genophoria

Genomics euphoria: ramblings of a scientist on genetics, genomics and the meaning of life

Category Archives: Non-coding RNAs

The rise of circular RNAs: a whole swath of circular Spongebobs

Recently, we’ve been bombarded by high-profile studies about a class of RNAs, called circular RNAs. Resulting from non-canonical splicing events (see below), circRNAs seem to be more prevalent than previously thought. They’re identified in mammals, plants and even archaea.

The formation and identification of circRNAs

The formation and identification of circRNAs

The recent papers in Nature (Memczak et al. and Hansem et al.) argue for a broad, even tissue specific, functionality for these type of RNAs. Memczak et al. report a comprehensive atlas of thousands of circRNAs in various organisms through a computational approach, to which they assign an impressive 75% sensitivity and very low false-discovery rate.

circRNA statistics according to Memczak et al.

circRNA statistics according to Memczak et al.

The significantly high stability of these RNAs, according to these authors, puts them in perfect position to function as post-transcriptional regulators through sponging other regulatory trans factors. They focused on miRNA sites to find circRNAs that show higher than expected occurrence of these elements. Ant they in fact find circRNAs that can bind and trap miR-7 loaded RISC, results that are corroborated in other recent papers.

Personally, I find sponging a very low-complexity function… meaning, they arise after the fact, with the cell taking advantage of non-coding RNAs that are already available. This means either that circRNAs first arose as aberrant splicing events, i.e. mistakes in donor-acceptor identification or either them or their splicing partners play other, more complex roles that we should be able to identify soon.

Source:

Memczak S, et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. doi:10.1038/nature11928

Hansen TB, et al. (2013). Natural RNA circles function as efficient microRNA sponges. Nature. doi:10.1038/nature11993

Solving the directionality problem of RNA polymerase

Every now and then, a study appears that reminds us how little we know about some of the most basic subjects in molecular biology, while at the same time expanding the connotations associated with these seemingly simple mechanisms. A recent paper in Science by a multinational collaborative team was a perfect example of one such moment for me. The problem statement is relatively simple: how does RNA polymerase recognize the orientation of DNA; in other words, how does it know towards which direction it should be heading? The answer as I knew it, was two parts: (i) there are certain promoter elements that are in of themselves directional, meaning the transcription complex specifically recognizes one strand and not the other (e.g. the world famous lac promoter is one such example). (ii) in cases where there is no directionality coded in the DNA or the epigenome, the polymerase in fact does go the wrong way, which produces the myriad anti-sense RNAs in the cell. Granted, there might be functionalities associated with these anti-sense RNAs, however, established examples are few and far between.

The more important observation, however, is the fact that there are genetic components to when the anti-sense RNA is transcribed and when it isn’t. The aforementioned study starts from one such mutant (ssu72) and goes on to dissect the mechanism through which Ssu27 establishes directionality of the RNA polymerase complex. The results are very simple and elegant: Ssu27 is a part of a bridging complex that demarcates the start and end of the gene, and consequently the correct direction for transcription (below you can see the figure from the main paper).

Ssu72-mediated loop formation

Ssu72-mediated loop formation

Now one might be wondering why all promoters are not directional at the sequence level? The short answer, I think, is “regulation”. There are a variety molecular mechanisms through which promoter directionality can be used in gene regulation, both for the downstream gene as well as the upstream ones. For the immediate gene, losing half of initiation complexes to the wrong direction ensures lower expression, a fraction that can very well be modulated (e.g. through regulating ssu72 in this example). And for the upstream of genes (as well as the downstream one), the presence of anti-sense RNA spells some form of doom or desist.

Peri-translational regulation… yes, I just made that up

A few years back, both ENCODE and FANTOM Consortium reported a comprehensive polling of transcription start and termination sites of transcribed RNAs in both human and mouse. Our first realization was that, most of the genome, it seemed, was being actively transcribed. A notable fraction of these transcripts, however, are not translated into proteins and are called non-coding RNAs (ncRNAs). There are further classifications (e.g. lncs and SINEs and…) but that is beside the point here. The discovery of ncRNAs started a race for a functional annotation of these molecules. After close to a decade however, the published functional examples are few and far in between. Now, either we over-estimated how relevant these ncRNAs are or they function in such nuanced and complex manner that evade our puny genetic and genomic methods.

Despite the scarcity of findings, one class of ncRNAs have been proved very promising, namely the antisense RNAs. As their name implies, these molecules are usually transcribed from the opposite strand of known protein coding RNAs. The complementarity between these anti-sense RNAs and their functional counterparts hints at a regulatory function mediated through direct interactions between these molecules. A paper published in Nature by an Italian group has functionally characterized an antisense RNA (anti-Uchl1) with impressive detail. Apparently, the export of anti-Uchl1 from nucleus can be controlled effectively. When in cytoplasm, anti-Uchl1 then activates polysome formation and active translation. These data reveal another layer of gene expression control at the post-transcriptional level, which I hereby dub peri-translational regulation.

Interaction between anti-Uchl1 and Uchl1