Systems biology of gene regulation fulfills its promise

A systems-level understanding of gene-regulation programs requires the synthesis of biological, computational, mathematical, and engineering approaches. One aim of a recent meeting on gene expression at the Cold Spring Harbor Laboratory was to promote this synthesis by bringing together experimentalists and computational biologists with a common interest in studying the organization and control of expression in complex biological systems. The presentations largely focused on identification and analysis of protein-DNA interactions, the discovery of cis-regulatory motifs, and the application of systems approaches to the study of post-transcriptional processes. Here we report on some of the remarkable experimental and computational advances in understanding gene regulation discussed at the meeting. A full list of abstracts is available at http://meetings.cshl.edu/meetings/abstracts/2006systems_absstat.html webcite.Chromatin immunoprecipitation followed either by DNA hybridization to microarrays (ChIP-chip) or by DNA sequencing of paired end tags (ChIP-PET) are two widely used approaches to map protein interactions with the genome. One focus of the meeting was on the data obtained from these genome-occupancy studies. Several presentations showed that researchers are expanding the analysis of genome occupancy to tissue and developmental systems.A strength of the ChIP-chip approach is its ability to define interaction sites for proteins with unknown targets. Peggy Farnham (University of California, Davis, USA) is exploiting this to investigate the protein Suz12, a component of the Polycomb Group complex. Her group has not only isolated DNA targets of Suz12, but has also found that Suz12 can silence large regions of the genome in a cell-type-specific manner. The application of ChIP-PET to studying genome occupancy of key transcription factors in embryonic stem (ES) cells was the subject of a presentation by Huck-Hui Ng (Genome Institute of Singapore, Singapore). Ng and his