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Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF


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 yeast1,2. 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 function4,5. A small number of SBF and MBF target genes have been identified3,6,7,8,9,10. 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 genes6,11. 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.

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Figure 1: Strategy for analysing genome-wide protein–DNA interactions.
Figure 2: Defining criteria for identifying SBF and MBF targets.
Figure 3: Genomic targets of SBF and MBF.
Figure 4: Expression profiles of SBF and MBF targets.


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We thank J. DeRisi for mapping software; O. Aparacio for immunoprecipitation protocols; A. Khodursky for help with significance tests; and J. Lieb for comments on the manuscript and discussion. This work was supported by grants from the National Institutes of Health, and by the Howard Hughes Medical Institute. P.O.B. is an associate investigator of the Howard Hughes Medical Institute.

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Correspondence to Patrick O. Brown.

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Iyer, V., Horak, C., Scafe, C. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533–538 (2001).

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