Research.

The research in Dr. Shen’s laboratory focuses on the regulation of gene expression in yeast with emphasis on the influence of chromatin structure and remodeling avtivities in gene activation. Recently, we have shown that CUP1 induction resulting in nucleosome repositioning over the entire gene, and its flanking sequence. The remodeling activity is recruited by a trancriptional activator (Shen et al, 2001), and is independent of targeted histone acetylation (Shen et al., 2002). We further identified Spt10p as a sequence-specific activator of histone genes (Eriksson et al. 2005). The zinc finger DNA binding domain of this transcription activator is homologous to that of foamy virus integrase, suggesting a targeted integration for foamy virus DNA into host DNA (Mendiratta et al., 2006).

One of our most recent works has focused on the mechanism of INO1 expression. Transcriptional activation in yeast INO1 chromatin was studied using the indirect end-labeling technique. INO1 chromatin is organized into an ordered, overlapping nucleosomal array under repressing conditions. Nucleosome positions were only disrupted at the promoter region under inducing conditions in the presence of SWI/SNF and INO80. Mutants lacking either remodeler demonstrated identical positioning patterns as the wild type under repressing conditions. This indicates that these two remodelers are responsible and essential for local nucleosomal mobilization at the INO1 promoter (Ford et al., 2007). The area of local nucleosome movement is consistent with the previously identified region of histone deacetylation activity. Consistent with these findings, chromatin immunoprecipitation revealed that both remodelers are restricted to the promoter and are not found over the entire gene, reinforcing the notion of local chromatin remodeling at the regulatory region. Furthermore, both SWI/SNF and INO80 are constitutively present at the INO1 promoter during repressing and inducing conditions, suggesting that the remodeling activity depends on a functional activator. We have also demonstrated that the presence of SWI/SNF is required for INO80 recruitment (Ford et al., 2008). Recently, we have shown that induction of INO1 resulted in acetylation of both histone H3 and H4 at the INO1 promoter and sequences farther downstream in the coding region, suggesting a gene-wide acetylation in response to transcriptional activation. Such chromatin remodeling activity also required the presence of activator Ino2p (Esposito et al., 2010). In light of these findings, we suggest that the localized distribution of chromatin remodelers at the INO1 promoter determine and result in a local nucleosome mobilization and a gene-wide histone acetylation. This remodeling activity is stimulated by the functional transcriptional activator, the Ino2p/Ino4p heterodimer in the absence of the Opi1p repressor under inducing conditions. Thus, a model has been proposed which describes the order of events in INO1 activation.

Ongoing research in our laboratory continues to focus on understanding the mechanism of gene expression, and the nature of metabolic signals triggered by changes in lipid metabolism or in heavy metal metabolism and their interaction with major cellular signal transduction pathways and transcriptional networks in the cell (Wimalarathna et al., 2011). Other projects in Dr. Shen’s laboratory include the transcriptional regulation of autism-associated genes (Zhang et al., 2009; Hong et al., 2011), neuroligin knock-down animal model and autism disorder, and the effect of serotonin 5-HT_1A receptor in feeding behavior.

A working model for transcriptional activation of INO1 chromatin.

In the presence of inositol, Opi1p translocates to the nucleus, and interacts with Ino2p/Ino4p, which is bound to the UAS_INO element. It is possible that the binding of Opi1p to Ino2p deactivates the heterodimer’s activity. Subsequently, Ume6p binds to the URS1 element and the Sin3p-Rpd3p complex is recruited to the promoter followed by histone deacetylation. Both SWI/SNF and INO80 are present at the promoter, but their activity is minimal as they are not stimulated by the non-functional activator. In the absence of inositol, Opi1p binds to phosphatidic acid and is anchored to the endoplasmic reticulum. The Ino2p/Ino4p activator becomes functional, stimulating the activity of SWI/SNF and INO80, resulting in nucleosome movement from Nucleosomes B through E. Meanwhile, the Ume6p-Sin3p-Rpd3p complex departs from the promoter and the Snf1 kinase is recruited. Next, histone acetylases Esa1p and the Gcn5p-SAGA complex are recruited to the promoter to acetylate the histone tails of Nucleosomes B through E. The resulting nucleosomal flux would allow the transcription initiation complex to access its binding site on the DNA template. As a result, INO1 becomes activated. Once INO1 is activated, it is possible that the transcriptional activator and some SWI/SNF are no longer required at the promoter and thus depart.