Last month, I wrote about the terrible botch journalists had made of an interesting paper in which tweaking regulatory sequences called enhancers transgenically caused subtle shifts in the facial morphology of mice. The problem in the reporting was that the journalists insisted on calling this a discovery of a function for junk DNA — the paper itself said no such thing, but somehow that became the dominant message of the popular press coverage. Strange. How did that happen?
So Dan Graur wrote to the corresponding author to find out how the junk crept in. He found out. It's because the author doesn't understand the science. Axel Visel wrote back:
When I talk to general audiences (or journalists) about my research, I generally explain that the function of most of the non-coding portion of the genome was initially unclear and many people thought of it as “junk DNA”, but that it has become clear by now that many parts of the non-coding genome are functional - as we know from the combined findings of comparative genomics, epigenomic studies, and functional studies (such as the mouse knockouts in our paper).
Aargh. Non-coding is not and never has been a synonym for junk. We've known that significant bits of non-coding DNA are functional for a period longer than I've been alive…and I'm not a young guy anymore. The mouse knockouts in his paper were tiny changes in a few very short sequences -- even if we had somehow been so confused that we though enhancer elements were junk, whittling away at such minuscule fragments of the genome weren't going to appreciably increase the fraction that is labeled functional. That focus on finding more functionality in the genome flags Visel as yet another ENCODE acolyte.
Man, I'm feeling like ENCODE has led to a net increase in ignorance about biology.
Graur does not mince words in his assessment:
My problem is that junk DNA does not equal noncoding or nontranscribed DNA, and I am sort of sick to see junk DNA being buried, dismissed, rendered obsolete, eulogized, and killed twice a week. After all, your findings have no bearing on the vast majority of the genome, which as far as I am concerned is junk. Turning the genome into a well oiled efficient machine in which every last nucleotide has a function is the dream of every creationist and IDiot (intelligent designer), so the frequent killing of junk DNA serves no good purpose. Especially, since the evidence for function at present is at most 9% of the human genome. Why not call noncoding DNA noncoding DNA? After all, if a DNA segment has a function it is no junk.
Larry Moran is also a bit peeved, and explains that we actually know what a lot of that noncoding DNA does. It's not a magic reservoir of hidden functionality.
I've said it many times but it bears repeating. A small percentage (about 1.4%) of our genome encodes proteins. There are many other interesting regions in our genome including ...
- ribosomal RNA genes
- tRNA genes
- genes for small RNAs (e.g spliceosome RNAs, P1 RNA, 7SL RNA, linc RNA etc.)
- 5' and 3' UTRs in exons
- centromeres
- introns
- telomeres
- SARs (scaffold attachment regions)
- origins of DNA replication
- regulatory regions of DNA
- transposons (SINES, noncoding regions of LINES, LTRs)
- pseudogenes
- defective transposons
These parts of noncoding DNA accounts for about 80% of the human genome. A lot of this noncoding DNA is functional (about 7% of the total genome [What's in Your Genome?]). None of it is mysterious in any way. We've known about it for decades. As Dan Graur says, it's a known known.
At least I'm in a position to do a little something about this ignorance. I'm teaching cell biology to our sophomores this semester, and next week I start the section on DNA replication, with transcription the week after. My students will know the meanings of all those terms and have a clear picture of genome organization.
And what that should tell all you employers out there is that you should hire UMM biology graduates, because they'll actually have some knowledge of the science. Unlike certain people who seem to have no problem publishing in Science and Nature.
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