Extensive studies in the past few years have begun to demonstrate that chro
mosome structure plays a critical role in transcriptional regulation. Two h
ighly conserved mechanisms for altering chromosome structure have been iden
tified: 1) post-translational modification of histones and 2) adenosine tri
phosphate (ATP)-dependent chromosome remodeling. Acetylation of histone lys
ine residues has been known for three decades to be associated with transcr
iptional activation. Recent discoveries, however, show that a number of tra
nscriptional regulators are histone acetylases or histone deacetylases. Spe
cific DNA-binding transcription factors recruit histone acetylases and deac
etylases to promoters to activate or repress transcription, These results s
trongly support the notion that histone acetylation and deacetylation play
an important role in transcriptional regulation. Recent findings have also
provided insight into the molecular mechanisms by which ATP-dependent chrom
osome-remodeling activities participate in transcriptional regulation. Furt
hermore, some ATP-dependent chromosome-remodeling activities have been show
n to complex with histone deacetylases. In the complexes studied to date, t
he ATP-dependent chromosome-remodeling activity enhances the histone deacet
ylase activity. Therefore, the two mechanisms appear to work in concert to
achieve precise control of transcription. Disruption of chromosome remodeli
ng has been linked to a number of diseases, and a complete understanding of
the complex chromosome-remodeling machinery may lead to the development of
new therapies.