Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Academic Article uri icon

Overview

abstract

  • Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.

authors

publication date

  • March 7, 2022

Research

keywords

  • Brain
  • RNA

Identity

PubMed Central ID

  • PMC9287170

Scopus Document Identifier

  • 85125715810

Digital Object Identifier (DOI)

  • 10.1101/gr.097857.109

PubMed ID

  • 35256815

Additional Document Info

volume

  • 40

issue

  • 7