Control of nucleosome positions by DNA sequence and remodeling machines

Recent studies have shown that promoter nucleosomes frequently adopt specific positions, and indicate that these positions functionally regulate transcription factor binding. Other studies indicate that DNA sequence has a major role in establishing these nucleosome positions, suggesting that evolution has selected for specific, default arrangements of promoter nucleosomes. Finally, recent studies indicate that ATP-dependent chromatin remodeling complexes move nucleosomes away from default positioning sequences, either to complex-preferred locations or to establish a complex-preferred spacing between nucleosomes. Here we will review these recent findings, and consider how combinations of promoter sequence and specific remodeling complexes may act to switch chromatin between permissive and repressive conformations.