Question

What is the ENCODE project? What was measured by the consortium? What was the ultimate conclusion of their work?

Answer 1

ENCODE PROJECT

•ENCODE is a public research consortium aimed at identifying all functional elements in the human and mouse genomes.

•The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.

•The conclusion that most of the genome is "functional" has been criticized on the grounds that ENCODE project used a liberal definition of "functional", namely anything that is transcribed must be functional. This conclusion was arrived at despite the widely accepted view, based on genomic conservation estimates from comparative genomics, that many DNA elements such as pseudogenes that are transcribed are nevertheless non-functional. Furthermore, the ENCODE project has emphasized sensitivity over specificity leading possibly to the detection of many false positives. Somewhat arbitrary choice of cell lines and transcription factors as well as lack of appropriate control experiments were additional major criticisms of ENCODE as random DNA mimics ENCODE-like 'functional' behavior.