Genome-Wide Chromosomal Targets of Oncogenic Transcription Factors
Annual rept. 31 Mar 2006-30 Mar 2007
TEXAS UNIV AT AUSTIN
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We originally proposed to develop a new genomic method named STAGE Sequence Tag Analysis of Genomic Enrichment to identify the direct downstream targets of transcription factors that are important in breast cancer. STAGE was based on high throughput sequencing of concatamerized tags derived from DNA associated with transcription factors isolated by chromatin immunoprecipitation. Over the last year, we have significantly improved the efficiency of our methodology by modifying the initial method to take advantage of new developments in sequencing technology. We first used a bead-based, pyrosequencing method developed by 454Roche to identify the targets of STAT1. We developed new methods to score target genes and independently verified targets using quantitative real time PCR. Secondly, we have adapted our approach to use even more high-throughput sequencing technology developed by Solexa to identify the targets of c-Myc, by sequencing millions of tags. We will also use Solexa sequencing to improve the coverage of E2F4 targets by significantly deeper sequencing.
- Anatomy and Physiology
- Medicine and Medical Research