All that “junk” DNA ain’t actually “junk” at all

For many years, no one has been able to understand why most human DNA didn’t seem to “do” anything. It didn’t code for proteins or enzymes or anything concrete that we could put our hands on (so to speak) … so we lumped it all into a vast mass called “junk” DNA … but the idea that we would have so much DNA that was irrelevant to the way that plants, animals, and humans actually functioned has never really made sense.

Now we know that it absolutely didn’t make sense.

The results of a massive study (the ENCyclopedia of DNA Elements or ENCODE study), carried out an extended group of interlinked investigators around the world, has shown that nearly all that junk DNA is really more like a massive, automated control system that manipulates the ways in which living things manage the levels at which specific genes are expressed (turned on) or not expressed (turned off) under specific circumstances … and this knowledge may be just the beginning of a whole new set of ways to look at the management of specific disorders (prostate cancer included).

To quote Clive Cookson in the Financial Times,

The so-called ENCODE study, published simultaneously in more than 30 papers in Nature and several other scientific journals, is the biggest investigation of DNA since the original project to decode the human genome was completed 10 years ago.

So what do we actually know now? We know that:

  • The human genome contains some 3 billion chemical “letters” (the Cs, As, Ts, and Gs that are the fundamental coding elements of our DNA).
  • Only about 2 percent of human DNA actually codes for the traditional genes (about 20,000 of them) that are used to make things like proteins and enzymes.
  • More than 80 percent of human DNA — including some 4 million genetic switches — actually has biochemical activity at specific cellular levels; in other words, it exerts control of some type in at least one of the thousands of different types and subtypes of human cell

These first results from the ENCODE study appear to offer us a preliminary map showing the genomic locations of the genetic switches in man (and woman). What we don’t know yet is:

  • Which switches actually control which genes
  • How the genes are switched on and off
  • What the “wiring system” looks like that interconnects all the elements

One way to think about this is the same way as we now think about the way the human brain works. The genetic operating control system is like a giant biochemical brain. Tiny adjustments to the system can have major physical and physiological impacts … both positive and negative … and the different types of prostate cancer mat reflect very, very small malfunctions in the operating system that play out over just a few months or over many, many years.

For more information about the ENCODE study, just click here. There is also more detailed coverage of the most recent findings on the ScienceDaily web site and good coverage for the lay person in an article in the New York Times.

2 Responses

  1. Thanks for posting this. It might be just in time! I am thinking of buying the standard work, “The Biology of Cancer,” by Weinberg. There’s a lot of information about genes and cancer in the book, but given this, an update might well be in order.

  2. Its interesting to compare the genomic DNA with the mitochondrial DNA — which is completely functional, with no junk DNA at all. Each part of the mitochondrial DNA codes for an important functional unit, including the ribosomal RNA, the transfer RNA, and the protein coding sequences of 12 important enzymes. The mitochondrial DNA is condensed, such that the same DNA sequence in some parts codes for two different proteins by reading two different frames of the DNA. The genomic DNA is completely different, having large sections of junk DNA. We now know that this DNA is functional in controlling expression of other regions of protein-expressing DNA. The key now is to understand the functional proteomics of the proteins expressed by the DNA.

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