Functional impacts of RNA modifications
August 30, 2015
Posted by on
My good friend and all-around awesome scientist Claudio has been working on this very cool idea the fruits of which is now available to all. I had the pleasure of being on his team and I’m personally fascinated by the problem. The broad question that Claudio is tackling is “what to RNA modifications do in the cell?” In particular he’s been focused on m6A modification and its role in miRNA processing.
But the real story is actually more fascinating. For the longest time, Claudio was looking for the molecular mechanism through which the miRNA mir-126 is down-regulated in highly metastatic cells. A possible solution formed in the form of the gene METTL3 which methylated RNA. Knocking down METTL3 indeed reduced mir-126 levels. But while doing the necessary controls, Claudio noticed that the reduction was not limited to mir-126 but was actually a more global effect impacting a large fraction of miRNAs. It was from this initial observation that his grand hypothesis was formed: RNA methylation (m6A) has a direct role in miRNA biogenesis. And this is were I came in…. a quick look at miRNA sequences showed that m6A sites were located close to but not on primary miRNA sequences. This suggested that m6A markings could serve as a beacon for recruiting the miRNA processing machinery (specifically the dsRNA-binding protein DGCR8). Claudio then used a series of focused experiment to prove this hypothesis (as much as anything can be proven in science). You can read all about this in his very nice paper in Nature.
However, as is usually the case in science, solving one problem leads to even more questions. As I mentioned earlier, m6A sites are not directly recognized by DGCR8, so there was a missing link between RNA modification and the recruitment of processing machinery. To approach this problem, Claudio did the an IP-mass spec of m6A-modified RNA and found a very good candidate in the form of the ubiquitous RNA-binding protein HNRNPA2B1. What was especially important was that the RGAC motif targeted by METTL3 actually has similarities to HNRNPA2B1 binding sequence. In fact the RGAC motif is very much enriched among the binding sites of HNRNPA2B1. Now the question is whether methylating these sequences can impact HNRNPA2B1 binding. In other words, are there sites where modifying the A to m6A will increase affinity to HNRNPA2B1. In a series of experiments (both high- and low-throughput) we showed that this is in fact the case. In general we observed a broad functional entanglement between METTL3 and HNRNPA2B1. These results were recently published in Cell and I invite everyone to read this paper.
HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events
My thoughts? I think this is just the beginning. There are two points to consider: (i) HNRNPA2B1 is not the only reader of m6A and (ii) m6A is not the only RNA modification. Together, I think these studies and those of other groups on m6A (and RNA modification in general) suggests the birth of a new field of research with broad functional consequences on gene expression regulation.