The Holstege Lab: Genome Control
The importance of understanding transcription regulation
Understanding gene regulation is fundamental to understanding almost any cellular process. This includes disease. Our current inability to properly combat many diseases is in part due to our incomplete knowledge of regulatory circuitry. The mission of the lab is to completely decipher our regulatory code so that we can more appropriately combat disease in various ways. This is a long-term goal. We are also already applying our genome-wide methods to improve health-care immediately. For example, we have recently shown that it is possible to accurately detect the presence of tumor metastases by DNA microarray expression-profiling of primary head-neck squamous cell carcinomas1. Most of our translational research is performed together with other laboratories at the UMC Utrecht, through collaboration with the microarray facility which is part of our group.Mapping the regulatory circuitry of an entire genome: a systems biology approach
The long-term goal of the lab is to develop an intricate molecular model that accurately describes how all genes are regulated: a genome control map. The initial focus is on transcription regulation. This will require quantitative measurements of transcription rates for all genes, determination of transcription factor occupancy across the genome, mechanistical insight into signal transduction induced protein-modifications and their consequences for transcription, analysis of chromatin structure and modifications, the activity of co-regulatory protein complexes, etc.
We have already put together a powerful tool-box for genome-wide analyses that includes DNA microarray expression-profiling, genome-wide localisation analysis by ChIP on chip and various bioinformatics tools. Based on literature and on our own experiments, we are putting together a molecular parts list: which proteins influence transcription of which genes in which way. The starting point is the important eukaryotic model organism Saccharomyces cerevisiae, otherwise known as bakers or brewers yeast. Our work typically results in finding novel regulatory mechanisms because of its genome-wide and unbiased nature2-4. Such discoveries often apply equally to other genes, transcription factors and organisms such as humans. We also include well-established tools to analyse and learn more about the underlying molecular mechanisms. Besides learning about eukaryotic transcription regulation, our lab is therefore also an excellent place to learn about biochemistry, molecular biology and molecular genetics as well as how to encorporate these into meaningful post-genomic science. Bioinformatics is also key to our goal of developing a genome control map and several members of our team focus entirely on bioinformatics.Transcription, signal-transduction, proteomics and genomics
Work from several laboratories world-wide has shown the feasibility of applying genome-wide methods such as DNA microarrays for studying transcription regulation. This includes the internationally recognized pioneering work performed by Frank Holstege during the early days of genomics5. Much of this previous work has focused on transcription factors6. Because transcription regulation is the result of an intricate cooperation between the transcription machinery and signal transduction pathways7, the lab is currently focused on better understanding this interplay by combining the powerful genome-wide technologies with newly developed mass-spectrometry based proteomic approaches in order to understand how the regulators themselves are regulated. Another pivotal study has been our recent demonstration that DNA microarray expression-profiling of gene deletions can be used to determine structure-function relationships within and between protein complexes, to discover new signal-transduction pathways, to determine epistatic relationships (which component is up- or downstream of the other) and to precisely pin-point the consequences of regulatory modifications by protein kinases3.The people involved
Although we believe strongly in molecular driven concepts as well as technology development, the most important asset of our lab is the people involved. Each member has their own projects and responsibilities. By working together, we believe that we can achieve both our personal goals as well as the long-term goal of the lab. Individual excellence combined with teamwork are key. Whether you are a prospective Ph.D. student, post-doc, technician, bioinformatician or a Masters student looking for an exciting internship, we invite you to join us. If you are intelligent, ambitious and like to work hard at something that is worthwhile, enjoy a challenge and are interested in performing meaningful science at the highest international level, our lab is an excellent place to test and develop your skills. We offer an environment that is internationally orientated, where it is fun to work and learn together. We take our work seriously and aim to publish in the best scientific journals because we believe that is where our work belongs.
For information regarding internships send us an email. We also welcome letters of interest and CVs from any prospective Ph.D. student, technician, post-doc, scientific programmer of bioinformatician. Useful past experience is in protein biochemistry, molecular biology, molecular genetics (especially yeast), mass-spectrometry, microarrays and bioinformatics. Previous experience in these subjects is not pivotal for a successful application. Previous excellence is.
Literature
(see our publications for a complete list)1. An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas Nature Genetics, (2005), 37, 182-6 Roepman, P., Wessels, L. F., Kettelarij, N., Kemmeren, P., Miles, A. J., Lijnzaad, P., Tilanus, M. G., Koole, R., Hordijk, G. J., van der Vliet, P. C., Reinders, M. J., Slootweg, P. J., and Holstege, F. C.
2. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit
Molecular Cell, (2005), 18, 171-83 Radonjic, M., Andrau, J. C., Lijnzaad, P., Kemmeren, P., Kockelkorn, T. T., van Leenen, D., van Berkum, N. L. and Holstege, F. C.
3. Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets Molecular Cell, (2005), 19, 511-22 van de Peppel, J., Kettelarij, N., van Bakel, H., Kockelkorn, T. T., van Leenen, D. and Holstege, F. C.
4. Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA Molecular Cell, (2006), 22, 179-92 Andrau, J. C., van de Pasch, L., Lijnzaad, P., Bijma, T., Koerkamp, M. G., van de Peppel, J., Werner, M. and Holstege, F. C.
5. Dissecting the regulatory circuitry of a eukaryotic genome Cell, (1998), 95, 717-28 Holstege, F. C., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S. and Young, R. A.
6. Transcription factor target practice Cell, (2006), 124, 21-3 Holstege, F. C. and Clevers, H.
7. Transcriptional regulation: contending with complexity Proc Natl Acad Sci U S A, (1999), 96, 2-4 Holstege, F. C. and Young, R. A.