- Tong Hao for questions regarding the database
- David Hill for questions regarding the ORFeome project
- Open Biosystems
for requesting any ORF clones
- Promoterome Database
Please email Yun Amanda Shen with your questions or comments.
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In addition to the human draft sequence, the complete genome sequences of an increasing number of model organisms are now available. (E. coli and a large number of microorganisms, S. cerevisiae, C. elegans, D. melanogaster and A. thaliana). This sequence information is expected to revolutionize the way biological questions can be addressed. Molecular mechanisms should now be approachable on a more global scale in the context of (nearly) complete sets of genes, rather than by analyzing genes individually.
However most protein-encoding open reading frames (ORFs) predicted from sequencing projects have remained completely uncharacterized at the functional level. For example, out of 19,000 ORFs predicted from the C. elegans genome sequence, the function of approximately 1,200 has been characterized during the last 30 years.
The field of functional genomics addresses this limitation by developing methods to annotate the function of large numbers of predicted ORFs simultaneously. But despite the urgent need for large-scale functional annotation projects, functional genomic approaches have remained relatively undeveloped, primarily because of the lack of suitable methods to clone large numbers of ORFs into many different expression vectors. Indeed, most strategies developed in these projects are based upon the expression of large numbers of proteins in exogenous settings and in fusion with relevant tags. In order to facilitate these different proteome-wide projects, for each organism, a complete set of ORFs (or "ORFeome" by analogy with genome, transcriptome and proteome) will need to be cloned multiple times into many different expression vectors. To achieve this goal, one solution is to clone ORFeomes once and for all in a referential vector allowing convenient transfer into various expression vectors.
This technical "tour-de-force", hard to imagine using classical cloning techniques, became possible with the emergence of recombinational cloning. Furthermore, this cloning technology is compatible with the automation of the procedures required for the cloning of such number of ORFs. Finally the generation of such a resource of cloned ORFeomes and its subsequent distribution to the scientific community would allow the use of sets of identical ORF constructs for many different functional experiments.
In this context, one of the goals of our lab is to clone the C. elegans ORFeome. This project, conducted in collaboration with Research Genetics, Life Technologies (now part of Invitrogen) and Agencourt. is likely to illustrate how to undertake ORFeome cloning projects for more complex multicellular organisms.