Free circular introns with an unusual branchpoint in neuronal projections.

Harleen Saini,Melissa J Moore,Alicia A Bicknell,Sean R Eddy

doi:10.7554/elife.47809

Abstract

The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.

Highlights

In polarized cells, such as neurons and oocytes, RNA localization to distinct subcellular compartments is important for spatial control of protein expression (Holt and Bullock, 2009)
Lysates prepared by scraping the underside are highly enriched for projections (“projection” samples), while lysates prepared from the top surface comprise whole cells with nuclei and projections (“whole cell” samples)
As we looked at randomly selected examples of the 1,632 intron regions in the rat genome browser, we found, unsurprisingly, that many cases represented an unannotated alternative splicing event or an unannotated transcription start site (TSS) or polyadenylation site (PAS) within an annotated intron

Summary

Introduction

In polarized cells, such as neurons and oocytes, RNA localization to distinct subcellular compartments is important for spatial control of protein expression (Holt and Bullock, 2009). A detained intron (i.e., an intron with regulated post-transcriptional splicing, as opposed to constitutive co-transcriptional splicing) restricts Srsf mRNA export from the nucleus (Boutz et al, 2015), and a retained intron (i.e., an alternative unspliced isoform) promotes dendritic localization of Calm (Sharangdhar et al, 2017). The Robo gene, which is important for commissural axon development in mice, expresses both a fully spliced mRNA and another retaining intron. 26, and these isoforms encode different proteins that have opposing functions in axon guidance (Chen et al, 2008). Spatial and temporal control of protein expression from the intron-retaining

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