Nucleosome-excluding sequences as barriers to the spread of silent chromatin. (A) Propagation of silent chromatin in S. cerevisiae. Silencer-binding proteins and Sir1p recruit the SIR complex. Sir2p deacetylates a nearby nucleosome (curved arrow). The hypoacetylated nucleosome (solid circle) then binds an incoming SIR complex. Repetition of this process leads to the spread of silent chromatin (indicated by the solid arrow). Shaded circles, acetylated nucleosomes; Ac, acetyl group. The inset illustrates interactions among silencer-binding proteins, SIR proteins, and the nucleosome. (B) DNA-binding proteins can form barriers to the spread of silent chromatin by excluding nucleosomes. DNA-binding proteins, such as LexA or Rap1p (solid diamond), bind to (multiple) sites in the path of the spread of silent chromatin and destabilize or remove one or more nucleosomes, thereby stalling the propagating SIR complex (curved line with bar). (C) Nucleosome-excluding sequences can form barriers to the spread of silent chromatin. Atypical DNA structures (zigzag line) formed by sequences such as (CCGNN)n or poly(dA-dT), which do not favor nucleosome formation, stop the spread of the SIR complex.