Projects

How do we identify and characterize factors that can lead to nucleosome depletion and how to mechanistically dissect long-distance chromosomal interactions that regulate gene expression? (Bai Lab)

We measure gene expression in single live cells to probe how these chromatin features affect gene expression in terms of the average level, cell-to-cell variability (noise), and dynamics. We are using budding yeast as our primary model system, but we are venturing into the mammalian cells as well. Method-wise, we are using a combination of imaging, genetics, genomics, and computational methods.

 

We are interested in understanding mechanisms of transcriptional control in eukaryotes and are currently focusing on the function and mechanism of promoter proximal pausing. (Gilmour Lab)

Using primarily Drosophila as a model system, we are combining biochemical, molecular genetic, and cytological methods to achieve a uniquely comprehensive approach to the study of promoter proximal pausing.  We have reconstituted promoter proximal pausing in Drosophila nuclear extracts and are using this to investigate the mechanism by which specific proteins control promoter proximal pausing.

 

Our work on epigenetic features and gene expression is complemented by a project using interspecies sequence alignments (comparative genomics) to find functional regions within noncoding DNA sequences. (Hardison Lab)

This long-standing collaboration with Drs. Webb Miller, Francesca Chiaromonte and others has led to the development of software for whole-genome alignments (Miller), use of machine-learning to predict regulatory regions from their patterns in multi-species sequence alignments (Chiaromonte and James Taylor), and the testing of these predictions for function as enhancers and promoters by gene transfer into mammalian erythroid cell lines.

 

Our research aims to understand where transcription factors (TFs) bind in the genome, and what they do once they get there. (Mahony Lab)

High-throughput sequencing assays are giving us unprecedented insight into the regulatory environment of the cell. ChIP-seq and ChIP-exo allow us to profile TF and histone modification occupancy at high resolution over the entire genome. RNA-seq lets us profile the global transcriptional activity. DNase-seq profiles the genome-wide accessibility landscape, while new assays such as ChIA-PET and Hi-C are opening a window on the three-dimensional architecture of the nucleus.

 

One of the main questions is understanding how the Plasmodium parasite controls its developmental progression within the red blood cell.  What are the factors that it uses to control this development? How does it interact with and sense the extracellular environment? And how are alternative developmental programs realized by the parasite? (Llinás Lab)

We are using a combination of genomics, biochemistry, and bioinformatics to address these issues with the goal of devising ways to disrupt the parasite lifecycle.

 

How are all gene regulatory proteins organized throughout the genome? (Pugh Lab)

There are nearly a thousand different gene and chromatin regulatory proteins which need to work together to regulate the genome. We want to know their precise positional organization relative to each other, within several bp of resolution. This will be achieved using our ChIP-exo assay applied to a thousand yeast TAP-tagged ORF strains. Such an all-encompassing view will help us better understand genome regulation. This will set the stage for an equivalent endeavor in human systems.

 

Uncover how multiple steps in gene expression are coordinated and regulated; define the functions of a highly conserved eukaryotic transcription factor complex implicated in human disease; and identify how specific mRNAs are marked for post-transcriptional control during transcription. (Reese Lab)

Our research exploits the powerful genetic systems of budding yeast and Drosophila melanogaster to examine the function of a complex proposed to perform multiple steps in gene regulation: the Ccr4-Not complex.  The Ccr4-Not complex is highly conserved across the eukaryotic kingdom. Initially purposed to be a nuclear transcription regulatory complex in yeast, it has since been identified as the major mRNA deadenylase in the cytoplasm and implicated in protein destruction and micro RNA (miRNA) processing.  Mutations in subunits of this complex cause altered DNA damage checkpoint functions, impaired cell cycle progression and sensitivity to stress. The human orthologues of these proteins are putative oncogenes and are implicated in regulating hepatitis C virus replication in human cells; thus, understanding the function of this complex is directly relevant to human disease.

 

Our overall goal is to provide fundamental insight into the systems and processes from biochemistry, using the principles and quantitative laws from physical chemistry. (Showalter Lab)

We aime to establish NMR methodology enabling quantitative and comprehensive structural biology for molecules that are traditionally under-represented in structural databanks.  Also to provide predictive connections between structure and function for highly flexible biomolecules, which are now agreed to be very common.

 

How do chromatin enzymes and transcription factors recognize nucleosomes and how is gene activity regulated on a chromatin template? (Tan Lab)

The two rate-limiting steps in structure determination of large complexes by X-ray crystallography are generating large quantities of high purity material and crystallizing the complexes. We have developed methods for reconstituting recombinant multicomponent complexes and we continue research to improve those methods. We are also investigating novel methods and tools for crystallizing multicomponent complexes.

 

Our working hypothesis is that Epigenetic Mechanisms regulate tumor suppressor gene expression in cancer cells. (Wang Lab)

Epigenetic repression of suppressor genes is a hallmark of cancer initiation and progression.  Epigenetic mechanisms, such as DNA methylation, histone deacetylation, and histone citrullination, play important roles in the repression of tumor suppressor genes.  As such, DNA methyltransferase (DNMT), histone deacetylase (HDAC) and peptidylarginine deaminase 4 (PAD 4) are promising anti-cancer drug targets.