Localization meets function: deciphering the role of lncRNAs and the synaptic transcriptome in motor neurons

In recent decades, RNA has become the focus of biotechnology. The COVID-19 pandemic revealed its potential as a therapeutic molecule in the case of mRNA vaccines, also highlighting the importance of pursuing basic science to discover new regulatory mechanisms that could drive future translational applications. Genome projects like the Human Genome Project, FANTOM, and ENCODE have shown that 98% of the genome is non-coding, raising attention to gene regulation mechanisms. In my PhD research, I focused on RNA localization as a regulatory mechanism, following the principle that “Localization is function”. Many cellular functions rely on cell polarization that, at a molecular level, depends on the differential subcellular partitioning of macromolecules like proteins and RNA. RNA localization is critical in cells like neurons that have distant structures like dendrites, axon and synapses that function independently of the cell body and in most cases are very far away. During this thesis, I concentrated on the biology of motor neurons and elucidated how coding and non-coding RNA molecules can localize in different subcellular compartments like the endoplasmic reticulum or the synapse, to mediate molecular functions critical for physiology and pathology. In the first part of my research, I studied the lncRNA Lhx1os function in vivo and in vitro in motor neurons. Lhx1os knockout mice displayed motor deficits and post-natal reduction in the number of motor neurons. In vitro, Lhx1os was found to localize to the Endoplasmic Reticulum (ER), interacting with the PDIA3 protein to regulate the ER stress response, a process implicated in the motor neuron pathology Amyotrophic lateral sclerosis (ALS). In the second part, using iPSC-derived motor neurons (iMNs), I analyzed the synaptic RNA composition and its response to stress and ALS mutations. Oxidative stress disrupted synaptic RNA localization, and ALS-associated FUS mutations affected mRNAs accumulation at synapses. Synapses are also enriched in many non-coding RNA molecules like lncRNAs, circRNAs and miRNAs, that could participate to mRNA shuttling and localization in the compartment. I also identified synaptic cis-regulatory sequences (zipcodes) in the coding sequences of RNAs that may direct synaptic localization. This thesis advances the understanding of RNA localization mechanisms, highlighting potential pathways relevant to ALS and other motor neuron disorders.