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Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.

Publication ,  Journal Article
Hardwick, SA; Hu, W; Joglekar, A; Fan, L; Collier, PG; Foord, C; Balacco, J; Lanjewar, S; Sampson, MM; Koopmans, F; Prjibelski, AD; Jarroux, J ...
Published in: Nat Biotechnol
July 2022

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.

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Published In

Nat Biotechnol

DOI

EISSN

1546-1696

Publication Date

July 2022

Volume

40

Issue

7

Start / End Page

1082 / 1092

Location

United States

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA
  • Protein Isoforms
  • Humans
  • Exons
  • Brain
  • Alternative Splicing
 

Citation

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Hardwick, S. A., Hu, W., Joglekar, A., Fan, L., Collier, P. G., Foord, C., … Tilgner, H. U. (2022). Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol, 40(7), 1082–1092. https://doi.org/10.1038/s41587-022-01231-3
Hardwick, Simon A., Wen Hu, Anoushka Joglekar, Li Fan, Paul G. Collier, Careen Foord, Jennifer Balacco, et al. “Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.Nat Biotechnol 40, no. 7 (July 2022): 1082–92. https://doi.org/10.1038/s41587-022-01231-3.
Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, et al. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol. 2022 Jul;40(7):1082–92.
Hardwick, Simon A., et al. “Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.Nat Biotechnol, vol. 40, no. 7, July 2022, pp. 1082–92. Pubmed, doi:10.1038/s41587-022-01231-3.
Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MM, Koopmans F, Prjibelski AD, Mikheenko A, Belchikov N, Jarroux J, Lucas AB, Palkovits M, Luo W, Milner TA, Ndhlovu LC, Smit AB, Trojanowski JQ, Lee VMY, Fedrigo O, Sloan SA, Tombácz D, Ross ME, Jarvis E, Boldogkői Z, Gan L, Tilgner HU. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol. 2022 Jul;40(7):1082–1092.

Published In

Nat Biotechnol

DOI

EISSN

1546-1696

Publication Date

July 2022

Volume

40

Issue

7

Start / End Page

1082 / 1092

Location

United States

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA
  • Protein Isoforms
  • Humans
  • Exons
  • Brain
  • Alternative Splicing