Invited Talks

GENE-CENTERED PROTEIN-DNA INTERACTOME MAPPING

Abstract
Transcription regulatory networks play a pivotal role in the development, function and pathology of metazoan organisms. Such networks are comprised of protein-DNA interactions between transcription factors (TFs) and their target genes[1]. We are interested in the architecture and functionality of such networks. We developed high-throughput gene-centered methods[2] for the identification of protein-DNA interactions between large sets of regulatory gene segments and various TF resources, including novel Steiner Triple System-based TF smart pools and a TF array[3]. So far, we mapped two gene-centered networks using C. elegans gene promoters[4,5]. These networks already provided insights into differential gene expression at a systems level. For instance, we found that most C. elegans genes are controlled by a layered hierarchy of TFs that sometimes function in a modular manner. Our data can be accessed in our database, EDGEdb[6].

1. Walhout, A. J. M. Unraveling Transcription Regulatory Networks by Protein-DNA and Protein-Protein Interaction Mapping. Genome Res 16, 1445-1454 (2006).
2. Deplancke, B., Dupuy, D., Vidal, M. & Walhout, A. J. M. A Gateway-compatible yeast one-hybrid system. Genome Res 14, 2093-2101 (2004).
3. Vermeirssen, V. et al. A C. elegans transcription factor array and Steiner Triple System-based smart pools: high-performance tools for transcription regulatory network mapping. Nat Methods In press (2007).
4. Deplancke, B. et al. A gene-centered C. elegans protein-DNA interaction network. Cell 125, 1193-1205 (2006).
5. Vermeirssen, V. et al. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res May 18; [Epub ahead of print] (2007).
6. Barrasa, M. I., Vaglio, P., Cavasino, F., Jacotot, L. & Walhout, A. J. M. EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics 8, 21 (2007).