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Novel Approach to Identify Co-Regulated Genes

Transcription factors activate or repress expression of particular genes by binding to specific DNA regulatory elements. An individual transcription factor can interact with hundreds, or even thousands, of genomic regulatory elements at a given time. The family of genes controlled by a transcription factor is termed its regulon. Regulons are not static, but rather change in response to various intracellular and extracellular signals. Understanding how a transcription factor drives the integrated genomic response to a particular stimulus, or set of stimuli, requires the definition of its target genes. Consequently, identifying transcription factor targets has been a long-standing goal of molecular genetics.

Considerable progress has been made on this problem in unicellular organisms, such as yeast, where the genomes are well characterized. In mammalian systems, which have more complex genomes, comprehensive analyses of transcription factor binding sites have been limited to the two smallest chromosomes, chromosomes 21 and 22, which represent less than 2% of the genome.

Co-Regulated Genes

Localization of genomic signature tags (designated by vertical lines) in two CREB-responsive genes. CpG designates CpG islands, regions typically associated with transcription. Predicted CREB binding sites are indicated.

The Goodman lab, working in collaboration with colleagues at Stony Brook and Brookhaven, has recently accomplished the first genome-wide analysis of transcription factor binding sites in a metazoan (multicellular) organism. Their study addressed the genomic targets for CREB, a transcription factor involved in many aspects of neurobiological and endocrine function. The method used to identify these targets combines chromatin immunoprecipitation with a modification of SAGE, an approach originally developed to analyze mixtures of RNA, and relies on the observation that a 21 nucleotide sequence of DNA (termed a genomic signature tag) generated from immunoprecipitated chromatin can be localized to a unique position within a mammalian genomic database with 75% accuracy. By collecting, sequencing, and analyzing these tags, the lab can identify and quantify transcription factor binding sites in an unbiased manner. Their study of CREB targets represents the most comprehensive analysis of transcription factor binding sites ever performed in a metazoan system and provides a powerful new tool for genomic analysis.

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