RNA localization mechanisms transcend cell morphology

Abstract

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.

Mammalian glial protrusion transcriptomes predict localization ofDrosophilaglial transcripts required for synaptic plasticity

“…We found a large overlap between the transcripts present at the periphery of both glia and neurons (Figure 1D). Our observations agree with a recent study highlighting conserved mRNA transport mechanisms between cell types (Goering, Arora and Taliaferro, 2022) and significant overlap of localized transcripts within astrocytes, radial glia and neurons (D’Arcy and Silver, 2020).…”

“…Certainly, the glial sub-types we characterized in Drosophila at the NMJ are also present, as defined by specific cell type markers, in association with neurons and synapses in the central brain. Furthermore, recent studies suggest that mRNA localization in one cell type mediated by interactions with RBPs can be predictive of the same interactions and localizations in other cell types with very different morphologies and functions (Goering, Arora and Taliaferro, 2022). It has also been shown that radial glia, astrocytes, and neurons, all of which have quite distinct morphologies and functions, share a significant overlap in the types of mRNAs localized to their protrusions (D’Arcy and Silver, 2020).…”

The role of midbody-associated mRNAs in regulating abscission

“…We next sought to identify specific cis-elements (LEs) within MBsome-localized RNAs that regulated their trafficking to the MB. We recently identified RNA elements that were necessary and sufficient for transport to both the neurites of neuronal cells and the basal pole of epithelial cells ( Goering et al, 2023 ). Both of these subcellular locations are associated with the plus ends of microtubules and we showed that these RNA elements directed RNAs to their destinations by targeting them to microtubule plus ends.…”

“…Using data from human intestinal epithelial cells ( Goering et al, 2023 ), we then compared enrichments across the apicobasal axis for MBsome RNAs and all other detected RNAs. Again, we found that MBsome-enriched RNAs were significantly enriched at the basal pole of these cells compared to non-MBsome-enriched RNAs ( Fig.…”

Distinct roles of LARP1 and 4EBP1/2 in regulating translation and stability of 5′TOP mRNAs

“…We do not observe any correlation between change in mRNA half-lives with either length of 5′TOP motif or the presence of a PRTE in the 5′UTR, suggesting that the position of the pyrimidines directly adjacent to the cap is necessary for this effect on mRNA stability. LARP1 was shown to promote the localization of ribosomal mRNAs in a PRTE-dependent manner but did not require the stricter 5′ TOP motif, suggesting that LARP1’s interaction with ribosomal mRNAs and its functional consequence could be context dependent ( 54 ).…”