Large-scale genomic sequencing projects have provided DNA sequence information for many genes, but the biological functions for most of them will only be known through functional studies. Bacterial artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs) are large genomic clones stably maintained in bacteria and are very important in functional studies through transfection because of their large size and stability. Because most BAC or PAC vectors do not have a mammalian selection marker, transfecting mammalian cells with genes cloned in BACs or PACs requires the insertion into the BAC/PAC of a mammalian selectable marker. However, currently available procedures are not satisfactory in efficiency and fidelity. We describe a very simple and efficient procedure that allows one to retrofit dozens of BACs in a day with no detectable deletions or unwanted recombination. We use a BAC/PAC retrofitting vector that, on transformation into competent BAC or PAC strains, will catalyze the specific insertion of itself into BAC/PAC vectors through in vivo cre/loxP site-specific recombination.Bacterial artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs), with their capacity for large inserts, stability, and lack of chimerism, play important roles in genome mapping and sequencing (Osoegawa et al. 2000). For these reasons and the fact that virtually every gene will have one or more corresponding BAC/PAC clones, they are the first choice for functional complementation or dose-effect studies in differentiated or embryonic stem (ES) cells. Mouse ES cells are of special interest for gene function studies because of their capacity for in vitro differentiation into different lineages (O'Shea 1999) and the ability to generate transgenic animals through germline transmission. The lack of a universal selection marker for mammalian cell transfection makes it difficult to include any particular marker in the BAC/PAC vectors. Therefore, the vectors for most current BAC or PAC libraries do not contain any mammalian selection marker for transfection studies. This necessitates the development of efficient ways to insert such selection markers into individual clones chosen from BAC/PAC libraries, a "retrofitting" operation.Several strategies have been developed to retrofit BACs/PACs on the basis of restriction digestion, transposition, homologous recombination, or site-specific recombination. Certain rare-cutter restriction enzymes have been used to linearize both the BAC clone and a retrofitting cassette. These sticky ends were then ligated to form retrofitted BACs with the selectable marker inserted (Mejia and Monaco 1997;Hejna et al. 1998). For this strategy to work, it has to be certain that there is no such restriction site in the genomic insert, which often is not the case with large inserts. It also requires subsequent transformation of the retrofitted BAC/PAC into Escherichia coli, which is both very inefficient and deleterious to the genomic insert. Recombination-based approaches allow the direct...

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