1. Department of Biochemistry and
2. Howard Hughes Medical Institute, Stanford University Medical Center, Stanford, California 94305, USA
3. Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
4. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
5. These authors contributed equally to this work
6. Present address: Institute of Molecular and Cellular Biology, University of Texas at Austin, Austin, Texas 78712, USA. Present address: Applied Biosystems, Foster City, California 94404, USA.

Correspondence to: Patrick O. Brown^1,7 Correspondence and requests for materials should be addressed to P.O.B. (e-mail: Email: pbrown@cmgm.stanford.edu) or M.S. (e-mail: Email:  michael.snyder@yale.edu).

Proteins interact with genomic DNA to bring the genome to life; and these interactions also define many functional features of the genome. SBF and MBF are sequence-specific transcription factors that activate gene expression during the G1/S transition of the cell cycle in yeast^{1, 2}. SBF is a heterodimer of Swi4 and Swi6, and MBF is a heterodimer of Mbp1 and Swi6 (refs 1, 3). The related Swi4 and Mbp1 proteins are the DNA-binding components of the respective factors, and Swi6 may have a regulatory function^{4, 5}. A small number of SBF and MBF target genes have been identified^{3, 6, 7, 8, 9, 10}. Here we define the genomic binding sites of the SBF and MBF transcription factors in vivo, by using DNA microarrays. In addition to the previously characterized targets, we have identified about 200 new putative targets. Our results support the hypothesis that SBF activated genes are predominantly involved in budding, and in membrane and cell-wall biosynthesis, whereas DNA replication and repair are the dominant functions among MBF activated genes^{6, 11}. The functional specialization of these factors may provide a mechanism for independent regulation of distinct molecular processes that normally occur in synchrony during the mitotic cell cycle.