Since the completion of the Human Genome Project in 2003, research efforts have been aimed at analyzing the functions of various sequences in the genome, using both experimental and computational strategies. The June issue of Genome Research (www.genome.org) is devoted to The ENCODE (ENCyclopedia Of DNA Elements) Project, whose goal is to characterize all functional elements in the human genome. Genome Researchs ENCODE issue includes 25 research papers, which report on the validation of the main results of the pilot project and are essential the community as they scale up to cataloguing functional elements in the whole genome.
In addition, the issue also contains commentary and perspectives on how our views of the genome have changed as a result of the ENCODE investigations. The major findings span the areas of chromatin and replication, gene transcription and regulation, and evolutionary constraint, some of which are highlighted below. The entire issue will be freely available online on June 14 to coordinate with the ENCODE consortium publication in the journal Nature.
1. Pervasive transcription, fewer boundaries
Dr. Alexandre Reymond and colleagues conducted a series of experiments to annotate all 399 protein-coding genes in the ENCODE regions. In doing so, they found that more than half of the genes produced transcripts that contained sequences mapping outside of the known boundaries of these genes. Interestingly, these transcribed sequences often overlapped with other genes, were located a significant distance from the main portion of the coding sequence, and spanned large genomic segments.
Our results modify our current understanding of the architecture and regulation of protein-coding genes, explains Dr. Reymond. Furthermore, some sequence polymorphisms hitherto considered to be located in non-coding regions may ultimately be related to disease.