Fang, W., Wang, X., Bracht, J. R., Nowacki, M., & Landweber, L. F. (2012). Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell, 151(6), 1243–1255. doi:10.1016/j.cell.2012.10.045
Most of us spent our childhood and teenage years under the impression the our genomes were dominated by "junk DNA." And if you're anything like me, you loved this fact. For me, there was nothing better than slowly waddling around on a Sunday morning with my genome full of total garbage. It's like my grandfather always used to tell me: "Keep your genome like you keep your pockets, boy: nearly 100% full of complete fucking trash from like a million years ago."
Given the centrality of useless DNA to my conception of myself, I was deeply dismayed when the consortium-with-the-mostest, the ENCODE project, pronounced that the human genome is NOT, in fact, dominated by "junk DNA," but is, in fact, chock full of highly useful, if non-coding, sequence. Reader, I was distraught.
But, thankfully for those of us who love roly-poly, useless DNA, there is still at least one loveable little fatty out there that keeps a solid 95% of its genome full of trash. This rosy-cheeked buddy goes by the name of Oxytricha, and the genomic haunted house of this single-celled protozoan is the subject of today's Sick Pape.
Unlike you y tu mama tambien, every single Oxytricha cell has two types of nuclei: one called the "somatic nucleus" and one called the "germline nucleus." This is profoundly unusual, but it is just the beginning. Every time that these organisms have sex, the somatic nucleus degenerates, and in the subsequent generation, the germline nucleus is used as a template to create a new somatic nucleus.
But here's the crazy part: 95% of the germline nucleus is edited out during in the creation of the somatic nucleus! In other words, 95% of the germline genome is so useless that it literally gets deleted in the somatic nucleus, and the nucleus is completely fine without it. Now that's the kind of junk DNA I'm talking about: real, honest-to-goodness trash. Furthermore, the germline genome, which exists as very long strands of DNA just like any normal genome, is physically fractured into hundreds of thousands of fragments, most of which contain a single gene, such that the somatic nucleus contains ~16,000 chromosomes, representing just 5% of the DNA content of the germline nucleus.
What Laura Landweber's lab wants to know is how the genome is properly edited during the creation of the somatic nucleus. How does the DNA know which fragments to keep and which to destroy? In the present Sick Pape, The first observations these wonderful authors make is that there is a class of small RNAs (~27 nucleotides long) that becomes abundant during this process. And amazingly, if you map these small RNAs to the germline genome, they blanket the parts of the genome that are saved in the somatic nucleus! Thus, the obvious hypothesis is that these small RNAs serve as the signal to protect a part of the genome from destruction. To definitively test this, these folks injected synthetic small RNAs mapping to a part of the genome that is usually deleted, and bazinga! These experimentally-protected DNA stretches are retained in the somatic nucleus!
We here at Sick Papes have drooled all over this type of small RNA (called piRNAs, for piwi-interacting RNAs), several times before, and this paper is another exhibit in the growing case that the Piwi pathway is one of the trippiest pathways out there, always popping up in the gnarliest situations, regulating. We here at Sick Papes offer a hearty seasons' greetings to the Landweber lab, and we thank them for continuing to share the secrets of this loveable ciliate.
