Gene Expression Focus Group
marks one year milestone

With initial support provided by a $1 million grant from the MSU Foundation, the Focus Group brings the interdisciplinary strengths of the member laboratories to bear on a range of new topics. Postdoctoral fellows have been recruited to launch new research in the area of gene expression in development and disease, and the first fruits of their efforts were described at a symposium in June at the Kellogg Center in which new research findings were presented to over fifty scientists of the participating eight research groups.

Transcriptional regulation involves the basal transcriptional machinery, which can be compared to an automobile’s engine, and regulatory factors, which function as the brakes and accelerator. Communication between these two classes of proteins is critical to regulation of gene expression. Postdoctoral researcher Stacy Hovde, working with the Geiger and Henry laboratories, has focused on one such interaction by solving the structure of the DNA binding domainof the Oct-1 transcription factor complexed to the DNA and to a component of the basal transcription machinery, SNAP190. Her high resolution molecular structures reveal critical contacts between the two proteins that allow Oct-1 to discriminate between sequences controlling expression of protein-coding genes regulated by RNA Polymerase II and small nuclear RNA genes regulated by RNA Polymerase III.

Retinoblastoma (Rb) proteins are transcriptional repressors that control expression of genes linked to the cell cycle, and mutations in Rb occur frequently in human cancers. The Henry laboratory has been studying the role of mammalian Rb in regulating a class of small nuclear RNA genes. Combining the Arnosti laboratory’s expertise with development and transcription in the fruitfly Drosophila melanogaster with the Henry’s biochemical prowess, postdoctoral researchers Scott Keller and Zakir Ullah have been analyzing the role of Rb proteins in Drosophila, where their role in development can be assessed. They have shown that the fly expresses two proteins of the Rb family, and that these proteins are likely to have distinct activities based on their complementary expression patterns and formation of complexes of distinct sizes. This research aims to functionally characterize the activities of the proteins using biochemical and molecular genetic means to better understand the role of Rb proteins in cancer.

Chromatin is the form in which cellular DNA is packaged within the tight constraints of the nucleus. Covalent and non-covalent modifications of histones and other chromatin proteins are integral events associated with gene activation and repression, and chromatin modification is known to play important roles in development and disease. To identify novel factors that associate with histone proteins and may play a role in chromatin structure, postdoctoral researcher Asha Acharya in the Kuo laboratory is using advanced genomic techniques in the yeast Saccharamyces cerevisiae to identify factors that bind to modified histone "tails", the portions of these proteins that are subject to modification in association with gene regulation. Analysis of histone acetyltransferase activities is being pursued in the Triezenberg laboratory, where postdoctoral researcher Amy Hark is examining the structure of promoters subject to regulation by the ADA2 and GCN5 proteins in the plant Arabidopsis thaliana. They find that these proteins regulate many aspects of development in this plant, and may provide an effective means to identify stress-tolerance genes of commercial importance.

Recent X-ray crystallographic analysis has afforded unprecedented views of the core enzyme of transcription, RNA polymerase. However, like a still photograph, these structural images do not convey the activity of the enzyme in operation. Using a novel "running-start" kinetic approach to transcriptional initiation, Xue Qian Gong in the Burton laboratory has been tracking the movements of human RNA polymerase II on a millisecond scale to understand the molecular transitions that allow this enzyme to work rapidly and accurately. In collaboration with the Geiger and Yan laboratory, they have identified a kinetic pathway for this enzyme that suggests that RNA polymerase preloads its NTP substrate prior to movement into the active site, contrary to conventional models. As medically important connections to this work, the actions of the deadly fungal toxin a -amanitin and the hepatitis B-associated hepatitis delta virus antigen are integrated into this picture to show how these factors inhibit and stimulate transcription, respectively.

While multicellular development is often thought the province of eukaryotic organisms, the lifestyle of some bacteria, such as Myxococcus xanthus, involves formation of elaborate multicellular structures, such as fruiting bodies. Gene regulation during development in this bacterium is the focus of research by Durairaj Srninivasan in the Kroos laboratory. Working with the Kuo laboratory, novel regulatory factors are being sought using yeast-based genetic screeens, and the binding of known transcription factors to promoters in vivo is being studied to better understand how genes are activated in response to cell-cell signaling during development.