Forkhead (Fkh) transcription factors influence cell death, proliferation, and differentiation and the cell cycle. In Saccharomyces cerevisiae, Fkh2 both activates and represses transcription of CLB2, encoding a B-type cyclin. CLB2 is expressed during G 2 /M phase and repressed during G 1 . Fkh2 recruits the coactivator Ndd1, an interaction which is promoted by Clb2/Cdk1-dependent phosphorylation of Ndd1, suggesting that CLB2 is autoregulated. Ndd1 is proposed to function by antagonizing Fkh2-mediated repression, but nothing is known about the mechanism. Here we ask how Fkh2 represses CLB2. We show that Fkh2 controls a repressive chromatin structure that initiates in the early coding region of CLB2 and spreads up the promoter during the M and G 1 phases. The Isw2 chromatin-remodeling ATPase cooperates with Fkh2 to remodel the chromatin and repress CLB2 expression throughout the cell cycle. In addition, the related factors Isw1 and Fkh1 configure the chromatin at the early coding region and negatively regulate CLB2 expression but only during G 2 /M phase. Thus, the cooperative actions of two forkhead transcription factors and two chromatin-remodeling ATPases combine to regulate CLB2. We propose that chromatin-mediated repression by Isw1 and Isw2 may serve to limit activation of CLB2 expression by the Clb2/Cdk1 kinase during G 2 /M and to fully repress expression during G 1 .The forkhead (Fkh) family of transcription factors is highly conserved in eukaryotes, with roles in cell cycle control, cell death, proliferative responses, and differentiation (1,3,4,27). All four forkhead factors have been characterized in Saccharomyces cerevisiae. Fhl1 and its coregulator Ihf1 regulate cell proliferation primarily through control of ribosomal protein gene expression (5,18,21,35,50,52,59). Different phases of the cell cycle are regulated by two forkhead factors, Hcm1 and Fkh2. Hcm1 regulates chromosome segregation genes and controls the S-phase transition (46). Fkh2 and its coactivator Ndd1 influence the expression of a wide range of genes (56), including the genes of the CLB2 cluster that control the G 2 /M and M/G 1 phases of the cell cycle (15,23,62) which are the best-characterized targets of Fkh2/Ndd1 regulation. Genes belonging to the CLB2 cluster, including CLB2 itself, contain one or more SFF binding sites at which Fkh2, Ndd1, and the MADS box protein Mcm1 bind. Both Fkh2 and Ndd1 are subject to extensive phosphorylation during the cell cycle. The Clb5/Cdc28 complex phosphorylates residues on the C-terminal region of Fkh2 between the S phase and G 2 (44). The interaction between Fkh2 and Ndd1 is optimal when both proteins are phosphorylated. Ndd1 is a substrate for the Clb2/ Cdc28 G 2 /M kinase, and phosphorylation promotes the interaction between Ndd1 and the FHA domain of Fkh2 (11,49). Thus, CLB2 expression is likely to be subjected to a positivefeedback loop (11,23,44,49) and may be regulated differently from other genes in the CLB2 cluster. Very little is understood about how this feedback loop is broken to repres...