The long-term goal of our lab is to identify chromatin features that affect the level, noise, and dynamics of gene expression, and to understand how these gene expression and chromatin features are encoded in the genome. Listed below are a few recently finished or on-going projects in the lab:

Identification and functional study of nucleosome-depleting factors

Nucleosomes present a barrier for the binding of most transcription factors. However, a special group of transcription factors can invade compact chromosome and deplete nucleosomes near their binding sites. These factors, known as nucleosome-depleting factors (NDFs) in yeast, direct the binding of other transcription factors and enable them to activate transcription. We are currently developing a high-throughput assay to identify NDFs among all the transcription factors in the genome and study their nucleosome-depleting property. We are also interested in how these NDFs affect gene regulation in single cells.

Long-distance gene regulation in budding yeast

Extensive long-distance chromosomal interactions have been discovered in budding yeast, but to what extent these interactions affect gene expression is not clear. We conducted two studies indicating that clustering of co-regulated genes in yeast can lead to enhanced gene expression. In the first case, we show that a wt GAL1 promoter can interact with a mutant GAL1 promoter at the allelic location in diploid yeast and accelerate its activation. In the second case, we show that a subset of Met4-targeted genes in the genome cluster together, and genes in the cluster gain higher activity. These results challenge widely held views of gene regulation in yeast and further our understanding of how the 3D organization of the genome contribute to gene regulation in eukaryotes.

Regulatory Mechanism and Functional Significance of Divergent Gene Pairs

Divergent gene pairs (DGPs) are abundant in eukaryotic genomes. In yeast, about 50% of the whole genome is organized in DGPs. Despite the fact that the two genes in a DGP are very close together and potentially share the same cis regulatory elements, most DGPs in the yeast genome are not co-regulated. We investigated how the two genes in a DGP can be “decoupled” in their regulation. Our bioinformatics analyses showed that co- versus differential regulation cannot be explained by several genetic features, including the promoter length, binding site orientation, TATA elements, nucleosome distribution, or presence of non-coding RNAs. Instead, for a differentially regulated DGP, PFK26-MOB1, we found that the decoupling is mainly achieved through two DNA-binding factors, Tbf1 and Mcm1. Similar to “enhancer-blocking insulators” in higher eukaryotes, these factors shield the proximal promoter from the action of more distant transcription regulators. Interestingly, this blockage mechanism is not 100% robust – the regulatory signal of PFK26 can occasionally “leak” to MOB1, increasing the cell-to-cell variability (noise) of MOB1 expression.