Junctional DNA.

JR Minkel at the Scientific American blog has responded to the post on Evolgen about his earlier story regarding “junk DNA” (did you catch all that?). At the end of the post, he asks:

Scientists and scientist bloggers: Again, do you care [if journalists call it junk DNA]? If so, what term would you propose instead, or how would you make the distinction between functional and nonfunctional noncoding DNA clear to a popular audience?

Yes, I care, and here are my suggestions. If you mean the general category without any speculation either way about function, then it is simply and accurately “noncoding DNA”. If it has a function, then you specify what that function is: “regulatory DNA” or “structural DNA” or what have you. If the type of sequence is known, then you can use that as well or instead: “transposable elements” or “mobile DNA” or “pseudogenes” or “introns”. Maybe readers won’t know what those terms mean. This is a good opportunity to inform them.

What is missing is a term to describe a given collection of noncoding DNA for which there is thought to be some function, but for which that function and/or the type of sequence is unknown. This would reside somewhere between “junk DNA” (in the vernacular sense) and “functional DNA” (to which specific names can be applied). I therefore suggest the neologism “junctional DNA” to encompass this category. Note that Petsko (2003) suggested “funk DNA” to represent “functionally unknown DNA”, but I think “junctional DNA” is a little less, uh, funky.

Let me be even more specific. The proposed term “junctional DNA” derives from a dual etymology: 1) a simple portmanteau of “junk” and “functional”; 2) an indication that the sequences so described reside at the crossroads between DNA with no evident function and that with a clear function.

Two terms in one day — “the onion test” and “junctional DNA” — how ’bout that.

Incidentally, my annoyance with such reports has less to do with the terminology than with the fact that the highly conserved sequences in question make up about 5% of the total genome. To jump from this to imply that all noncoding DNA is recognized as functional is inappropriate and misleading. I also wish they would cite the source papers they reference; some of us would like to look up the primary material when we see a summary in a news story.

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Update: Other bloggers (RPM of Evolgen in personal correspondence, Sandwalk) seem to think this term is not needed. I point out that this post was given in direct response to Minkel’s appeal for a term that would “make the distinction between functional and nonfunctional noncoding DNA clear to a popular audience”. In light of the fact that a journalist sees the need for such a term, and that it was coined in response to that need, I think ‘junctional DNA’ could be a useful term.



6 comments to Junctional DNA.

  • TheBrummell

    I like the term. But I find the term “Funky-junctional DNA” even more entertaining, if too long and unwieldy for normal conversation.

    Get down with your bad selves, chromosomes!

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  • Nick (Matzke)

    Hi again Ryan,

    I had another look for your posts, this was all I could find about issue of the “junctional DNA” using the already-defined word “junctional”:

    The proposed term “junctional DNA” derives from a dual etymology: 1) a simple portmanteau of “junk” and “functional”; 2) an indication that the sequences so described reside at the crossroads between DNA with no evident function and that with a clear function.

    I guess I missed what you meant by “crossroads.” I was thinking of a conceptual crossroads. Were you suggesting a semi-“literal” crossroads, as if this junctional DNA physically sits between DNA of known function and DNA with no clear function? This at least needs to be clarified I think.

    An unrelated problem I just came across is that the term is already in the literature, i.e. in V(D)J recombination elsewhere: google scholar on junctional DNA. It appears to have the very meaning I was worried about, i.e. DNA joining other pieces of DNA.

    I’m really not trying to just get on your case, I promise! I just worry that this particular issue is already so confused among the public, the journalists, and many scientists, that new terms should be very carefully looked at to see if they will be helpful or not.

    Maybe we could come up with something like “disposable DNA” or “poorly conserved DNA” or “inessential DNA” for the chunks of DNA that really do appear to have little-to-no function, or appear to be present only as an expression of the c-value/cell volume correlation (whatever the fundamental causes are behind that).

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  • TR Gregory

    I responded to this same basic comment when you made it over on Sandwalk as follows:

    Actually, “joining” is part of the intended meaning, in that it is “an indication that the sequences so described reside at the crossroads [or ‘junction’] between DNA with no evident function and that with a clear function”. As Larry argues, if there is evidence of non-function it is “junk” in the sense commonly used. If it has a clear function then it should be labeled according to the function. In the middle, joining these two ends of the spectrum, is something else — in the present term, “junctional DNA”. It also represents a joining of two levels of selection in many instances. And finally, it may involve the joining of former parasites with the rest of the functional portion of the genomes of their hosts.

    Many new terms in genetics have made use of previously defined words, so this seems like a real non-problem. Examples include “junk DNA”, “satellite DNA”, “genetic code”, “DNA sequence”, “transposable element”, “restriction enzyme”, “primers”, “base pair”, “DNA fingerprint”. Since I mean “junctional DNA” to imply a junction, I think it falls in the same category of using existing words in a new application.

    You’re also arguing two mutually exclusive points: 1) “junctional DNA” is already defined in common usage so it can’t be used in genetics, 2) “junctional DNA” is already used in genetics.

    Others have pointed out the existing use of “junctional” in genetic usage with regard to splicing (e.g., in V(D)J recombination of immunoglobins). As I said, these are minor usages, and already my post is the top hit on Google in a search of “junctional DNA”. Interestingly, if indeed key components of the V(D)J system (namely RAG1 and RAG2) are derived from transposable elements, then this would be a great example of junctional DNA in both a literal and metaphorical sense.

    So far I haven’t seen any objections that didn’t also apply to “junk DNA” and many other terms, but if “junctional DNA” is too problematic, then so be it.

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  • Nick (Matzke)

    Thanks Ryan, I missed that previous reply.

    I don’t think the “it’s already in the dictionary” and the “it’s already in the V(D)J recombination literature” arguments conflict — because the usage in V(D)J recombination actually has something obvious to do with junctions and joining.

    Nevertheless, I deeply appreciate your blogging and your commentary on the c-value and DNA-occasionally-known-as-junk issues — e.g. your latest post on the marsupial genome and the media reporting of it is golden!

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  • TR Gregory

    Nick — please feel free to use whatever term you like.

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  • arvind mishra

    Hi,
    Is there any term like meta DNA ? Do you find any corelation in between meta and junk DNA ?
    best,
    arvind
    Varanasi,India

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