The chicken embryo has been
for many years the most advanced model organism suitable for experimental
embryology. Post-implantation mouse embryos are essentially unavailable
for experimental manipulation, and are not suitable for ex utero culture
for more than a few hours. By contrast, the large and robust chick embryos
are accessible during the stages when most important developmental decisions
are taken so that a large variety of methodologies can be used to analyze
the genetic regulation of a many different developmental processes.
repertoire of the chick embryo includes:
manipulations and tissue grafting
of developing embryos
With these unique experimental
advantages the chick has made major contributions in our understanding
of the regulation of:
development (Fallon, Ide, Izpisua-Belmonte, Martin, Nisswander,
Nohno, Tabin, Tickle)
(Anderson, Cepko, Le Douarin, Jessell, Lumsden, Tessier-Lavigne)
development (Le Douarin, Schoenwolf, Stern)
(Emerson, Lassar, Le Douarin, Ordahl, Pourquié, Tabin)
asymmetry (Noji, Ros, Tabin)
development (Chuong, Dhouailly, Morgan, Nisswander)
Our understanding of skeletogenesis,
myogenesis, lineage, embryonic patterning, craniofacial development, vasculogenesis,
angiogenesis, wound-healing, immunology, and mechanisms of teratogenic
effects has also progressed significantly as a result of studies on the
Many mutations that result
in developmental abnormalities are available. These have been, and continue
to be, extremely valuable tools for the study of developmental processes.
Chicken eggs are plentiful,
inexpensive and extraordinarily convenient. Large numbers of eggs can
be incubated at one time to obtain embryos at precise stages of development.
Chick embryos are much cheaper to maintain and study than mouse embryos.
Most institutes' facilities for maintaining and growing transgenic mice
are already inadequate, and it is inevitable that this shortage of space
will become more severe, even if funding is diverted into expanded infrastructure.
The chick represent the model
system which most resembles other higher vertebrates while still permitting
experimental intervention in ovo. As such it represents an important
complement to mouse model systems.
Chicks offer a further unique
system for studying cellular processes: DT40 cells whose high-frequency
of mitotic recombination allows the ready generation of somatic cell
lines homozygous for targeted mutations. This system is already being
used to analyze many gene products that control general processes, such
as cell-cycle control, chromosome structure, etc.
Rapid advances are being
made in chicken transgenics, ES cell technology and the cryopreservation
of sperm, blastdisc cells, primordial germ cells and ES cells. These
newer technologies, coupled with the already well established experimental
manipulations, will make the chicken an extremely useful and economical
organism for studying vertebrate development and for the generation
of model systems for human diseases.
Perhaps the major current
barrier to efficient use of the above biological systems in the chick
is the extensive effort spent re-isolating chick homologues of human,
mouse or Drosophila genes. This is usually conducted in laboratories
whose major expertise lies elsewhere, in developmental and cellular
biology, and so often involves considerable consumption (waste) of time,
effort and money. This hurdle could be overcome by a relatively small
investment in a chick genome project conducted by professional genomics
We propose four approaches
to greatly enhance the contributions of the chicken in studies on developmental
processes and as model systems for human diseases. They are:
a chicken EST database with support for data management.
a physical map of the chicken genome.
and support relevant mutant chicken repositories.
a unified website for chicken genomics.
A) Generate a chicken
A series of normalized cDNA
libraries would be used to determine ~200,000 ESTs. The primary need
for chick ESTs is to generate probes to analyze endogenous gene expression.
Normal gene expression profiles are an important part of interpreting
the effects of gain or loss of function experiments. Furthermore, analysis
of gene expression has proven to be an effective way to assess the effects
of both gene and embryological manipulations. A second need for chick
ESTs would be to clone full-length chick sequences to manipulate gene
With current technology,
the generation of an EST database could be achieved very rapidly and
at an estimated cost of $1-2 million. The savings in effort and resources
currently spent on gene isolation alone would justify the latter expenditure.
Individual cDNA libraries would be derived from a series of hand-dissected
tissue samples which, together, would enlarge the diversity of low level,
tissue specific transcripts represented in the database. These would
derive from a genetically defined chick strain, e.g. that for which
ES cells are available. Tissues for the libraries would be isolated
by various laboratories within the chick community according to their
biological speciality and suitable
normalization would minimize library redundancy.
In the slightly longer-term,
the ESTs would be used to generate gridded cDNA microarrays for expression
screening. The chick will offer a unique opportunity for in vivo expression
screening in developmental and pathological contexts.
B) Generate a physical
map of the chicken genome.
Techniques are currently
being developed for analyzing gene regulation in chick embryos. These
include electroporation of embryos, retroviral vectors for analyzing
gene function and regulation, gene knock-out utilizing ribozymes, and
chicken ES cells for germ-line studies. These experimental approaches
are much cheaper and faster than their mouse equivalents which, as mentioned
above, require facilities that are, or soon will be, saturated in most
institutions. The chick also offers excellent material for analyzing
gene regulatory sequences and genome organization. The chick genome
is one-third the size of that of the mouse. In addition, it has been
argued that most chick genes are organized in gene-rich microchromosomes
at densities equivalent to those of Fugu. Analysis of gene organization
in the chick would also contribute to our understanding of human gene
and chromosome organisation as syteny between chick and human chromosomes
seems to be much higher than that between mice and humans.
