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

Autor: Simon A. Hardwick, Wen Hu, Anoushka Joglekar, Li Fan, Paul G. Collier, Careen Foord, Jennifer Balacco, Samantha Lanjewar, Maureen McGuirk Sampson, Frank Koopmans, Andrey D. Prjibelski, Alla Mikheenko, Natan Belchikov, Julien Jarroux, Anne Bergstrom Lucas, Miklós Palkovits, Wenjie Luo, Teresa A. Milner, Lishomwa C. Ndhlovu, August B. Smit, John Q. Trojanowski, Virginia M. Y. Lee, Olivier Fedrigo, Steven A. Sloan, Dóra Tombácz, M. Elizabeth Ross, Erich Jarvis, Zsolt Boldogkői, Li Gan, Hagen U. Tilgner
Přispěvatelé: Molecular and Cellular Neurobiology, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience - Neurodegeneration
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Nature Biotechnology, 40(7), 1082-1092. Nature Publishing Group
Hardwick, S A, Hu, W, Joglekar, A, Fan, L, Collier, P G, Foord, C, Balacco, J, Lanjewar, S, Sampson, M M G, Koopmans, F, Prjibelski, A D, Mikheenko, A, Belchikov, N, Jarroux, J, Lucas, A B, Palkovits, M, Luo, W, Milner, T A, Ndhlovu, L C, Smit, A B, Trojanowski, J Q, Lee, V M Y, Fedrigo, O, Sloan, S A, Tombácz, D, Ross, M E, Jarvis, E, Boldogkői, Z, Gan, L & Tilgner, H U 2022, ' Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue ', Nature Biotechnology, vol. 40, no. 7, pp. 1082-1092 . https://doi.org/10.1038/s41587-022-01231-3
ISSN: 1087-0156
DOI: 10.1038/s41587-022-01231-3
Popis: 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.
Databáze: OpenAIRE
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