The story behind the preprint: circRNA leading to oscillations

Dear readers, as always, my apologies for the long delay in between posts. I’m sure you have missed reading them as much I have missed writing them! In this post, I’ll try and tell the story of my latest preprint, and final chapter of my thesis! You can find the preprint here: https://www.biorxiv.org/content/early/2018/03/31/292029

Jake outlined a bit of the story behind the preprint on twitter, but I wanted to elaborate a bit here, in a few more characters.

New analysis from @andrewdhawan showing novel (?) function of circular RNA – creating tunable, stable oscillations in gene expression. Would love feedback! https://t.co/1caEi5TAIW pic.twitter.com/CBPi1NKPlz

— Jacob G Scott (@CancerConnector) March 31, 2018

The beginnings

The story began last summer, when I started thinking about circular RNA – a strange form of non-coding RNA that is formed by back-splicing of exons together (like an alternative splicing event, just resulting in a circularised RNA moleucle). These circRNA are very interesting because they are thought to be more stable (i.e. degraded less) within the cell than linear RNA because their lack of free ends means that certain RNA degradation enzymes won’t work on them. No one really knows what they do, why they exist, and even their very existence is controversial in nature (they can be hard to detect — more on that in a future blog post, promise!).

One of their purported functions is to act as a miRNA sponge – something that I imagine floating around the cell, binding up miRNA as it encounters them, and preventing these from repressing their targets. This finding is supported by the discovery of a few circRNA that have huge (~70) numbers of binding sites in their sequence for the same miRNA, suggesting that this may be its primary purpose. Even this remains controversial, but let’s go with it. After hearing about this, I was intrigued, dear reader, because the week before I learned about this, I had read a number of papers about the ceRNA hypothesis.

The connection: ceRNA

The ceRNA hypothesis refers to mRNA transcripts that effectively compete in the pool of all cells for the same miRNA, and so overexpressing one mRNA might cause the de-repression of another, when the overexpressed mRNA binds up all of the repressive miRNA on both. Effectively this is another form of miRNA sponge.

I looked further, and it seemed that there were many other types of RNA that were predicted to, at least sometimes, act as miRNA sponges, which led to my central question.

Why are there so many types of miRNA sponges?

Given the lack of experimental evidence or data from evolutionary studies for these RNA, I turned to theory to help me understand where these RNA could differ. The lesson from the circRNA is that different conformations of RNA molecules have intrinsically different kinetic rate constants in a cell. As a result, even when acting as a sponge in the same system, they can give different dynamics. This was exciting, but I needed a proof of concept.

An over-represented network helps us design the proof of concept

Happily, I had stumbled upon a work that helped to find miRNA-mRNA-transcription factor motifs that were over-represented in the transcriptome. This gave me a chance to see how the different dynamics might play out in this network if a sponge were present, and might help us to understand when different sponges might be used in different cases, and this is the basis of our paper!

As always, I’d love to have feedback, and seems we’ve got a number of cool ideas bouncing around on twitter, but the more the merrier.