A study of gene silencing within the mating-type region of fission yeast defines two distinct pathways responsible for the establishment of heterochromatin assembly. One is RNA interference-dependent and acts on centromere-homologous repeats (cenH). The other is a stochastic Swi6 (the fission yeast HP1 homolog)-dependent mechanism that is not fully understood. Here we find that activating transcription factor (Atf1) and Pcr1, the fission yeast bZIP transcription factors homologous to human ATF-2, are crucial for proper histone deacetylation of both H3 and H4. This deacetylation is a prerequisite for subsequent H3 lysine 9 methylation and Swi6-dependent heterochromatin assembly across the rest of the silent mating-type (mat) region lacking the RNA interference-dependent cenH repeat. Moreover, Atf1 and Pcr1 can form complexes with both a histone deacetylase, Clr6, and Swi6, and clr6 mutations affected the H3/H4 acetylation patterns, similar to the atf1 and pcr1 deletion mutant phenotypes at the endogenous mat loci and at the ctt1 ؉ promoter region surrounding ATF/CREbinding site. These data suggest that Atf1 and Pcr1 participate in an early step essential for heterochromatin assembly at the mat locus and silencing of transcriptional targets of Atf1. Furthermore, a phosphorylation event catalyzed by the conserved mitogen-activated protein kinase pathway is important for regulation of heterochromatin silencing by Atf1 and Pcr1. These findings suggest a role for the mitogen-activated protein kinase pathway and histone deacetylase in Swi6-based heterochromatin assembly.Methylation of histone H3 lysine 9 (H3 Lys-9) by the conserved H3 Lys-9-specific methyltransferase, Su(var)3-9 in flies, SUV39H1 in human, and Clr4 in the fission yeast Schizosaccharomyces pombe (1-4) correlates with heterochromatin assembly. The methylated Lys-9 residue recruits another conserved heterochromatin protein, which is called Swi6 in S. pombe and HP1 (heterochromatin protein 1) in higher eukaryotes (5, 6), leading to regional silencing of chromatin. In the fission yeast, recent studies (6 -8) addressing the silencing of the mating-type region provide insights for understanding the regulation of heterochromatin assembly in eukaryotes. Of particular interest, previous work (9) has defined sequential requirements for the establishment and maintenance of regional heterochromatic domains.Heterochromatin assembly at the mating-type region containing the mat2 and mat3 silent donor loci and an 11-kb interval (K region) between them requires several cis-acting DNA sequences as well as trans-acting factors (8, 10 -13). Heterochromatin formation at the centromeres and within the silent mat2/3 interval requires many of the same silencing factors, including Clr3 and Clr6 (H3/H4-specific histone deacetylases), the Clr4-Rik1 complexes, and Swi6 (2, 14 -19). The DNA elements involved in silencing within the entire 20 kb of the mat2/3 silent mating-type interval include REII (20), the mat3-M element including putative ATF 1 /CREB-binding sites (21), and the ...