Chromatin structure exerts vital control over gene expression, DNA replication, 
recombination, and repair. In addition to altering RNA polymerase II's (Pol II) 
accessibility to DNA, histones are involved in the recruitment of activator and 
repressor complex(es) to regulate gene expression. Histone deacetylase Rpd3 
exists in two distinct forms, Rpd3S and Rpd3L. Several recent studies 
demonstrated that the Eaf3 chromodomain, an Rpd3S subunit, recognizes 
Set2-methylated histone H3K36, initiating Rpd3 deacetylase activity in the wake 
of transcribing Pol II. Eaf3 and Set2 inhibit internal initiation within mRNA 
coding regions, similar to the transcription elongation factor and histone 
chaperone, FACT. Recent studies reviewed here demonstrate that histone 
deacetylation on the body of a transcribed gene is regulated via Set2-mediated 
methylation of histone H3-K36. These modifications provide restoration of normal 
chromatin structure in the wake of elongating Pol II and prevent inappropriate 
initiation within protein-coding regions masked by chromatin.