The S. cerevisiae Rpd3 large (Rpd3L) and small (Rpd3S) histone deacetylase 
(HDAC) complexes are prototypes for understanding transcriptional repression in 
eukaryotes [1]. The current view is that they function by deacetylating 
chromatin, thereby limiting accessibility of transcriptional factors to the 
underlying DNA. However, an Rpd3 catalytic mutant retains substantial repression 
capability when targeted to a promoter as a LexA fusion protein [2]. We 
investigated the HDAC-independent properties of the Rpd3 complexes biochemically 
and discovered a chaperone function, which promotes histone deposition onto DNA, 
and a novel activity, which prevents nucleosome eviction but not remodeling 
mediated by the ATP-dependent RSC complex. These HDAC-independent activities 
inhibit Pol II transcription on a nucleosomal template. The functions of the 
endogenous Rpd3 complexes can be recapitulated with recombinant Rpd3 core 
complex comprising Sin3, Rpd3, and Ume1. To test the hypothesis that Rpd3 
contributes to chromatin stabilization in vivo, we measured histone H3 density 
genomewide and found that it was reduced at promoters in an Rpd3 deletion mutant 
but partially restored in a catalytic mutant. Importantly, the effects on H3 
density are most apparent on RSC-enriched genes [3]. Our data suggest that the 
Rpd3 core complex could contribute to repression via a novel nucleosome 
stabilization function.