Abstract
BackgroundRNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different cell functions, e.g., in neuronal dendrites, localization is a critical step for long-lasting synaptic potentiation. However, there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. A comprehensive catalog of localized RNA can help dissect RBP/RNA interactions and localization motifs. Here, we utilize a single cell sub-cellular RNA sequencing approach to profile differentially localized RNAs from individual cells across multiple single cells to help identify a consistent set of localized RNA in mouse neurons.ResultsUsing independent RNA sequencing from soma and dendrites of the same neuron, we deeply profiled the sub-cellular transcriptomes to assess the extent and variability of dendritic RNA localization in individual hippocampal neurons, including an assessment of differential localization of alternative 3′UTR isoforms. We identified 2225 dendritic RNAs, including 298 cases of 3′UTR isoform-specific localization. We extensively analyzed the localized RNAs for potential localization motifs, finding that B1 and B2 SINE elements are up to 5.7 times more abundant in localized RNA 3′UTRs than non-localized, and also functionally characterized the localized RNAs using protein structure analysis.ConclusionWe integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource. This catalog of transcripts, including differentially localized isoforms and computationally hypothesized localization motifs, will help investigators further dissect the genome-scale mechanism of RNA localization.
Highlights
RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which mediate localization to specific sub-cellular compartments
A few specific examples of differentially localized 3′UTR isoforms have already been characterized [11], such as BDNF [12, 13], and this phenomenon was recently surveyed on a genome-wide scale in brain-derived cell lines and cortical neurons [8] and rat hippocampal tissue slices [14] resulting in the identification of hundreds of cases of differential localization of alternative 3′UTR isoforms
We identify a total of 2225 candidate dendritic RNAs, including 298 that showed differential localization of 3′UTR isoforms that was consistent across the individual cells
Summary
RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which mediate localization to specific sub-cellular compartments. We generated a pool of “non-localized” background 3′ UTR sequences based on the list of genes that were significantly higher expressed in the soma from the gene-level DESeq analysis described above (3811 genes) We filtered this set to remove any overlap with one of the other localized lists (i.e., the consDend list and the isoDend list) and any overlap with previously annotated dendritically localized genes in order to make this list as specific to non-localized genes as possible, which resulted in removal of 471 and 531 genes respectively leading to a final pool of 2809 genes from which to draw 3′UTR sequences to make up a background. The background sets used for enrichment testing were the lengthmatched non-localized sets described above
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