The mRNA cap epitranscriptome: Understanding an essential novel layer of gene expression in neuronal differentiation and function

The information for life is encoded in the DNA of the genes harboured in our chromosomes. The DNA in a chromosome is a very long chain consisting of four different nucleotides: G, A, C and T. For most genes this code is then converted into a messenger RNA intermediate (mRNA) that has a cap structure and a polyA tail to protect it from degradation.

This mRNA is then translated in the cytoplasm into a chain of amino acids called proteins, which fulfil a function; for example an enzymatic reaction to generate energy from the nutrients we eat to allow for the electrical communication among neurons in our brain.

Although the sequence of mRNA only consist of four nucleotides, many can be modified by addition of small chemical groups to increase the regulatory portfolio and coding capacity. The most prominent modification in mRNA are methyl groups added to the nucleotides adjacent to the cap structure. Animals including humans have two cap methyltransferase enzymes (CMTrs) that add these modifications.

Also many parasites have a CMTr gene in their genome that is required for their propagation. In mice, CMTrs are essential and required for neuronal development, however, the biological functions of CMTrs and the mRNA cap modifications remain largely unexplained.

We recently discovered that mutant Drosophila lacking both CMTrs are viable, although they suffer from neurological and learning defects. Intriguingly, we further discovered that in these mutant flies, mRNAs were not properly transported to synapses, which are the sites where signals are transmitted to neighbouring neurons. In particular, we could show that some mRNAs are only made into protein at synapses.

Hence, the cap modifications have an essential role in directing the synthesis of new proteins locally at synapses suggesting that this process is required for learning of new associations, that are then stored as memory in the brain. However, we currently do not know which genes are expressed in this way at synapses nor what the sequence code is to direct mRNAs to synapses for localized expression.

We now have the ideal animal model to address the very fundamental questions about how this enigmatic modifications direct local expression of genes to synapses. Our preliminary data indicate that the cap modifications vary between different animals and conditions. Since CMTrs also localize to synapses, our data suggest a dynamic code important for local protein synthesis.

In a first step to crack this code, we will identify specific mRNAs that localize to synapses allowing us to build a reporter system to test the code. To complement this analysis we will further determine the sequence preferences of CMTrs in biochemical assays and identify proteins important for CMTr specificity and decoding of the cap modification code.

These studies are essential to understand the vital function of the cap modifications in the regulation of gene expression and how its aberrant regulation can lead to neurological defects in humans, or can be exploited to interfere with viral replication such as in SARS-CoV-2.