Keystone, Green Edition
Look to the plant. Look at ’em; eat ’em; use ’em for medication; and appreciate them because they offer numerous biological fruits, including well studied RNAi. Here are some things overheard at this year’s RNA Silencing Mechanisms in Plants Keystone Symposium, which met in Santa Fe late last month. (Thanks a bunch to my friend M. for helping with this.)
A couple heavy-hitters described a class of predominantly 22 nt miRNAs in Arabidopsis, Dcr-like 1 products, that initiate secondary siRNA biogenesis by an unknown mechanism. This has also been seen in rice, where they are also Dcr-like 4 dependent. They key point is that specific miRNAs only appear to be able to initiate secondary siRNA biogenesis if they are 22 nt, and not 21 nt. (Most miRNAs in Arabidopsis are 21 nt.) The implication is that Argonaute can decipher a 1 nt difference in length of a miRNA, and this may induce some structural change that could, for example, lead to recruitment of RdRP and other factors responsible for producing secondary siRNAs. Pretty fascinating that such a minute difference could be responsible for such critical decision making.
Another speaker presented work showing some elegant, and very technically challenging, grafting experiments in Arabidopsis that show 24 nt siRNAs can move through tissues, and cause RNA induced DNA methylation. [Hearing this caused me flashbacks to my first-year grad Development course in which we learned about pioneering grafting experiments in newts in the early part of last century, and how crazy it is that these Franksteinian techniques work so well.] Using a different technique, particle bombardment, another speaker demonstrated spreading of siRNAs through cells. Very fascinating to think of how spreading is regulated/controlled to remain specific. They’d be potent little things to be sending out without exact destinations/address labels.
Although it is worth pointing out that 24 nt siRNAs repress transposons and repeat elements, so it may not be so bad to have this activity be somewhat constituitive in a given region when such a challenge is detected. When silencing components were removed, transposition was observed to grow slowly. When silencing components were re-introduced, it took several generations to re-establish silencing, in reproductive tissues.
One of the above speakers also described experiments mating tomatoes. [I love tomatoes myself, and, did you see The Simpsons episode where Homer see’s Ralph Wiggum’s alcohol powered car at the Springfield Elementary science fair? “One for you; one for me” Homer says, as he dreams sipping half of his fuel purchase. That would be me if I was mating tomatoes in lab.] What was really cool is that after a few generations they saw the emergence of new siRNAs that were neither present in the parental nor F1. These progeny with novel siRNAs expressed new traits as well. Maybe I’m overinterpreting the result, but, wow! It’s unlikely perhaps, but the traits could be solely due to the fresh siRNAs. Or more interestingly, could evolution be dictating some sort of package deal for the emergence of new traits? “I’ll give you a new trait, but you’ve gotta take small RNA(s) along with it.” Or maybe it’s simply coincidence–you mate two non-isogenic things, and all kinds of stuff comes out.
Also mentioned was a new set of 24 nt miRNAs in rice, Dcr-like 3 dependent, present in reproductive organs, that direct methylation of their target genes in trans, in a strand specific manner. Yeah, but what kind of rice? Was it brown basmati?
Finally, comparing two different Arabidopsis strains, one Columbia (from Missouri) and one from the Cape Verde islands, a speaker described that they produced vastly different genome-wide Cytosine methylation patterns. Promoter methylation appeared to be conserved while gene body methylation was greatly reduced in the Cape Verde Island strain. Presumably this has some significant functional consequence, perhaps due to the differential environmental responses that the two strains have evolved.
I wish I was in Cape Verde right now, on the beach, eating a salad.