Breakthrough study overturns theory of 'junk DNA' in genome

[Techne]

Breakthrough study overturns theory of 'junk DNA' in genome

The international Encode project has found that about a fifth of the human genome regulates the 2% that makes proteins.

Long stretches of DNA previously dismissed as "junk" are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists' understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture...

From Nature:
Presenting ENCODE

2001 will always be remembered as the year of the human genome. The availability of its sequence transformed biology, and the exemplary way in which hundreds of researchers came together to form a public consortium paved the way for 'big science' in biology. It was an incredible achievement but it was always clear that knowing the 'code' was only the beginning. To understand how cells interpret the information locked within the genome much more needed to be learnt. This became the task of ENCODE, the Encyclopedia Of DNA Elements, the aim of which was to describe all functional elements encoded in the human genome. Nine years after launch, its main efforts culminate in the publication of 30 coordinated papers, 6 of which are in this issue of Nature.

Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome's components have now been assigned at least one biochemical function...

More from one of the scientists on the project:
http://genomeinformatician.blogspot.com/2012/09/encode-my-own-thoughts.html

And an interesting read:
http://sandwalk.blogspot.com/2012/09/encode-leader-says-that-80-of-our.html

And a video:
[video=youtube;Y3V2thsJ1Wc]http://www.youtube.com/watch?v=Y3V2thsJ1Wc[/video]

 

[porchrat]

This title also seems kind of misleading just in the other direction.

I have always understood junk DNA to be noncoding DNA. Correct me if I am wrong but I don't see that this study overturned that, the amount of DNA that codes for proteins still sits in the single digit percentages. They just used the word "functional" more liberally than others have in the past.

Don't get me wrong it is awesome work on a large scale and it is going to benefit researchers for ages to come but the titles we are getting in the journalistic pieces are ridiculous.

 

[RiaX]

Its because they start with the title then do science to fit it. Its a big problem all over the world.

 

[Techne]

I have always understood junk DNA to be noncoding DNA.

This is a common misconception. The term "junk DNA" merely applies to DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. No function for noncoding DNA was found so they labeled it junk. Studies like these just decrease our ignorance about noncoding portions of the genome.

 

[porchrat]

This is a common misconception. The term "junk DNA" merely applies to DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. No function for noncoding DNA was found so they labeled it junk. Studies like these just decrease our ignorance about noncoding portions of the genome.

Ah interesting. Thanks for clearing that up.

Title not misleading at all then. Very cool.

 

[Jab]

Most of what you read was wrong: how press releases rewrote scientific history

So even as the paper was released, we already knew the ENCODE definition of "functional impact" was, at best, broad to the point of being meaningless. At worst, it was actively misleading.

 

[porchrat]

Most of what you read was wrong: how press releases rewrote scientific history

Seems the issue is not so cut and dry after all.

Techne, response?

 

[Techne]

I think I provided links from various sides in the OP when the story broke. The arstechnica article fails to provide a coherent definition of junk DNA and part of the issue is also providing a coherent and consistent definition of what it means to be "functional".

No research has actually demonstrated clearly that any piece of DNA is actually complete functionless junk. The common definition of junk DNA is just, as pointed out, DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. This does not imply that it is actually functionlless junk. The arstechnica article appears to imply that it is, which is a mistake.

 

[porchrat]

I think I provided links from various sides in the OP when the story broke. The arstechnica article fails to provide a coherent definition of junk DNA and part of the issue is also providing a coherent and consistent definition of what it means to be "functional".

No research has actually demonstrated clearly that any piece of DNA is actually complete functionless junk. The common definition of junk DNA is just, as pointed out, DNA that is a provisionally labelled for sequences of DNA for which no function has been identified. This does not imply that it is actually functionlless junk. The arstechnica article appears to imply that it is, which is a mistake.

Yup got to agree with you there your logic is undeniable. Just because we currently don't have a function for it doesn't mean it is necessarily functionless.

Still if their definition of "functional" is as loose as that article claims it is (I will need to take a look at the study itself) then I do have to conclude that the media has been pretty wild with the titles of those articles. I can't, for example, consider something functional if it is merely being transcribed into RNA and then having that RNA rapidly digested.

Just seems like a war of semantics rather than something truly revolutionary.

 

[Techne]

Not really, the study shows activity for at least 80% of the genome i.e. it doesn't just sit there and do absolutely nothing, and this is likely to become 100% as someone mentioned before (can't remember). The trick is now to find out what exactly the activity can be associated with e.g. fine-tuning of metabolism, replication, gene expression, protein folding etc.
Studies like these pave the way for completely new avenues of study.

 

[porchrat]

Not really, the study shows activity for at least 80% of the genome i.e. it doesn't just sit there and do absolutely nothing, and this is likely to become 100% as someone mentioned before (can't remember). The trick is now to find out what exactly the activity can be associated with e.g. fine-tuning of metabolism, replication, gene expression, protein folding etc.
Studies like these pave the way for completely new avenues of study.

I don't get the impression that people have recently been saying that these things sit and do nothing but this is a discussion for another time. As I have said the "activity" found in this study apparently can easily include stuff like portions of the genome that are transcribed into RNA which is pretty much immediately digested (do you disagree?). Does that strike you as particularly functional? Sure it means the stuff is transcribed but if the product is digested immediately then that to me shouldn't be considered a function, not in any real sense.

Note I'm not saying the particular genome portion can't potentially have a function, just that calling stuff like transcription and followed by immediate digestion of the product "functional" seems like a stretch to get a big sensational figure. That the massive difference we see between this percentage and previous percentages that all the journalists are leaping on stems from semantics, in particular the definition of the word "functional".

What I am saying is that this doesn't seem to be a massive revelation that has turned the world of genomics on its head but rather just the next step along a similar line of research. Just suddenly they expand the reach of the word "functional" and journalists go bananas over this 80% figure.

 

[Techne]

Well, I thought the research was pretty awesome and groundbreaking. Certainly more than just "the next step".

 

[empirex]

I don't get the impression that people have recently been saying that these things sit and do nothing but this is a discussion for another time. As I have said the "activity" found in this study apparently can easily include stuff like portions of the genome that are transcribed into RNA which is pretty much immediately digested (do you disagree?). Does that strike you as particularly functional? Sure it means the stuff is transcribed but if the product is digested immediately then that to me shouldn't be considered a function, not in any real sense.

Not at all. That RNA can serve to enhance the expression of a protein-coding gene.

The longer messenger RNA can avoid said digestion the more protein can be created.
The duplicate RNA runs interference, thus allowing for translation to continue by avoiding degradation.

An expressed pseudogene regulates the messenger-RNA stability of it's homologous coding gene,
Nature 423 (2003): 91 - 96

 

[porchrat]

Not at all. That RNA can serve to enhance the expression of a protein-coding gene.

That wasn't part of this study as far as I am aware and was not considered when they were deciding whether or not something was "functional".