The ISWI class of chromatin remodeling factors exhibits potent chromatin re
modeling activities in vitro. However, the in vivo functions of this class
of factors are unknown at a molecular level. We have found that S. cerevisi
ae Isw2 complex represses transcription of early meiotic genes during mitot
ic growth in a parallel pathway to Rpd3-Sin3 histone deacetylase complex. T
his repressor function of lsw2 complex is largely dependent upon Ume6p, whi
ch recruits the complex to target genes. Nuclease digestion analyses reveal
ed that Isw2 complex establishes nuclease-inaccessible chromatin structure
near the Ume6p binding site in vivo. Based on these findings, we propose a
model for the mechanism of transcriptional repression by two distinct chrom
atin remodeling complexes.