With the recent completion of the DNA sequence of the euchromatic portion of the human genome, the inherited information that determines cellular and organismal function is available. The next challenge lies in understanding how to connect the information in the genome sequence with the functions it encodes. This project aims to refine and implement efficient high throughput experimental methods to identify the sequence features that encode regulatory and maintenance functions of the human genome. Specifically the project will aim to design and construct micorarrays consisting of 1.5kb PCR products covering the entire unique genomic sequence of the 30 Mb targeted by the ENCODE project. In parallel a collection of BAC and other sequencing tilepath clones will be establish to cover the targeted regions in a tile-path BAC subarray. At the same time we will optimize assays to provide DNA fractions enriched for specific functional elements from three actively dividing cell lines representing B cells, T cells and fibroblasts. These DNA fractions will be assayed using the genomic microarrays to identify DNA fragments containing functional elements. This will establish a map of various functional properties for 1% of the physical genome, specifically replication timing, location of replication origins, chromatin modification, and common transcription factor binding sites. These maps will be analyzed in comparison to other properties of the genome sequence including G+C content, gene content, repeat content, and sequence conservation. All data will be deposited with the ENCODE consortium as soon as it is shown to be reliable by replication and preliminary analysis.
