Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology DOI Creative Commons
Sergio Alan Cervantes-Pérez,

Sandra Thibivillliers,

Sutton Tennant

et al.

Plant Science, Journal Year: 2022, Volume and Issue: 325, P. 111486 - 111486

Published: Oct. 3, 2022

Language: Английский

Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing DOI Creative Commons
Zhiping Zhang, Bongmin Bae, Winston H. Cuddleston

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 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.

Language: Английский

Citations

16
Single-cell and spatial transcriptomics: Bridging current technologies with long-read sequencing DOI
Chengwei Ulrika Yuan, Fu Xiang Quah, Martin Hemberg

et al.

Molecular Aspects of Medicine, Journal Year: 2024, Volume and Issue: 96, P. 101255 - 101255

Published: Feb. 17, 2024

Language: Английский

Citations

6
Steering research on mRNA splicing in cancer towards clinical translation DOI
Olga Anczuków, Frédéric H.‐T. Allain, Brittany Angarola

et al.

Nature reviews. Cancer, Journal Year: 2024, Volume and Issue: 24(12), P. 887 - 905

Published: Oct. 9, 2024

Language: Английский

Citations

6
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns DOI Creative Commons
Alla Mikheenko, Andrey D. Prjibelski, Anoushka Joglekar

et al.

Genome Research, Journal Year: 2022, Volume and Issue: 32(4), P. 726 - 737

Published: March 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.

Language: Английский

Citations

27
Review: Challenges and perspectives in applying single nuclei RNA-seq technology in plant biology DOI Creative Commons
Sergio Alan Cervantes-Pérez,

Sandra Thibivillliers,

Sutton Tennant

et al.

Plant Science, Journal Year: 2022, Volume and Issue: 325, P. 111486 - 111486

Published: Oct. 3, 2022

Language: Английский

Citations

25