RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins (RBPs). Generally, our knowledge of the mechanistic details behind the localization of a given RNA is restricted to a particular cell type. Here, we show that RNA/RBP interactions that regulate RNA localization in one cell type predictably regulate localization in other cell types with vastly different morphologies. To determine transcriptome-wide RNA spatial distributions across the apicobasal axis of human intestinal epithelial cells, we used our recently developed RNA proximity labeling technique, Halo-seq. We found that mRNAs encoding ribosomal proteins (RP mRNAs) were strongly localized to the basal pole of these cells. Using reporter transcripts and single-molecule RNA FISH, we found that pyrimidine-rich motifs in the 5' UTRs of RP mRNAs were sufficient to drive basal RNA localization. Interestingly, the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells. In both cell types, the regulatory activity of this motif was dependent on it being in the 5' UTR of the transcript, was abolished upon perturbation of the RNA-binding protein LARP1, and was reduced upon inhibition of kinesin-1. To extend these findings, we compared subcellular RNAseq data from neuronal and epithelial cells. We found that the basal compartment of epithelial cells and the projections of neuronal cells were enriched for highly similar sets of RNAs, indicating that broadly similar mechanisms may be transporting RNAs to these morphologically distinct locations. These findings identify the first RNA element known to regulate RNA localization across the apicobasal axis of epithelial cells, establish LARP1 as an RNA localization regulator, and demonstrate that RNA localization mechanisms cut across cell morphologies.
Keywords: RNA localization; RNA trafficking; TOP motif; chromosomes; gene expression; genetics; genomics; human; mouse.
The information required to build a specific protein is encoded into molecules of RNA which are often trafficked to precise locations in a cell. These journeys require a complex molecular machinery to be assembled and set in motion so that the RNA can be transported along dynamic ‘roads’ called microtubules. The details of this mechanism are known only for a handful of RNAs in a few cell types; for example, scientists have uncovered the signals presiding over the shuttling of certain RNAs to the axon, the long and thin projection that a neuron uses to communicate. Yet these RNAs are also present in cells that lack axons. Whether the molecular processes which preside over RNA movement apply across cell types has so far remained unclear. To investigate this question, Goering et al. tracked the location of RNA molecules in two types of polarized mouse cells: neurons which feature an axon, and ‘epithelial’ cells which line the intestine. The experiments revealed that the signals sending RNAs to the axons also directed the molecules towards the bottom pole of epithelial cells. In both cases, the RNAs travelled towards the extremity of the growing, “plus” end of the microtubules. Overall, this work suggests that RNA transport mechanisms should not be thought of as leading to a particular location in the cell; instead, they may be following more generalisable instructions. This knowledge could allow scientists to predict where a particular RNA will be sent across cell types based on data from one cell population. It could also aid the development of synthetic RNAs that target specific parts of the cell, offering greater control over their actions.
© 2023, Goering et al.