Decoding the complex journeys of RNAs along neurons

Abstract

Neurons are highly polarized, specialized cells that must overcome immense challenges to ensure the health and survival of the organism in which they reside. They can spread over meters and persist for decades yet communicate at sub-millisecond and millimeter scales. Thus, neurons require extreme levels of spatial-temporal control. Neurons employ molecular motors to transport coding and noncoding RNAs to distal synapses. Intracellular trafficking of RNAs enables neurons to locally regulate protein synthesis and synaptic activity. The way in which RNAs get loaded onto molecular motors and transported to their target locations, particularly following synaptic plasticity, is explored below.

Graphical Abstract

Figure 1.

The complexity of neuronal transport. Arrows illustrate just a few of the thousands of potential paths motors and cargo can take. For simplicity, only anterograde tracks (transport away from the soma) are highlighted in panels (A), (B), and (E). (A) In the brain, axons from individual neurons, such as those in the hippocampus, can project to and form synapses with neurons in several different brain regions centimeters away. Orange arrows illustrate these anterograde axonal tracks to circuitry underlying learning and memory. (B) Pyramidal neurons typically have a single axon (orange arrow) while dendrites split off from the soma and branch multiple times, resulting in dozens of different splits on the road and potential paths to take (dark blue arrows show just anterograde transport for simplicity) [141]. (C) Within each dendrite, there are typically hundreds of dendritic spines (the receiving end of the synapse) at various stages of maturity [142, 143]. Each spine is a ∼ micron-sized compartment. RNAs may be localized between spines, at the base of spines, or within spines. This may vary depending on the type of spine and neuronal activity. Dendrites also contain microtubules with mixed polarity (dark blue arrows: plus-end-out microtubules, white arrows: minus-end-out microtubules). This further complicates and informs transport as motor proteins will walk to the plus or minus ends depending on which family they belong to [144]. (D) Taking a closer look within the dendrite, more options for RNA localization emerge (i) the endoplasmic reticulum (ER), (ii) rough ER entering a spine, (iii) on/in elongated dendritic mitochondria, (iv) in filopodia (which participate in “silent synapses” [145]), (v) in the postsynaptic density (PSD; an electron-dense hub of receptors and scaffolds indicative of excitatory synapses), (vi) the base of mushroom spines (mature synapses), (vii) in stubby spines (likely a variation of mushroom spines [146]), or (viii) in thin spines (immature synapses). (E) Within axons, RNA cargoes are trafficked along uniformly plus-end-out microtubules. On their journeys, RNA pass through or dock at the synaptic boutons [the presynaptic side of the synapse] they encounter. (F) In a more detailed axonal view we see that RNAs may also localize to (i) synaptic vesicles, (ii) between boutons, (iii) synaptic mitochondria, or (iv) at an ER tubule or other sites not illustrated here. Estimated scale bars are shown.

Figure 2.

(A) Potential interactions of coding and ncRNAs at dendritic spines. Kinesins deliver RNPs near the base of spines. miRNAs in the RISC complex can bind to the 3′UTR of the target mRNA, stalling, or inhibiting translation of the protein. CircRNAs and lncRNAs can act as sponges for miRNAs, enabling translation of the target protein. LncRNAs can also promote translation through recruiting initiation factors (eIFs) to bind to mRNAs. Additionally, lncRNAs can act as scaffolds and encourage protein activity. (B) Both cis- and trans- regulatory elements such as zip codes, the length of 3′UTRs, and alternative splicing allow for differential targeting of RNAs. The structure or post-transcriptional modification of lncRNA protein-binding elements can affect their interaction with specific proteins. For example, (A) the composition of dendritic spines may result in an altered lncRNA structure compared to within the dendritic shaft (B, C) and thus what proteins the lncRNA can interact with. Post-transcriptional modifications, such as m6A methylation can recruit initiation factors, potentially initiating local translation.

Figure 3.

Model of RNA transport. (A) The dendritic region of interest is highlighted on the excitatory pyramidal neuron in black. (B) During basal conditions RNAs, particularly those required for the early (<10 min) phases of plasticity (black), are transported bidirectionally throughout neurons. This transport follows a modified sushi-belt model, where cargoes dissociate from motors, at sites of potential need. If no stimulus occurs, these RNAs could reattach to motors to be carried to a new site. This deposition and re-recruitment may depend on current abundance at that site and possibly a molecular timer to ensure molecules do not persist too long at sites that lack the required stimulus. (C) Following synaptic plasticity, RNAs involved in early processes of plasticity are transported to and accumulated at the stimulated spine (large arrow). This prompt accumulation is largely driven by “stealing” nearby RNAs (red RNAs at the spine base and in the RNPs) in the same dendrite rather than from the soma. A third wave of newly transcribed RNAs (green RNAs coming from the soma) required for the consolidation of early changes at the spine may also be directed to the stimulated site.

Figure 4.

Cartoon illustration depicting outstanding questions: Although we have advanced significantly, there are several major gaps in our knowledge regarding RNA transport in neurons. Among them are: How are different types of RNAs loaded into their “car seat” and how is this association determined? How many RNAs can fit in one “seat”? How do RNPs form (do they have specific partners, is it based on demand, or self-assembly via intrinsically disordered regions)? How do interactions with organelles affect RNA transport? Is this interaction dependent on the organelle’s reliance on that protein product/regulatory element of the mRNA/ncRNA? Or is it based on the organelle being targeted to its final destination? How do RNA granules associate with specific motors? How does transport differ in axons, with “one-way” streets (all plus-end-out microtubules) compared to dendrites, with “two-way” streets (with mixed plus- and minus-end-out microtubules)? How do different compositions of microtubule associated proteins and post-translational modifications affect RNA traffic? How does transport differ in varying “city plans”, with changes to the numbers and types of highways? How might transport be altered in highly polarized neurons (i.e. pyramidal) versus bipolar neurons versus those with highly complex dendritic arbors (i.e. Purkinje cells)? Lastly, how is RNA transport altered in neuronal disease, where brain regions may atrophy, and highways become fragmented?