Isoform cell type specificity in the mouse primary motor cortex

Abstract

Full-length SMART-Seq single-cell RNA-seq can be used to measure gene expression at isoform resolution, making possible the identification of isoform markers for cell types and for an isoform atlas. In a comprehensive analysis of 6,160 mouse primary motor cortex cells assayed with SMART-Seq, we find numerous examples of isoform specificity in cell types, including isoform shifts between cell types that are masked in gene-level analysis. These findings can be used to refine spatial gene expression information to isoform resolution. Our results highlight the utility of full-length single-cell RNA-seq when used in conjunction with other single-cell RNA-seq technologies.

Robust and annotation-free analysis of alternative splicing across diverse cell types in mice

“…However, the authors only considered annotated skipped exons, a subset of the events we quantify, and they used a different dimensionality reduction technique. Figure 4b highlights PSI from some of the top differentially spliced intron groups across cell types, defining “marker introns” as a complement to marker genes (similar to isoform markers defined in [28]). We are able to detect well-known cell-type-specific alternatively spliced genes such as Nrxn1 , which encodes a key pre-synaptic molecule (Figure 4c) [34].…”

“…Cells were filtered to those from three month-old mice present in this collection: https://czb-tabula-muris-senis.s3-us-west-2.amazonaws.com/Data-objects/tabula-muris-senis-facs-processed-official-annotations.h5ad (filtering details in [41]). BICCN Cortex data were downloaded from http://data.nemoarchive.org/biccn/lab/zeng/transcriptome/scell/SMARTer/raw/MOp/ and filtered as in [28].…”

Acorde: unraveling functionally-interpretable networks of isoform co-usage from single cell data

“…Alternative Splicing (AS) is known to be a tightly-regulated process in which splicing factors interact to create cell type-specific isoform expression patterns 78 . The transcriptome-level consequences of AS regulation have been studied in different ways, including, but not limited to, the detection of within-isoform coordination of alternative sites 40,41 , the generation of gene-isoform networks to uncover novel regulatory relationships [79][80][81][82] and the application of single-cell data to unravel cell type-specific expression patterns for same-gene isoforms 27,83 . However, the extent to which AS regulation creates co-expression patterns among alternative isoforms from different genes has not yet been fully addressed.…”

“…Notwithstanding this limited scenario, there are a number of relevant questions regarding the importance of splicing for cell identity and function that can only be resolved by evaluating isoform expression at the single-cell level. In point of fact, splicing differences have been shown to discriminate cell types with an accuracy comparable to that obtained using gene expression 33 , while integrating AS and gene expression changes has led to the discovery of cell subtypes and states that were otherwise not detected 27,[34][35][36] . Especially relevant among these inquiries is the much-debated issue of whether individual cells express one or several isoforms, that is, whether the isoform diversity observed in bulk studies is recapitulated by each single cell or, alternatively, arises as a result of the combination of multiple cells, each of In the present study, we hypothesize that isoform expression coordination exists as a result of AS regulation, and that this can be computationally detected in the form of isoform groups showing co-variation across cell types.…”

Isoform-specific regulation of rhythmic gene expression by alternative polyadenylation

“…Differences in rhythmic expression between APA isoforms does not appear to rely on a single mechanism, but rather seems to involve several independent processes. While many transcript isoforms are expressed in specific cell subtypes (e.g., 24.4% in mouse liver; Figure 2) (Booeshaghi et al, 2020;Hu et al, 2020;Lianoglou et al, 2013), cell subtypespecificity only contributes moderately to the differential rhythmicity between of APA isoforms. In contrast, posttranscriptional regulation is highly prevalent, especially for the generation of rhythmic APA isoforms from arrhythmically transcribed transcripts (i.e., Group 1 isoforms, Figure 3).…”