Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

Abstract

Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 (www.isoformAtlas.com). Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain (www.isoformAtlas.com). Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function.

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

“…Of note, novel approaches for using long-read sequencing approaches in single cells will enable a more granular approach to exploring transcript diversity in the cortex. Although such approaches are currently limited by technological and analytical constraints, a recent study used long-read transcriptome sequencing to identify cell-type-specific transcript 21 diversity in the mouse hippocampus and prefrontal cortex 67 . Finally, although we explored the extent to which novel transcripts contained ORFs, the extent to which they are actually translated and contribute to cortical proteomic diversity is not known.…”

Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed

“…A natural application of CLOC is to control these features to enable stronger inference of their relationship to downstream variables. Examples of these potential targets for control include the activity of different cell types [93,94,95,96,97,98]; the type [99,100,101], frequency [102], amplitude [102], spike coherence [103,104] and interactions [105,106] of different oscillatory patterns [107]; discrete phenomena such as bursts [79], sharp wave ripples [87], oscillatory bursts [108,109,110,111,112], traveling waves [113,114,115,37,81,116], or sleep spindles [117]; and latent states describing neural dynamics [118,119,120,121,122,123,124,125], including those most relevant to behavior [20,126,127].…”

Ex uno, plures–From One Tissue to Many Cells: A Review of Single-Cell Transcriptomics in Cardiovascular Biology

“…Short-read sequencing of end-primed transcripts hampers the detection of transcript isoforms, although some scRNAseq methods provide full-length transcript information [ 186 , 187 ]. Methods are currently being developed to combine short-read and long-read sequencing from barcoded cells to identify cell-type specific isoforms through barcode deconvolution [ 188 ].…”