Calling cards for DNA-binding proteins * Haoyi Wang, Mark Johnston, and Robi David Mitra^1 * / Department of Genetics, Washington University, School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA / Identifying genomic targets of transcription factors is fundamental^ for understanding transcriptional regulatory networks. Current^ technology enables identification of all targets of a single^ transcription factor, but there is no realistic way to achieve^ the converse: identification of all proteins that bind to a^ promoter of interest. We have developed a method that promises^ to fill this void. It employs the yeast retrotransposon Ty5,^ whose integrase interacts with the Sir4 protein. A DNA-binding^ protein fused to Sir4 directs insertion of Ty5 into the genome^ near where it binds; the Ty5 becomes a "calling card" the DNA-binding^ protein leaves behind in the genome. We constructed customized^ calling cards for seven transcription factors of yeast by including^ in each Ty5 a unique DNA sequence that serves as a "molecular^ bar code." Ty5 transposition was induced in a population of^ yeast cells, each expressing a different transcription factor--Sir4^ fusion and its matched, bar-coded Ty5, and the calling cards^ deposited into selected regions of the genome were identified,^ revealing the transcription factors that visited that region^ of the genome. In each region we analyzed, we found calling^ cards for only the proteins known to bind there: In the /GAL1--10/^ promoter we found only calling cards for Gal4; in the /HIS4/ promoter^ we found only Gcn4 calling cards; in the /PHO5/ promoter we found^ only Pho4 and Pho2 calling cards. We discuss how Ty5 calling^ cards might be implemented for mapping all targets of all transcription^ factors in a single experiment. -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================