In eukaryotic organisms chromatin plays a key role in the highly efficient regulation of gene expression. The genome is organized into discrete structural and functional chromatin domains with different potentials for gene expression. Our major goal is to understand the mechanisms underlying the establishment and maintenance of genomic domains in the highly tractably yeast model system by addressing the following questions.
How do silencers initiate the formation of transcriptionally silent chromatin?
Silencers are small regulatory sequences flanking HML and HMR in yeast that are responsible for the initiation of formation of a special silent chromatin across these loci. An outstanding question concerning silencer function is whether they act in an orientation-dependent or –independent fashion. We have recently demonstrated that a silencer is intrinsically unidirectional but its genomic context can regulate its directionality. We are examining cis-acting DNA elements and trans-acting protein factors that contribute to the determination of the directionality of silencers.
How do barriers block the propagation of silent chromatin?
The Sir complex is an integral part of silent chromatin. It is recruited to the silencers during the initiation of formation of silent chromatin. Sir complexes have the ability to spread along the chromatin fiber in a step-by-step fashion thereby encroaching upon transcriptionally active chromatin. This poses the question of how an active chromatin domain is protected from adjacent silent chromatin. We and others have identified various special sequences referred to as barrier elements that could block the spread of silent chromatin. Barriers exist near the silent HM loci but the mechanisms of their functions have not been resolved. We are investigating how these elements restrict silent chromatin to limited domains.
How does silent chromatin repress gene expression?
Silent chromatin in yeast is equivalent to the condensed heterochromatin in higher organisms. Compared to active chromatin (euchromatin), silent chromatin has a more compact structure, is associated with reduced histone acetylation, and is covered by the Sir silencing complexes. It is generally believed that the compactness of silent chromatin hinders the initiation and/or elongation of transcription by RNA polymerases. However, this contention is challenged by our recent findings. We are currently testing the hypothesis that it is histone hypoacetylation, not the special chromatin structure that is mainly responsible for the repression of genes residing in silent loci.
How does a chromatin-associated histone acetyl transferase (HAT) acetylate nucleosomes at a distance?
Histone acetylation by HATs is intimately linked to gene expression, as transcriptionally active chromatin domains are usually hyperacetylated. HATs are recruited to gene enhancers/promoters by transcriptional activators. We have recently shown that a targeted HAT could acetylate at least eight consecutive nucleosomes on either side. We are examining the mechanism(s) underlying how a targeted HAT “reaches” and acetylates nucleosomes at a distance.