New Class of Genes Discovered

HarryGenes writes "Reuters is reporting that Scientists Find New Type of Gene in Junk DNA. The research from Harvard Medical School describes a discovery in the Yeast Genome of a new class of gene that regulates the neighboring gene through the production of its RNA product. This has much broader implications than the article lets on to. Assuming these same type of genes exist in Humans and other organisms, the whole science behind gene expression and gene mapping will be changed dramatically. This type of mechanism can explain a lot of the 'unexplainable'. This is really exciting. I have been working in gene mapping for years and always felt that the 'junk' was there for a reason."

Good article

[cariaso1]

Until this article was published, 'junk dna' would be considered the correct term for this region. Broadly speaking, the term suggests that there is no known function for the region. We don't know much beyon "is a region is a coding region?" and "is a region regulatory?". Now this region can be classified as regulatory, but it uses a mechanism never before observed. That is news.

Much more information can be found in this article taken from pubmed.

Stealth regulation: biological circuits with small RNA switches [genesdev.org]

Re:Paper search

[HarryGenes]

If you visit the story at The Scientist, [biomedcentral.com] they have a much better article and a link to the PubMed, full text article.

On the other hand...

[Indomitus]

New Scientist [newscientist.com] has an article about some scientists who removed pretty huge chunks of a mouse's "junk DNA" and the mouse was just fine in every way they could measure.

So the moral is, we have a lot to learn about DNA.

Re:The more you know.......

[FlyingOrca]

Man, I don't know. Animals are one thing, but plants are quite another. Ever check out plant genetics?

I'm more of an animal guy, but my ex was into plant biology, and her take on the whole plant genetics thing is nothing less than... very worrisome. Plants swap and adopt chromosomes, hybridize, etc. much more freely than animals.

The problem therefore is not that the actions of a gene in one species aren't known (though I'm not convinced they're know well enough); it's that the gene can get into other species far too easily. There are bigger nightmares in that scenario than a few allergic reactions.

I'll be the first to admit I'm no expert in plant genetics - but a fair number of people who ARE experts are concerned. I'm inclined toward caution. I'd suggest that the best thing to do is to clearly label products containing material from GMOs and let the consumers decide, but the shee^H^H^H^Hconsumers are the same folks with unpatched Windoze boxen. Cheers!

context.

[gregorsamsa11]

I agree. Of course there is some inherent risk in foods modified using modern recombinant DNA technologies, but no more than with conventional breeding, in my opinion.

Many food producing species have been crossed with outside species (usually closely related, but not always). Crossing with outside species introduces a host of unknown factors, combining genes in a totally unique, unpredictable way. However, this was never a matter of heated public debate. Now if you want to add a single gene culled from some other organism, there is an outcry.

Seedless fruit varieties are generally the result of an uneven cross, where the offspring ends up with an uneven number of chromosome sets, and is thus sterile. These lineages are perpetuated by vegetative cloning (cutting).

Genetic manipulation of food producing plants has been around for some time. Now we have the technology to modify organisms in a more careful, precise way (although the outcomes are still unpredictable), but there is resistance. I think this stems mostly from sensationalist coverage of the new technology. Without the proper background information, people are shocked.

Of course this is a public health issue, and new food products should only be introduced to the public after careful testing. What irks me is the hyteria (not that the parent is hysteric).

Re:Precedent for "junk DNA"

[GeoGreg]

For example, a few centuries ago some mathematicians started studying the funny numbers like the diagonal of a unit square, and proved that they weren't the ratio of two integers. The idea that there were such numbers was widely ridiculed. The mathematicians' reaction was to say "We need a name for these new numbers. People are calling us irrational for talking about them. Why don't we just call them `irrational' numbers?" And so it was.

Actually, irrational numbers are so named because they can't be formed from the ratio of two integers. It so happens that in Latin, ratio can mean either "reason" or "computation". Thus the name describes a mathematical property, not any perceived faulty reasoning.

Complexity = unintended consequences

[garyebickford]

Patent and legal issues are the easiest. Foresight is essentially impossible in any practical sense. Identifying potential interactions of genetic modifications is many orders of magnitude more complex than, for example, nuclear waste management. The state space for the interactions between genes has dimensionality (IIRC) 2^2^log(n) for n genes, and each dimension has variance 2^n. For as few as 20 genes, you have a space too large to search for significant interactions.

Now, expand that space to account for the 98% of the DNA once thought to be junk that has now been shown to have unidentified and mysterious interaction with the "proper" genes.

To make matters worse, you are working with a dynamically stable ecosystem, within which a minor change in a single gene in a single plant can cause transformation or collapse of an entire ecosystem - usually not, but it has happened. The recent debacle [nerage.org] of Monsanto's Round-up resistant seed crops is instructive, as it shows that the genetics is just one small part of the puzzle. The relationships between all the other parts of the system are altered, like dropping a bowling ball on a multidimensional trampoline. Ecosystems adapt, usually in ways that are not convenient for anyone trying to force them into a particular pattern. This article [web-dictionary.org] is worth reading and well-linked to related facts and definitions.

Also, as someone who regularly suffers allergic reactions to foods that are improperly labelled, Inote that statistics mean something entirely different to statisticians than to victims. Does this mean you're volunteering to be one of those two or three? :O)

Re:Multi-dimensional

[Coos]

Boy, I can't wait till they find out that genes are multi-dimensional, the same way a fugue is.

Sorry, but they already are!

A single gene can contain up to three overlapping reading frames, and some virii and bacteria can generate three completely different and functional proteins from the same gene sequence by this method. Add to that that certain gene products may be broken into subunits at different points along their sequence, and a highly-evolved (or carefully designed) gene could encode >10 proteins.

This isn't exactly new...

[dnaboy]

Researchers have been discovering these genes for some time now. They're generally extremely short (~21 nucleotides) and in their endogenous form are referred to as micro RNAs (miRNA).

Interestingly, the mechanism was actually understood before functional miRNAs had been discovered. Back in the 90s there was an upswelling of new biotech companies (Isis, for one) looking at antisense technology. Basically, the idea is that if you insert a complementary RNA strand to a messenger RNA (mRNA- The RNA's which code for proteins), you could block the expression of that gene into protein. The problem was that these weren't very specific (relative to what people would expect, since it was the exact complement of the gene sequence). Also, it's a bitch to get a full length RNA strand into cells reliably, short of using viruses. Generally a bad stigma.

Over time, people started realizing that these antisense targets being inserted were being cleaved into really small (~20 to 25 nucleotide) pieces by an enzyme group called the RISC complex (It's a lot more complecated than that, but whatever). This explained one thing. ~20 nucleotide chunks are much more likely to stick to another gene. There's a much better chance that the 20 bases are identical to 20 bases in another gene, than several hundred to several thousand being repeated. What it didn't answer is what was going on.

It was assumed that the complex that large antisense targets made blocked translation into protein. 20 base pieces were much less likely to do that. What people came to realize is that another enzyme called DICER was chomping up the genes where these ~20 nucleotide pieces stuck. This technique isa called RNA interference, or RNAi, and these ~20 nucleotide sequences were called short interfering RNAs or siRNAs. The sweet thing is these, relative to their much longer antisense couterparts are relatively trivial to insert into cells.

Anyway, to make a long story short, researchers didn't really know why this worked at first, and consensus was that it was either an evolutionary legacy, a mechanism to fight RNA viruses, or a fluke (which generally, very few things in biology end up being).

Anyway, this article points out what researchers all over are finding which is that these little guys appear to be present all over the human and other genomes. They are much more likely to be a mechanism for regulating gene expression. For more info, google 'micro RNA'.

Cheers