Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 7, 2023

Abstract Nervous system development is associated with extensive regulation of alternative splicing (AS) and polyadenylation (APA). AS APA have been extensively studied in isolation, but little known about how these processes are coordinated. Here, the coordination cassette exon (CE) Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown Nanopore combined an analysis pipeline to quantify inclusion exons connection 3’ ends. Using PL-Seq, identified genes that exhibit significant differences CE depending on connectivity short versus long 3’UTRs. Genomic 3’UTR deletion found alter upstream isoforms ELAV loss differentially affected work highlights importance considering 3’UTRs when monitoring events.

Язык: Английский

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Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing

Molecular Aspects of Medicine, Год журнала: 2024, Номер 96, С. 101255 - 101255

Опубликована: Фев. 17, 2024

Язык: Английский

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Steering research on mRNA splicing in cancer towards clinical translation

Nature reviews. Cancer, Год журнала: 2024, Номер 24(12), С. 887 - 905

Опубликована: Окт. 9, 2024

Язык: Английский

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Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns

Genome Research, Год журнала: 2022, Номер 32(4), С. 726 - 737

Опубликована: Март 17, 2022

Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing sequence cDNA copies representing molecule on both Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT). We these pairs in terms of content isoform patterns. Although read show high similarity, find differences (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation (poly(A)-site) assignment, (4) exon–intron structures. Overall, 25% disagree either TSS, poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors microexons complicated sites. Our single-molecule technology comparison reveals inconsistencies are often caused by error–induced inaccurate ONT alignments, especially downstream GUNNGU donor motifs. However, annotation-disagreeing upstream shifts NAGNAG acceptors confirmed PacBio thus likely real. In barcoded nonbarcoded reads, intron number proximity GU/AGs better predict with the annotation than quality alone. summarize findings annotation-based algorithm spliced correction improves subsequent transcript construction reads.

Язык: Английский

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Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology

Plant Science, Год журнала: 2022, Номер 325, С. 111486 - 111486

Опубликована: Окт. 3, 2022

Язык: Английский

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