Cooperation at a distance between silencers and proto-silencers at the yeast HML locus.

Abstract

Transcriptional repression at the silent yeast mating type loci is achieved through the formation of a particular nucleoprotein complex at specific cis‐acting elements called silencers. This complex in turn appears to initiate the spreading of a histone binding protein complex into the surrounding chromatin, which restricts accessibility of the region to the transcription machinery. We have investigated long‐range, cooperative effects between silencers by studying the repression of a reporter gene integrated at the HML locus flanked by various combinations of wild‐type and mutated silencer sequences. Two silencers can cooperate over >4000 bp to repress transcription efficiently. More importantly, a single binding site for either the repressor activator protein 1 (Rap1), the autonomous replicating sequence (ARS) binding factor 1 (Abf1) or the origin recognition complex (ORC) can enhance the action of a distant silencer without acting as a silencer on its own. Functional cooperativity is demonstrated using a quantitative assay for repression, and varies with the affinity of the binding sites used. Since the repression mechanism is Sir dependent, the Rap1, ORC and/or Abf1 proteins bound to distant DNA elements may interact to create an interface of sufficiently high affinity such that Sir‐containing complexes bind, nucleating the silent chromatin state.

Long-Range Communication between the Silencers of HMR

“…HMR-I cooperates with HMR-E, but it cannot initiate silencing on its own (42,50). Therefore, HMR-I is analogous to proto-silencers that have been found at telomeres and HML (6,13). At telomeres, proto-silencers and proteins with barrier activity are interspersed in the subtelomeric blocks to yield domains of discontinuous silencing (24,25,38), and these functional assays have led to models where the protosilencer elements might interact with one another, but direct long-range interactions at telomeric loci have not been demonstrated using the 3C technique.…”

Asymmetric Positioning of Nucleosomes and Directional Establishment of Transcriptionally Silent Chromatin by Saccharomyces cerevisiae Silencers

“…For instance, the binding sites for Abf1p, Rap1p, or ORC in the silencers are actually distinct variants of a consensus sequence (see the legend to Fig. 1A) that may have different affinities for the corresponding protein (4,7). Moreover, the arrangement of the factor-binding sites in each silencer concerning the distance and intervening sequence between any pair of adjacent sites is unique.…”

Differential Requirement of DNA Replication Factors for Subtelomeric ARS Consensus Sequence Protosilencers in Saccharomyces cerevisiae

“…At these positions the telomeric (TG 1-3 ) repeats, which contain binding sites for Rap1p (Gilson 1989;Marcand et al 1996;Grunstein 1997), cooperate with Abf1p-binding sites (ABF1-BS) and ACS, which are found in the core X-and Y9-subtelomeric elements. ABF1-BS and ACS do not act as silencers on their own and hence they are referred to as protosilencers (Boscheron et al 1996;Fourel et al 1999;Pryde and Louis 1999;Lebrun et al 2001). In the core X-and Y9-elements, protosilencers coreside with sequences that have chromatin partitioning or antisilencing activities that are referred to as subtelomeric antisilencing regions (STARs) (Fourel et al 1999(Fourel et al , 2004Pryde and Louis 1999).…”