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Thematic Minireview Series on the ENCODE Project

Thematic Minireview Series on the ENCODE Project

The Encyclopedia of DNA Elements (ENCODE) Project (http://www.genome.gov/10005107) is an international collaboration of research groups funded by the National Human Genome Research Institute, with the goal of delineating all functional elements encoded in the human genome (1). This project began in 2003 with a targeted analysis of a selected 1% of the human genome. The results from the pilot project were published in 2007 , and a second phase of funding was then provided to scale the project to the entire human genome. Genome-scale projects in ENCODE involve the identification and quantification of RNA species in whole cells and subcellular compartments, mapping of noncoding and protein-coding genes by manual review and experimental methods, delineation of chromatin and DNA accessibility, mapping of histone modifications and transcription factor-binding sites by ChIP, and measurement of DNA methylation. More recently, ENCODE has adopted additional approaches that have not yet resulted in extensive data sets, including the examination of long-range chromatin interactions, analysis of RNA-binding proteins, and validation of transcriptional enhancers and silencers. To date, >2000 data sets have been deposited for public use by the ENCODE Project at the University of California Santa Cruz (UCSC) Genome Browser ; to encourage public use of the data sets, a user's guide to the ENCODE data sets has been published . As the second phase of the ENCODE Project nears completion, the ENCODE Consortium has prepared a large integrative manuscript that includes analyses of experiments from 147 cell types and provides a summary of their.

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