Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Genome Biol. 2021 Nov 11;22(1):310. doi: 10.1186/s13059-021-02525-6.

Abstract

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, and mutation detection in single cells. We identify thousands of unannotated isoforms and find conserved functional modules that are enriched for alternative transcript usage in different cell types and species, including ribosome biogenesis and mRNA splicing. Analysis at the transcript level allows data integration with scATAC-seq on individual promoters, improved correlation with protein expression data, and linked mutations known to confer drug resistance to transcriptome heterogeneity.

Keywords: Long-read sequencing; Single-cell gene expression; Single-cell multi-omics; Splicing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Animals
  • Exons
  • Gene Expression Profiling / methods
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Mice
  • Nanopore Sequencing / methods*
  • Protein Isoforms / genetics*
  • Protein Isoforms / metabolism*
  • RNA Splicing
  • RNA, Messenger
  • Transcriptome

Substances

  • Protein Isoforms
  • RNA, Messenger