These experimental advantages
that are offered by the chick need to be supported by a physical map
of the chick genome that would allow efficient recovery of chick genes.
There are a number of laboratories associated with chicken genomics.
These are listed in Burt and Cheng (See chicken matrix for reference)
and any efforts that result from the present proposal should be integrated
with existing efforts.
A library of BAC clones sufficient
to provide 10X genome coverage would be constructed and gridded. This
would be supplemented by a 3X YAC library. These would be derived from
the same chick strain as used in the EST project. Filters of gridded
clones would be made available to investigators who would screen and
identify specific genes. Such gene identification would also aid in
clone assembly. Assembly of the physical map would involve fingerprinting
techniques utilizing robotic sequencing techniques. Clone end-sequences
would also be determined. Assembly software and other informatics could
be adapted from already existing software developed for other genome
projects. It is anticipated that complete assembly of the physical map
could be largely completed within 3 years.
Although complete genome
sequencing is not proposed at this time, this should ultimately be considered
to maximize the usefulness of this organism in studying development
and generating model systems for human diseases.
C) Identify and support
relevant mutant chicken repositories.
A number of chick mutants
have played key roles towards our understanding of morphogenesis in
vertebrates. This is particularly true for the development of the limb,
the integument and the skeleton. In addition the chicken has proven
to be useful as model systems for autoimmune forms of avian vitiligo,
scleroderma, thyroiditis, scoliosis and the autosomal recessive form
of muscular dystrophy. Thus in addition to their enormous value in studies
on development these mutants are also useful as models for human diseases.
A listing of all chicken mutations has been compiled as part of a report
entitled "Avian Genetic Resources at Risk: An Assessment and Proposal
for Conservation of Genetic Socks in the USA and Canada". The complete
data on the extant genetic resources of the chicken are presented in
Appendix 2 of the report which will be published by the Genetic Resource
Conservation Program of the University of California at Davis.
The mutations that are relevant
to the mission of the NIH should be identified and supported.
D) Establish a unified
website for chicken genmomics.
A number of websites on chicken
genomics already exist. These are:
It is proposed that the information
on chicken genomics generated from proposals (A) and (B) above be integrated
with existing public information resources. In this manner all chicken
genomic information would be made available to the scientific community.
Such a resource would maximize the usefulness of the chicken in studying
development and human diseases.
- The chick
is the cheapest advanced model system for studying embryonic development
and gene function in higher vertebrates.
- It offers
several unique experimental advantages, most particularly, accessibility
- The above
proposal would greatly extend the contributions that can be made by
the chicken in fundamental biological research.
- The above
projects would be cheap and rapid, provide excellent value for money,
and be of immediate utility to a wide community.
Submitted by Paul Goetinck
on behalf of:
Ursula Abbott, David Anderson,
Richard Andrew, Jacques Balthazart, Tibor Bartha, Darwin Berg, Paola Bovolenta,
Philip Bradley, Paul Brickell, Marianne Bronner-Fraser, Annie Burke, David
Canning, Jean Champagnat, Qian Chen, Vincent Chiappinelli, Bodo Christ,
Cheng-Ming Chuong, Jonathan Cooke, Douglas Cotanche, Jeffrey Corwin, John
Couchman, Alun Davies, Flora de Pablo, Mary Delany, C. R. Dermon, Chao
Deng, Danielle Dhouailly, Susanne Dietrich, Jane Dodd, Stuart Dryer, Delphine
Duprez, Charles Emerson, John Fallon, Donna Fekete, Donald Fischman, Doug
Foster, Balasz Gereben, Scott Gilbert, Joel Glover, Paul Goetinck, Anthony
Graham, Andy Groves, Stan Halvorsen, Richard Harvey, Stefan Heller, Paul
Henion, Hans-Dieter Hofmann, Gabriel Horn, Richard Hume, David Ish-Horowicz,
Michele Jacob, Tom Jessell, Jean Jiang, Christy John, Robert Kosher, Cathy
Krull, Haymo Kurz, Paul Layer, Nicole Le Douarin, Julian Lewis, Luis Puelles
Lopez, Andrew Lumsden, Susan Mackem, Christophe Marcelle, Ivor Mason,
Bruce Morgan, Andrea Munsterberg, Linda Musil, Angela Nieto Toledano,
Rae Nishi, Lee Niswander, Robert Oakley, Toshihiko Ogura, Charles Ordahl,
Ketan Patel, Olivier Pourquie, Cliff Ragsdale, Mehandra Rao, Guy Richardson,
Robert Riddle, Hermann Rohrer, John Rostas, David Rowe, Ariel Ruiz i Altaba,
Helen Sang, John W. Saunders, Roger Sawyer, Gary Schoenwolf, Matthew,
Scott, Paul Scotting, Jane Sowden, Claudio Stern, Andrew Stoker, Jennifer
Stone, Kate Storey, Georg Striedter, Cliff Tabin, Marc Tessier-Lavigne,
Cheryll Tickle, Kathryn Tosney, Robert Trelstad, William Upholt, Marion
Wassef, Andrea Wizenmann, Anne Woods.