Science-related social media was abuzz on September 5, 2012 in regards to the launch of the Nature ENCODE database. @NatureMagazine could not contain their excitement, with a variety of tweets: announcing the new venture, linking to the database, movies about the database, and even pictures of aerial silk dancers at their Nature ENCODE launch press conference.
Aerial silk dancers? Yes, these dancers were imitating various DNA elements, including looped DNA (as seen above) and primed DNA polymerases, found here.
What was the reason for all this fanfare? What is Nature ENCODE?
ENCODE stands for the Encyclopedia of DNA elements. The ENCODE Project Consortium set out to map the functional of the human genome.1 These elements include “regions of transcription, transcription factor association, chromatin structure and histone modification.”1 A pilot phase, released in 2007, mapped 1% of the human genome and the 2012 release celebrates the culmination of a vast array of methods and data analysis applied to the whole of the human genome. At least one biochemical function has been assigned to ~80% of the human genome.1 Simplifying and summarizing the approaches used to amass and analyze this data is beyond the scope of this article; instead, click here, for the introductory research article by the Nature ENCODE project consortium, and here for the “Making a Genome Manual.”
The Nature ENCODE project release included the publication of thirty papers in Nature, Genome Biology, and Genome Research. The busy graduate student may be hesitant to add these to their ever-growing list of papers. Not surprisingly, ENCODE anticipated this and created the ENCODE explorer which puts “your favorite part of the genome” just a click away. This explorer starts with thirteen threads with topics such as “RNA and chromatin modification patterns around promoters” and “three-dimensional connections across the genome.” Interested in characterizing non-coding RNA? Click on thread 6 and the ENCODE explorer has spliced relevant sections from the ENCODE consortium papers right here at your fingertips.
The tech-savy scientist can access the ENCODE genome annotations at their fingertips with the Nature ENCODE iPad app. Still overwhelmed with the massive amount of data? Try viewing this introductory video containing interviews with scientists involved in the project, or this animated video entitled “ENCODE: The story of you,” which starts at Gregor Mendel, moves through Watson and Crick to the Human Genome Project, then focuses on the ENCODE launch.
Where will ENCODE go from here? What surpasses aerial silk dancers imitating primed DNA polymerases? For that, we will have to wait and see.
The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.