The effects of inhibiting histone deacetylation on the maturation of newly 
replicated chromatin have been examined. HeLa cells were labeled with 
[3H]thymidine in the presence or absence of sodium butyrate; control experiments 
demonstrated that butyrate did not significantly inhibit DNA replication for at 
least 70 min. Like normal nascent chromatin, chromatin labeled for brief periods 
(0.5-1 min) in the presence of butyrate was more sensitive to digestion with 
DNase I and micrococcal nuclease than control bulk chromatin. However, chromatin 
replicated in butyrate did not mature as in normal replication, but instead 
retained approximately 50% of its heightened sensitivity to DNase I. Incubation 
of mature chromatin in butyrate for 1 h did not induce DNase I sensitivity: 
therefore, the presence of sodium butyrate was required during replication to 
preserve the increased digestibility of nascent chromatin DNA. In contrast, 
sodium butyrate did not inhibit or retard the maturation of newly replicated 
chromatin when assayed by micrococcal nuclease digestion, as determined by the 
following criteria: 1) digestion to acid solubility, 2) rate of conversion to 
mononucleosomes, 3) repeat length, and 4) presence of non-nucleosomal DNA. 
Consistent with the properties of chromatin replicated in butyrate, micrococcal 
nuclease also did not preferentially attack the internucleosomal linkers of 
chromatin regions acetylated in vivo. The observation of a novel chromatin 
replication intermediate, which is highly sensitive to DNase I but possesses 
normal resistance to micrococcal nuclease, suggests that nucleosome assembly and 
histone deacetylation are not obligatorily coordinated. Thus, while 
deacetylation is required for chromatin maturation, histone acetylation 
apparently affects chromatin organization at a level distinct from that of core 
particle or linker, possibly by altering higher order structure.