Free circular introns with an unusual branchpoint in neuronal projections

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.

Expansion Sequencing: Spatially PreciseIn SituTranscriptomics in Intact Biological Systems

“…Splicing of RNA is known to play a role in synapse specification (31), and neurons contain one nucleus vs. thousands of potentially molecularly distinct synapses, raising the question of whether splicing of expressed mRNAs, including those that contribute to synaptic function, is regulated in a spatially dependent manner along dendritic trees (32). We examined 5 reads that corresponded to intron-containing regions, and found that, while most (70%) of reads that mapped to intronic regions were located inside the soma (as is the case for most genes), we also observed introns in YFP-containing dendritic projections up to 100 microns away from the cell body layer, consistent with previous reports of cytoplasmic intron-retaining transcripts throughout neural processes (33,34). For example, Glutamate ionotropic receptor kainate type 10 subunit 2 (Grik2), which encodes a receptor subunit involved in excitatory glutamatergic neurotransmission that is implicated in autosomal recessive cognitive disability, appears in our data as a dendritic mRNA with a retained intron (Fig.…”

An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization

“…IR has previously been implicated in regulating the transcriptome by coupling to RNA degradation pathways 1,2,[10][11][12] . Although intron-retaining transcripts (IRTs) have predominantly been identified as residing within the nucleus where they are degraded 4,7,8 , there is an expanding body of evidence demonstrating the cytoplasmic localisation of stable IRTs [13][14][15][16][17] . It is noteworthy that neural cells, with their exceptional polarity and compartmentalisation, exhibit higher degrees of IR compared with other tissues [1][2][3] .…”

Subcellular Spatial Transcriptomes: Emerging Frontier for Understanding Gene Regulation

“…circRNAs have received a lot of interest in recent years, and it is known that they can code for proteins (Jeck and Sharpless 2014) and show asymmetric subcellular localization (Saini et al 2019). Initial studies, for example, suggest circRNAs localize differently relative to other RNAs in neuronal projections (Saini et al 2019). In addition, immunogenic circRNAs that are sensed as foreign are localized to distinct locations in the cytoplasm compared to endogenous circRNAs (Chen et al 2019b).…”

“…Cells contain many different RNA species, and extending our current understanding of mRNA localization to other RNA species, including tRNAs and circular RNAs (circRNAs), will be important in understanding the regulation of these molecules. circRNAs have received a lot of interest in recent years, and it is known that they can code for proteins ( Jeck and Sharpless 2014 ) and show asymmetric subcellular localization ( Saini et al 2019 ). Initial studies, for example, suggest circRNAs localize differently relative to other RNAs in neuronal projections ( Saini et al 2019 ).…”