ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome”

by Max Andrews

A groundbreaking paper in Nature reports the results of the Encyclopedia of DNA Elements (ENCODE) project, which has detected evidence of function for the “vast majority” of the human genome. Titled “An integrated encyclopedia of DNA elements in the human genome,” the paper finds an “unprecedented number of functional elements,” where “a surprisingly large amount of the human genome” appears functional. Based upon current knowledge, the paper concludes that at least 80% of the human genome is now known to be functional:

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.(The ENCODE Project Consortium, “An integrated encyclopedia of DNA elements in the human genome,” Nature, Vol. 489:57-74 (September 6, 2012) (emphasis added))

In the past we’ve frequently read about studies reporting function for many thousands of base pairs (see here or here for a few of many examples), but it’s often hard to get a sense of just how much of the genome has had function detected for it. Through the collaboration of hundreds of researchers, the ENCODE project determined that “The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.” As discussed further below, Tom Gingeras, a senior scientist with the ENCODE project, contends in an interview that “[a]lmost every nucleotide is associated with a function.”

“Surprisingly Large” Amount of the Human Genome is Functional

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One Comment to “ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome””

  1. Why is it that it is “Surprisingly Large”? What is it about the new evidence that makes it surprising?

    Isn’t it surprising only if you had the preconceived or predisposed view that it was nothing more than junk?

    Statistical probability studies constantly reveal the unlikelihood of random mutation and natural selection as a satisfying solution and driver for complex and innovative code.

    If it couldn’t happen in 17 Trillion Years, why would we need to accept 3.4 billion years? It seems that if 3.4 billion years is not sufficient then any number less than 3.4 would be more likely.

    Does the question even make sense?

    My point is that code when first presented is somewhat complete. And when it is pre-designed to allow for expansion and innovation then this even more evidence that the definition of the code comes from something other than the code and that is general it doesn’t take that much time because agreement comes from mind. Not the random chemical predisposition that with enough (magic fairy dust) time you have the molecules of life. And since all life comes from ubiquitous carbon life necessarily must be somewhere or everywhere. It is not a matter of if, only when.

    YEC seems entirely plausible from an information science point of view in that the foundation of alpha-numerics and control codes used in all computing systems today rely on pre-established rules or standards. Without those standards this message could not be read. Those same standards exist with the base pairs of DNA. And with amino acids of protein.

    How much time did it take to author or encode the current English Alphabet, ASCII, C++?

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