Silencing_coevolution_PLoS_113010
Co-evolution of Transcriptional Silencing Proteins and the DNA Elements Specifying Their Assembly
Chromatin immunoprecipitation of either Sc-Sir4 or Sb-Sir4 was performed in five separate S. cerevisiae/S. bayanus hybrid diploid strains.  Each Sir4 allele was separately myc-tagged, and the ChIPs were performed using anti-c-myc affinity resin.  Input and IP fractions for each ChIP experiment were sequenced on individual lanes of an Illumina flow cell using 36-bp paired end reads.  Data were collected between 5/18/09 - 5/26/09.  Except for the "No tag" sample, only IP reads are stored under this accession.  The matching Input reads can be found under accession SRP000997.
Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated.  Here we provide experimental evidence of such co-evolution in yeast silent chromatin, a finding that emerged from studies of hybrids formed between two closely related Saccharomyces species.  A unidirectional silencing incompatibility between S. cerevisiae and S. bayanus led to a key discovery: asymmetrical complementation of divergent orthologs of the silent chromatin component Sir4.  In S. cerevisiae/S. bayanus interspecies hybrids, ChIP-Seq analysis revealed a restriction against S. cerevisiae Sir4 associating with most S. bayanus silenced regions; in contrast, S. bayanus Sir4 associated with S. cerevisiae silenced loci to an even greater degree than did S. cerevisiae’s own Sir4.  Functional changes in multiple silencer DNA elements across the genome paralleled changes in Sir4 sequence and a reduction in Sir1 family members in S. cerevisiae.  Critically, species-specific silencing of the S. bayanus HMR locus could be reconstituted in S. cerevisiae by co-transfer of the S. bayanus Sir4 and Kos3 (the ancestral relative of Sir1) proteins.  As Sir1/Kos3 and Sir4 are structural chromatin proteins that bind conserved transcription factors, but not specific DNA sequences, these rapidly evolving proteins served to interpret differences in the two species’ silencers presumably involving emergent features created by the transcription factors that bind sequences within silencers.  The results presented here, and in particular the high resolution ChIP-Seq localization of the Sir4 protein, provided unanticipated insights into the mechanism of silent chromatin assembly in yeast.