVD                   |
| gcy-7*  | ASEL	  | sra-6   | PVQ, ASH                   |
| gcy-10* | AWB, AWC	  | tbh-1   | RIC                        |
| gcy-33  | BAG	  	  | tph-1*  | NSM, ADF, HSN, (AIM, RIH)  |
| glr-6*  | RIA		  | unc-4*  | SAB, DA, I5, VA, AVF, VC   |
| gpa-4*  | ASI		  | unc-47* | DD, VD, AVL, DVB, RME, RIS |
| gpa-8*  | URX, AQR, PQR | 	    |                            |
  ----------------------------------------------------------------

* indicates that the expression pattern has been verified; cells in 
parentheses
   fluoresced faintly.




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