Periodic Reporting for period 4 - Neuro-UTR (Mechanism and functional impact of ultra-long 3’ UTRs in the Drosophila nervous system)
Reporting period: 2023-07-01 to 2024-12-31
The nervous system is composed of highly polarized cells of complex and dynamic architecture. The formation and maintenance of neurons and neural circuits require the coordinated expression of genes at each step of RNA metabolism: from transcription, processing, localized transport and translation, to degradation. To achieve this level of complexity, neurons employ mechanisms that increase RNA regulatory potential: alternative splicing, alternative polyadenylation, and non-coding RNA expression.
One particularly striking process is the drastic lengthening of the 3’ untranslated region (3’ UTR) of hundreds of genes, which occurs in neurons from flies to humans. The function of the resulting ultra-long 3’ UTRs is unknown. RNA deregulation plays a central role in neurological diseases, which constitute a growing health concern in ageing populations; to understand underlying causes, it is essential to study regulatory processes and define the function of these RNA sequences. In this study, we integrate the molecular processes governing biogenesis and function of neuronal RNAs, from nucleus to synapse, in an animal model, the fruit fly Drosophila melanogaster.
Conclusions of the action: we found molecular mechanisms that govern the biogenesis of neuron-specific RNA signatures, and more generally, of gene expression regulation. We uncovered how ultra-long 3’UTRs are post-transcriptionally regulated, and the important contribution of highly conserved neuronal RNA-binding proteins in the processes of mRNA stability, localisation, and translation. One important aspect of our research is the demonstration of crucial functions carried out by neuronal 3’UTRs, individually and globally, during neurogenesis and in adult neuron physiology.
Overall, the results of this research made a major impact on our understanding of neuronal gene regulation in health and disease.
One particularly striking process is the drastic lengthening of the 3’ untranslated region (3’ UTR) of hundreds of genes, which occurs in neurons from flies to humans. The function of the resulting ultra-long 3’ UTRs is unknown. RNA deregulation plays a central role in neurological diseases, which constitute a growing health concern in ageing populations; to understand underlying causes, it is essential to study regulatory processes and define the function of these RNA sequences. In this study, we integrate the molecular processes governing biogenesis and function of neuronal RNAs, from nucleus to synapse, in an animal model, the fruit fly Drosophila melanogaster.
Conclusions of the action: we found molecular mechanisms that govern the biogenesis of neuron-specific RNA signatures, and more generally, of gene expression regulation. We uncovered how ultra-long 3’UTRs are post-transcriptionally regulated, and the important contribution of highly conserved neuronal RNA-binding proteins in the processes of mRNA stability, localisation, and translation. One important aspect of our research is the demonstration of crucial functions carried out by neuronal 3’UTRs, individually and globally, during neurogenesis and in adult neuron physiology.
Overall, the results of this research made a major impact on our understanding of neuronal gene regulation in health and disease.
We identified the master regulator that generates neuronal RNA signatures —neuronal 3’UTRs, but also splicing patterns and circular RNAs—, and described several cellular strategies of how the robust function of this protein is maintained and safeguarded throughout development and adult neuronal function. These results were published in two research papers (Carrasco et al., Molecular Cell 2020; Alfonso-Gonzalez et al., under review and in BioRxiv 2024)
We discovered a fundamental principle of gene expression regulation that is applicable broadly, beyond neuronal systems: sites of transcription initation determine mRNA isoform selection, including alternative RNA processing choices such as alternative splicing and alternative polyadenylation. These results were published in two research papers (Alfonso-Gonzalez et al., Cell 2023; Alfonso-Gonzalez et al., STAR Protocols 2023).
We identified neuronal RNA signatures that play a particularly crucial role in neurogenesis, and defined a developmental window in which they need to be deployed in order to ensure a functioning nervous system in adults. These results were published in a research paper (Carrasco et al., Cell Reports 2022)
We characterized a long non-coding neuronal RNA that acts as a scaffold for neuronal granules, identified its interaction partners and condensation properties. Generating a unique animal model to study the physiological function of neuronal granules, we found that individual RNA/protein condensates play a crucial role in neuron maturity, memory, and preventing neurodegeneration phenotypes. These results were published in a research paper (Grzejda et al., Science Advances 2022).
We found that neuronal 3’UTRs are regulated in concert by subsets of neuronal RNA-binding proteins. This 3’UTR-dependent post-transcriptional regulation is essential for the proper stability, localisation and translation of mRNAs encoding synaptic proteins, and represents a way to modulate synaptic protein expression and function. These results were published in a research paper (Grzejda and Hess et al., in press at EMBO Reports and in BioRxiv 2024).
We discovered a fundamental principle of gene expression regulation that is applicable broadly, beyond neuronal systems: sites of transcription initation determine mRNA isoform selection, including alternative RNA processing choices such as alternative splicing and alternative polyadenylation. These results were published in two research papers (Alfonso-Gonzalez et al., Cell 2023; Alfonso-Gonzalez et al., STAR Protocols 2023).
We identified neuronal RNA signatures that play a particularly crucial role in neurogenesis, and defined a developmental window in which they need to be deployed in order to ensure a functioning nervous system in adults. These results were published in a research paper (Carrasco et al., Cell Reports 2022)
We characterized a long non-coding neuronal RNA that acts as a scaffold for neuronal granules, identified its interaction partners and condensation properties. Generating a unique animal model to study the physiological function of neuronal granules, we found that individual RNA/protein condensates play a crucial role in neuron maturity, memory, and preventing neurodegeneration phenotypes. These results were published in a research paper (Grzejda et al., Science Advances 2022).
We found that neuronal 3’UTRs are regulated in concert by subsets of neuronal RNA-binding proteins. This 3’UTR-dependent post-transcriptional regulation is essential for the proper stability, localisation and translation of mRNAs encoding synaptic proteins, and represents a way to modulate synaptic protein expression and function. These results were published in a research paper (Grzejda and Hess et al., in press at EMBO Reports and in BioRxiv 2024).
We developed and optimized experimental and computational techniques that advanced the fields of both molecular neuroscience and gene expression regulation.
These methods and their application in the scope of this project have not only revealed mechanisms of how alternative UTRs regulate gene expression complexity in neurons, but are also useful for the broader scientific community.
These methods and their application in the scope of this project have not only revealed mechanisms of how alternative UTRs regulate gene expression complexity in neurons, but are also useful for the broader scientific community.