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Thursday, April 05, 2018

Peter Larsen: "There is no such thing as 'junk DNA'"

The March 2018 issue of Chromosome Research is a Special Issue on Transposable Elements and Genome Function. I found it as I was doing my routine search for papers on junk DNA in order to see whether scientists are finally beginning to understand the issue. Peter Larsen (guest editor) wrote the introduction to the special issue. He says ...
There is no such thing as “junk DNA.” Indeed, a suite of discoveries made over the past few decades have put to rest this misnomer and have identified many important roles that so-called junk DNA provides to both genome structure and function (this special issue; Biémont and Vieira 2006; Jeck et al. 2013; Elbarbary et al. 2016; Akera et al. 2017; Chen and Yang 2017; Chuong et al. 2017). Nevertheless, given the historical focus on coding regions of the genome, our understanding of the biological function of non-coding regions (e.g., repetitive DNA, transposable elements) remains somewhat limited, and therefore, all those enigmatic and poorly studied regions of the genome that were once identified as junk are instead best viewed as genomic “dark matter.”

This is very disappointing. Anyone working on transposons should know that more than half of our genome is composed of various bits and pieces of defective transposons. Nobody has ever provided convincing evidence that most of that flotsam and jetsam is functional. The default explanation is that it is junk and that makes a lot of sense since it certainly looks like junk.

Larsen proposes that transposable elements are involved in the third and fourth dimensions of the genome. The third dimension is DNA & chromatin structure and the fourth dimension is time-related biological processes. He provides no evidence that half of our genome plays a functional role in these "dimensions."

There is evidence that some transposon-related sequences have been co-opted to perform regulatory and structural roles but that doesn't mean that all of them do. That crazy form of argument has been ridiculed so many times that I'm surprised to see it resurface in 2018. It's almost as though the scientists who use it don't even read the literature on junk DNA.

Five Things You Should Know if You Want to Participate in the Junk DNA DebateFurthermore, the evidence for junk DNA is not confined to speculation about the role of transposon fragments. There's lots of other data that must be refuted before you announce the death of junk DNA. If you don't know what that evidence is, then you have no business writing about the subject.

I'm also annoyed about sloppy use of the term "dark matter." As far as I can tell, it's an attempt to: (1) shift the burden of proof, and (2) glamorize ignorance. The default explanation for transposon fragments is junk. The burden of proof is on those who want to prove function. By saying that it's "dark matter" they ignore the default explanation and shift the burdon of proof on to those who say it's junk DNA. The glamorous part is due to associating the term with the dark matter of the universe. There's plenty of evidence for the existence of that kind of dark matter even though astronomers don't know exactly what it's composed of. The idea here is that by referring to the 'dark matter' of the genome you imply that there really is something mysterious and important going on but we just don't know what it is.

That's not true. We know a lot about genomes and there are no great mysteries [What's In Your Genome? - The Pie Chart]. We know that most of the human genome is junk in spite of what Peter Larsen says.

Can someone explain what's going on? There really isn't much of a controversy any more. Knowledgeable scientists have examined the data and concluded that about 90% of our genome is junk. How can you write about junk DNA without mentioning that data and how does an article like this get past peer review?

Peter Larsen has received a link to this post. I'm looking forward to his response.

Larsen, P.A. (2018) Transposable elements and the multidimensional genome. Chromosome Research, 26:1-3. [doi: 10.1007/s10577-018-9575-2]

1 comment :

  1. Ahh, the "it's wrapped up into chromatin"-fallacy, a favorite of Sal Cordova.

    Yes, what the hell else would it be? As the genome size has inflated over time, so has chromatin packaging co-evoled to keep it tightly packaged. That doesn't mean that DNA "does" something, all it means is that selection to get rid of it hasn't been strong enough to counteract the mechanisms responsible for it's accumulation. But the components necessary to package additional DNA in an expanding genome already existed, so didn't have to be invented de novo.