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Friday, March 27, 2015

Plant biologists are confused about the meanings of junk DNA and genes

A recent issue of Nature contains a report on plant micro-RNAs (Lauressergues et al., 2015). The authors found that certain genes for plant micro-RNAs encoded short peptides in the micro-RNA precursors and those peptides seemed to have a biological function. What this means is that part of the longer precursor RNA that is cleaved to produce the final micro-RNA may have a function that wasn't recognized. If you thought that the part of the precursor that was thought to be discarded as useless junk was, in fact, junk, then you were wrong—at least for some genes.

This is not a big deal and the authors of the paper don't even mention junk DNA.

The paper was reviewed by Peter M. Waterhouse and Roger P. Hellens in the same issue (Waterhouse and Hellens, 2015). They think it's a big deal. Here's what they say,
In the 1970s, as it started to become clear that the genomic regions that encode proteins (the genes) swim in a sea of non-protein-coding sequences, the idea of meaningless, or 'junk', DNA became a hot topic of discussion. Biologists are now well aware of introns, the sequences within genes that separate the coding regions (exons) and which are spliced out at the messenger-RNA level, as well as their notable regulatory roles. However, the term junk DNA has survived and is used loosely to describe genomic sequences between genes, giving them an implied lack of importance.
There's a lot of confusion here. First, not all genes encode proteins so right off the bat the paragraph begins to sound uninformed. Second, there's lots of function in "non-protein-coding sequences," including lots of genes, so they seem to combining multiple misconceptions. Third, the concept of junk DNA was supported by far more knowledge that the authors are aware of. Fourth, introns are junk DNA (mostly). Fourthly, no knowledgeable scientist thinks that all of the DNA between genes is junk. (And many of them think that most of the DNA of eukaryotic genes (introns) is junk.)
The debate about the usefulness of non-protein-coding DNA sequences continues to rage3, 4
References 3 and 4 are the original ENCODE summary paper and the backtracking PNAS paper published 18 months later. There is no debate among knowledgeable scientists about the usefulness of some noncoding sequences. It would be helpful to explain that the debate is about whether 90% of our genome is junk of whether most of it is functional.
However, within these intergenic regions of a genome are the sequences that produce most plant and many animal pri-miRs. Clearly, these sequences are not useless.
If there are regions of the genome that specify functional small RNAs then the proper word for those regions is "genes." You can't have genes "within" intergenic regions. This is very confusing.

The rest of the review is also confusing. If the small RNAs are functional then they aren't junk. If they encode small functional peptides then they aren't junk. The Lauressergues et al. paper doesn't seem to have anything to do with junk DNA, so why all the fuss in the review?

If all the suspected small RNAs were actually functional in plants then how much of the genome does this cover? I suspect it's about 1% or less. That's just background noise in the junk DNA debate.

Lauressergues, D., Couzigou, J-M., San Clemente, S., Martinez, Y., Dunand, C., Bécard, G., and Combier, J-P. (2015) Primary transcripts of microRNAs encode regulatory peptides. Nature Published online March 25, 2015. [doi:10.1038/nature14346]

Waterhouse, P.M. and Hellens, R.P. (2015) Plant biology: Coding in non-coding RNAs. Nature Published online March 25, 2015. [doi: 10.1038/nature14378]


Claudiu Bandea said...

LAURENCE A. MORAN: “Plant biologists are confused about the meanings of junk DNA and genes”

I completely disagree; they are not confused, they just want to hype the significance of the research they are writing about.

Anonymous said...

How is this possible and why would they do that?

Larry Moran said...

They can be both confused AND want to hype.

Georgi Marinov said...

Well, that's a small fraction of miRNA genes, which are a very small fraction of the genome to begin with...

Claudiu Bandea said...

This is elementary knowledge that any undergraduate if not high school student with interest in genome biology would easily understand.

jb said...

Well, as a nonbiologist, I'm confused. I enjoy reading the posts here but I'm a bit out of my depth. Can someone point me to a good (brief?) description of the various functional roles bits of DNA can play. I was under the (mistaken?) impression every gene codes for a protein. Larry's writing above implies to me that there are non-protein coding functional parts called genes, and other functional parts of DNA that are not called genes, and then DNA that is truly junk. Is this right? Does that completely partition DNA? Help!

Anonymous said...

jb, Here's a post that tells is in your genome.

Yes, you're right. There are genes that code for proteins and genes that code for useful RNA's, like the ones that make the ribosome and some regulatory RNA's.

There are also parts of the genome that have other functions, like attachment points for centromeres or other fibers, or the telomeres that terminate chromosomes. There are regulatory sequences, and biologists disagree greatly about how much of the genome actually has regulatory function (probably not much). There are some other useful bits.

Within each gene, there are regulatory parts, coding parts (exons), and non-coding parts that produce products that are cut out during processing (introns).

Also in our genome are sequences that used to be genes but mutated to uselessness (pseudogenes), sequences that used to be viruses or transposons but have mutated so they're not functional, and a few functional viruses and transposons.

Our DNA is weirder and more diverse than I would ever have thought.

roger shrubber said...

Claudiu, yes and no. The misinformation is that junk DNA equals non-coding DNA. That's the oversimplification that keeps getting in the way. Come on, the assertion that DNA that encodes for small peptide is "non coding DNA" is really over-the-top. I'm stuck with the notion that oversimplification, and naive acceptance of oversimplification, is being promulgated in programs that are training "genetic engineers". Meanwhile, actual biologists sign and despair over the future of biological sciences. Being a curmudgeon is sad. Put another way, the worst thing about being a pessimist is being right all the time.

Petrushka said...

"Our DNA is weirder and more diverse than I would ever have thought."

Not trying to change the subject, but so are brains. The first order of analysis of anything always leaves out some important things.