%0 Journal Article
%T Large-scale discovery and validation of functional elements in the human genome
%A Bradley E Bernstein
%A Manolis Kellis
%J Genome Biology
%D 2005
%I BioMed Central
%R 10.1186/gb-2005-6-3-312
%X Computational and experimental genomics researchers convened at Cold Spring Harbor Laboratory at the end of 2004 to address the ambitious goal of identifying all the functional elements in the human genome. The functional elements discussed at the meeting included protein-coding genes, regulatory elements, RNA genes and DNA sequences that dictate chromosome structure or replication. The presentations described diverse approaches to the problem, ranging from innovative comparative genomic methods to high-throughput functional assays designed to identify and validate such elements.The meeting followed a gathering of the ENCODE consortium, which aims to identify a comprehensive 'Encyclopedia of DNA elements' in the human genome http://www.genome.gov/10005107 webcite. The consortium, organized and funded by the National Human Genome Research Institute, is initially focusing on designated regions comprising approximately 1% of the human genome, and it strongly emphasizes technology development. Participating laboratories are developing computational techniques for sequence assembly, gene identification and regulatory motif discovery, as well as experimental methods for identifying transcripts, chromatin structures and regulatory regions. Against this backdrop, most speakers described experimental and computational approaches that generated vast numbers of candidate functional elements, from comprehensive transcript catalogs to lists of highly conserved sequence elements. They were complemented by a smaller number of presentations dealing with the daunting task of systematically validating these elements.Mike Snyder (Yale University, New Haven, USA) and Tom Gingeras (Affymetrix, Santa Clara, USA) covered genome-scale technologies for transcript identification and the large numbers of new candidate elements emerging from these studies. Snyder described a complete tiling of the non-repetitive human genome, with 134 arrays containing 52 million oligonucleotide probes. In an
%U http://genomebiology.com/2005/6/3/312