TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
08 08 2023
08 08 2023
Historique:
received:
03
12
2022
accepted:
11
07
2023
medline:
10
8
2023
pubmed:
9
8
2023
entrez:
8
8
2023
Statut:
epublish
Résumé
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
Identifiants
pubmed: 37553321
doi: 10.1038/s41467-023-40083-6
pii: 10.1038/s41467-023-40083-6
pmc: PMC10409798
doi:
Substances chimiques
RNA
63231-63-0
Protein Isoforms
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
4760Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM088342
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM121827
Pays : United States
Organisme : NHGRI NIH HHS
ID : R56 HG012310
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA233074
Pays : United States
Informations de copyright
© 2023. Springer Nature Limited.
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