• Overview
• Protein-DNA Interactions
• Cis Regulatory codes
• Cis Regulatory Elements

Research Overview

The ability of a cell to respond to environmental stresses, differentiate properly, and progress normally through the cell cycle requires a specific and coordinated gene expression program involving regulated transcription of thousands of genes. The initiation of transcription is in large part controlled by the sequence-specific DNA binding of transcriptional activators and repressors. Despite their importance, the sequence specificities of most transcription factors (TFs) remain unknown, underscoring the need for a rapid and universal method to discover TF binding sites.

Previously we developed a novel DNA microarray-based in vitro technology, termed protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the DNA binding site sequence specificities of TFs in a single day (Mukherjee et al., Nature Genetics (2004) 36(12):1331-9; Berger et al., Nature Biotechnology (2006) 24(11):1429-1435). Using PBMs, we have identified the DNA binding site sequence specificities of a large number of TFs from a wide range of organisms, including Vibrio harveyi, Plasmodium falciparum, yeast, worm, fly, mouse, and human. In addition to identifying novel sequence-specific putative regulatory proteins, PBM data aid in the identification of cis regulatory elements and gene regulatory networks, as the resulting binding specificity data allow for improved prediction of genomic TF binding sites and TFs' combinatorial co-regulation of target genes.

To this effect, we have developed computational approaches for analyzing cis regulatory modules (including transcriptional enhancers). We have developed algorithms that include a rigorous statistical consideration of TF binding site clustering, their combinatorial co-occurrences, and cross-species conservation in order to identify candidate cis regulatory modules (CRMs). We have seen that our predicted CRMs are bound by the corresponding TFs in mammalian cells, and that predicted transcriptional enhancers drive temporal- and cell-specific gene expression in the developing Drosophila embryo. A newer algorithm of ours can refine a prior hypothesis of TFs' combinatorial co-regulation of the expression of their target genes. These and newer strategies under development in our lab can be applied widely for analyzing metazoan transcriptional regulatory networks.

This page was last updated September 1, 2008