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A story-tail ending for the guardians of the genome

 5 January 2021   Research News

By Dr Sophie Arthur

If I asked you to imagine what your DNA looks like, what comes to mind? Probably the classic double helix structure? Maybe the bundles of DNA that form your chromosomes, or it might even be just a simple string of letters that code for all of our genes. What these standard images fail to convey, however, is that our DNA is always in motion – unwinding to be copied, being pulled apart to be divided between cells or having other smaller molecules added to or removed from it. Perhaps most remarkably of all, while the DNA molecule jiggles rapidly, the sequence of letters itself is slowly on the move – through a process called mutation whereby some letters change into different ones.

Our DNA mutates over time normally. Some mutations are bad, some are good and others have no effect. Yet, there are also sections of our DNA sequence that can move around and selfishly insert themselves into random places of our genome. They are called transposable elements, or ‘jumping genes’, and they can cause many problems if they insert themselves into essential genes and stop them from doing their job. These ‘genomic enemies’ need to be controlled and one way to do that is by creating thousands of tiny RNAs known as piwi-interacting RNAs (piRNAs). These piRNAs bind to the RNA that is produced from the transposable elements, and stop them from moving around. However, how the cell makes these ‘guardians’ against transposable elements is not fully understood.

In a previous study, the Epigenetic Inheritance and Evolution group at the MRC LMS began to unravel this question in nematode worms. They found that piRNA production evolved by repurposing the machinery already found in the cells. A motif, or short DNA sequence, that helps to create another type of short RNAs – called small nuclear RNAs (snRNAs) – had mutated slightly to create piRNAs that could help protect our genome against transposable elements. In their latest study, published in the journal EMBO, the team unravel another aspect of how nematodes create these ‘guardians of the genome’.

DNA is transcribed into RNA by an enzyme called RNA polymerase II. Cells do this to create all the proteins encoded by our genes. They create RNA molecules that are usually very long, whereas piRNAs are only around 30 nucleotides – or ‘letters of the DNA’ – long. The mystery lies in how the same enzyme creates both long RNA molecules and very short piRNAs. Usually there is a complex mechanism for cutting the end of an RNA molecule and includes lots of hidden coded messages in the DNA sequence, and the resulting RNA molecule. These coded signals are usually hundreds of nucleotides long, but to create these tiny piRNAs, there simply isn’t the space to include these ‘scissor signals’. So, just how are these small RNAs made?

Since piRNA production evolved from the creation of snRNAs, the team hypothesised that perhaps the secret to understanding how these short RNA molecules are cut might also borrow machinery from snRNA production. The Integrator complex was known to be responsible for making the end of snRNAs, and this work, pioneered by PhD student and first author of the paper Toni Beltran, reveals that the Integrator also plays a role in making the ends of piRNAs in nematode worms.

Collaborating with the Computational Regulatory Genomics group at the LMS, the groups combined a technique called CAGE (Cap Analysis Gene Expression) with an innovation to purify RNA with the RNA polymerase enzyme still bound in the laboratory. These two things together helped to capture the very first events of transcription and to work out how the Integrator complex produces piRNAs.

The researchers show in this study that the Integrator complex is actually a backup mechanism for creating piRNAs. From their previous study, the team found that there was a sequence that caused the RNA polymerase to pause very shortly after starting transcription. The short RNA molecule then gets cleaved and released. The new idea from this study is that the RNA polymerase sometimes gets going again, but only moves a short distance further along the DNA before pausing again.  This “budging” of the RNA polymerase allows the Integrator complex access to the RNA molecule to again cut and release the short piRNA. This elegant system means that if the first attempt fails to make a piRNA, then the Integrator complex can step in, so a short piRNA can still be made before the RNA molecule gets too long.

Dr Peter Sarkies, Head of the Epigenetic Inheritance and Evolution group at the LMS and senior author of this paper, discussed this paper further:

“The rapid evolution of piRNAs, which makes the piRNA biogenesis mechanism so different in worms, flies and humans, seems to be possible because they borrow tools from other molecular processes in the cell that are conserved across organisms. Importantly then, we can gain insight into the molecular capabilities of these other processes by working out what they do in piRNA production. As an example, in this work, we have uncovered a role for the Integrator complex in cutting RNA at paused RNA polymerases when piRNAs are made. It’s possible that Integrator might cut RNA at paused polymerases at other places in the genome, including protein-coding genes and indeed there is already some evidence that this takes place in mammals.”

 

‘Integrator terminates promoter-proximal Pol II to generate C.elegans piRNA precursors’ was published in the journal EMBO on 19 December. Read the full article here.