Genomic and Functional Analyses of Conserved Noncoding Regions in Vertebrates

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A bidirectional promoter is defined as the shared regulatory region that falls in the intergenic space between two oppositely oriented genes, which are separated by no more than 1,000 bp. These genes are organized in a head-to-head arrangement and transcribed away from one another. The closely spaced arrangement of the transcription start sites (TSSs) for such a pair of genes is recognized as a nonrandom event in the genome, proven by the fact that a greater than expected number of promoters have this architecture. One plausible scenario for the creation of bidirectional gene pairs is chromosomal recombination bringing the ends of two TSSs in close proximity. This formation is likely to be irreversible because breakage of the union (within or near the bidirectional promoter) would interrupt the normal regulation of two genes profoundly affecting normal genomic function. We have mapped bidirectional promoters in multiple genomes. In doing so, we are creating the first high-confidence regulatory map of promoter sequences in multiple vertebrate lineages. In addition to characterizing promoter regions, we are interested in identifying novel types of elements such as negative regulators of gene expression (NREs). In contrast to the large body of literature on positively acting elements such as enhancers and promoters, cis-acting NREs have not been extensively studied. Despite their scarcity in the literature, these elements are likely to be abundant in the genome. Examples of NREs include silencers, which decrease expression of a gene under their regulation and enhancer-blocking (EB) elements, which prevent the action of an enhancer on a promoter when placed between the two, but not otherwise. By developing a strategy to experimentally identify NREs, we have identified novel elements with these functions in the human genome. Both of these research projects examine cis-acting elements and converge on the identification of transcription factor binding sites, which as trans-acting elements, act as the basic components of gene regulation. Regulatory motifs have been published for each of the projects. During the course of our work, novel motifs were implicated as silencers and new biological insights were revealed for the regulation of alternative promoters. A collaborative effort has been established to define the regulatory networks involving these motifs and epigenetic events that control gene expression in these pathways during cancer.