Understanding how chromatin structure influences DNA-mediated processes has become a fundamental problem in cellular biology. Chromatin is known to influence the regulation of eukaryotic gene expression, DNA replication, DNA repair, and recombination. Abnormal chromatin structure can therefore deregulate these processes, which often leads to cellular transformation and ultimately tumorigenesis. Chromatin effects on gene expression can be either local (gene-specific) or global (non-specific). A classic example of a global chromatin effect is silencing, which is the epigenetic transcriptional repression of a large chromosomal locus, a phenomenon also called position effect. There is a specialized chromatin structure associated with these domains that prevents transcription of genes located either within or adjacent to these heterochromatin regions.

The powerful genetic techniques available in the yeast Saccharomyces cerevisiae have led to its use as a model organism for studying silencing. The classic examples of silencing in yeast are repression of the HML and HMR mating-type loci and telomeres, which are the heterochromatin equivalents in yeast. These forms of silencing depend on a series of shared trans-acting factors that includes the products of the silent information regulator (SIR) genes. Among the four SIR genes, SIR2 is unique in that it is evolutionarily conserved from bacteria all the way up to humans, implying that it has an important and basic cellular function.

The research in our lab is mainly focused on a recently identified form of silencing in yeast called rDNA silencing, which is the transcriptional repression of reporter genes located in the ribosomal DNA. There is a specialized Sir2p-dependent chromatin structure associated with the rDNA that is responsible not only for silencing reporter genes, but also for suppressing recombination between rDNA repeats. We are using genetic and biochemical approaches aimed at 1) identifying structural and regulatory genes associated with rDNA silencing, 2) determining the molecular mechanism of SIR-mediated gene silencing, and 3) investigating the role of rDNA silencing in other cellular processes. Preliminary work from our lab and others already suggests that rDNA silencing has effects on rRNA transcription, regulation of telomeric silencing, and cellular aging. rDNA silencing is unique in that the SIR3 and SIR4 genes are not required, suggesting that a separate Sir2p-associated complex may function at the rDNA. Given the evolutionary conservation of SIR2, exploiting rDNA silencing as a model for SIR2-mediated gene silencing is likely to be applicable to the chromosomal biology of higher eukaryotes, including humans.

Selected References

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Smith JS, Caputo E, Boeke JD. (1999) "A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors." Mol Cell Biol. 19:3184-97. [PubMed]

Smith JS, Brachmann CB, Celic I, Kenna MA, Muhammad S, Starai VJ, Avalos JL,Escalante-Semerena JC, Grubmeyer C, Wolberger C, Boeke JD. (2000) "A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family." Proc Natl Acad Sci U S A. Jun 97(12):6658-63. [PubMed]

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Loewith R, Smith JS, Meijer M, Williams TJ, Bachman N, Boeke JD, Young D. (2001) "Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae." J Biol Chem. Jun 276(26):24068-74. Epub 2001 Apr 16. [PubMed]

Smith JS, Avalos J, Celic I, Muhammad S, Wolberger C, Boeke JD. (2002) "SIR2 family of NAD(+)-dependent protein deacetylases." Methods Enzymol. 353:282-300. [PubMed]

Sandmeier JJ, Celic I, Boeke JD, Smith JS. (2002) "Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway." Genetics. 160:877-89. [PubMed]

Smith J. (2002) "Human Sir2 and the 'silencing' of p53 activity." Trends Cell Biol. 12:404-6. [PubMed]

Sandmeier JJ, French S, Osheim Y, Cheung WL, Gallo CM, Beyer AL, Smith JS. (2002) "RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase." EMBO J. Sep 21(18):4959-68. [PubMed]