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Genes that encode proteins are the structural genes, the binding of the protein, or several proteins at a set of nearby cis sites, can turn the second structural gene on or o.
More generally, the binding of diusible factors, called “trans acting factors,” to cis sites, can tune graded rates of transcription of the nearby structural gene.
The human cell is estimated to have about eighty to a hundred thousand structural genes and between ten thousand to perhaps a hundred thousand cis acting sites.
In general, any structural gene may be regulated by zero to ten dierent trans acting factors that may bind at one or more nearby cis acting sites.
Real genes show graded levels of activities as a function of the concentrations of their trans acting inputs and the bound states of their cis regulatory loci.
Steve had carefully read about sixty papers on regulated genes with K = known inputs, where the data was available at the level of actual binding of trans acting factors to cis sites and the turning on of transcription.
But then we can clone controllable cis sites such as promoters into cells at one or more randomly chosen sites and study the eects of transiently perturbing the activities of one or a few genes.
And yet more: My colleague Marc Ballivet, with a minor bit of help from me, has come up with a means to rapidly clone most or all cis sites from cells.
If the thousands of cis sites can be cloned, each can be used to anity purify the trans factors binding it.
We have spun out a biotechnology company, CIStem Molecular, that aims to clone the small cis acting DNA regions that control turning genes on and o in development and disease, a European daughter company, Euro-Bios, as well as EXA, a company spun out with NASDAQ to make tools for financial markets.
The current database version, At cis DB 1.
One of the main features of At cis DB is mapping of experimentally known and computationally predicted (see Methods for details) TF binding sites to their respective gene promoters, and display in graphical form.
We also provide a web page at our database, where the users of At cis DB can report back any of the validated annotations of At cis DB from their experiments.
This facilitates the generation of a draft-annotated version of At cis DB.
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