Protosilencers as building blocks for heterochromatin

Abstract

DNA repetitions may provoke heterochromatinization. We explore here a model in which multiple cis-acting sequences that display no silencing activity on their own (protosilencers) may cooperate to establish and maintain a heterochromatin domain efficiently. Protosilencers, first defined in budding yeast, have now been found in a wide range of genomes where they appear to stabilize and to extend the propagation of heterochromatin domains. Strikingly, isolated or moderately repeated protosilencers can also be found in promoters where they participate in transcriptional activation and have insulation functions. This suggests that the proper juxtaposition of a threshold number of protosilencers converts them from neutral or transactivating elements into ones that nucleate heterochromatin. Interactions might be transient or permanent, and are likely to occur over distances by looping. This model provides a conceptual framework for as varied phenomena as telomere-driven silencing in Drosophila, X inactivation in mammals, and rDNA silencing in S. cerevisiae. It may also account for the silencing that occurs when multiple copies of a transgene are inserted in tandem.

Long-Range Communication between the Silencers of HMR

“…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. Long-range interactions between the proto-silencers and terminal telomeric sequences, which function as silencers, may indeed be occurring, similar to what we observe at HMR.…”

Chromatin Domain Boundaries Delimited by a Histone-binding Protein in Yeast

“…Chromatin was then digested by adding 50 units of XbaI for 45 min at 37°C to cleave the DNA between the URA3 and the TRP1 genes. Immunoprecipitation was performed with precoated Dynabeads overnight at 4°C and using specific antibodies against tetra-acetylated histone H4 (K5, 8,12,16), diacetylated histone H3 (K9, 14) (Upstate), or against SIR2, SIR3, and SIR4 proteins (Santa Cruz). An aliquot of each sample was not immunoprecipitated (Input).…”

“…6B). Alternatively, a proto-silencer present over the TRP1 gene might recruit additional Sir4 proteins over this gene (8).…”

“…This phenomenon is referred to as telomere position effect and is similar to the position effect variegation (PEV) initially described in Drosophila (6). Transcriptional silencing at yeast telomeres is associated with a heterochromatin-like structure (7,8). DNA wrapped in transcriptionally silent chromatin replicates late in S phase and is refractory to some modifying agents.…”

“…A series of physical and genetic arguments imply that this SIR complex may nucleate from the telomere and spread along the chromosome to coat more centromeric regions and thereby silence intervening genes (14,15). Silencing in natural subtelomeric regions further involves auxiliary recruitment at protosilencer relay elements found in the middle-repetitive X and YЈ subtelomeric elements (1,8,16).…”