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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
..., rely on short reads and offer the ability to transcriptomically compare different cell types but are limited in their ability to measure differential isoform expression. More recently, long-read sequencing methods have been combined with single-cell and spatial technologies in order to characterize...
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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
...variants in the transcriptome (Glinos et al. 2022). Furthermore, long-read sequencing enables comprehensive analysis of splicing (Tilgner et al. 2015, 2018; Joglekar et al. 2021) which has fundamental importance for determining mRNA modifications due to their dependence on splicing patterns and transcript...
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Method: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns
- Alla Mikheenko,
- Andrey D. Prjibelski,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. April 2022 32: 726-737; Published in Advance March 17, 2022, doi:10.1101/gr.276405.121
...than read quality alone. We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.Long-read sequencing is being increasingly used in transcriptomics, particularly for barcoded unique molecules (Gupta et...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...of individual snRNAs drove widespread gene-specific differences in alternative splicing but not transcriptome-wide splicing failure. Genes that were particularly sensitive to variations in snRNA abundance in a breast cancer cell line model were likewise preferentially misspliced within a clinically diverse...
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Research: In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
- F.X. Reymond Sutandy,
- Stefanie Ebersberger,
- Lu Huang,
- Anke Busch,
- Maximilian Bach,
- Hyun-Seo Kang,
- Jörg Fallmann,
- Daniel Maticzka,
- Rolf Backofen,
- Peter F. Stadler,
- Kathi Zarnack,
- Michael Sattler,
- Stefan Legewie,
- and Julian König
Genome Res. May 2018 28: 699-713; Published in Advance April 11, 2018, doi:10.1101/gr.229757.117
..., Germany; 7Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt a.M., Germany ↵8 These authors contributed equally to this work. Corresponding authors: s.legewie@imb-mainz.de, j.koenig@imb-mainz.deAbstractAlternative splicing generates distinct mRNA isoforms...
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Method: Single-molecule long-read sequencing reveals the chromatin basis of gene expression
- Yunhao Wang,
- Anqi Wang,
- Zujun Liu,
- Andrew L. Thurman,
- Linda S. Powers,
- Meng Zou,
- Yue Zhao,
- Adam Hefel,
- Yunyi Li,
- Joseph Zabner,
- and Kin Fai Au
Genome Res. August 2019 29: 1329-1342; Published in Advance June 14, 2019, doi:10.1101/gr.251116.119
...widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...independently of one another in S. pombe. To globally investigate the progression of splicing during transcription, nascent RNA (nRNA) prepared from proliferating S. pombe cells was analyzed by both short- and long-read sequencing (LRS). We report an unexpected coordination between splicing of neighboring...
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Method: From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
- Georgi K. Marinov,
- Brian A. Williams,
- Ken McCue,
- Gary P. Schroth,
- Jason Gertz,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. March 2014 24: 496-510; Published in Advance December 3, 2013, doi:10.1101/gr.161034.113
...-acceptor pair). The presence of alternative splice sites is thus widespread in the cell population. Nevertheless, in most cases, c was close to 1, suggesting quantitative dominance of one isoform. The vastmajority of novel splices received very low inclusion scores (Fig. 5C) and would generally be considered...
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Research: The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
...and androgenotes (Nikaido et al. 2003; Morison et al. 2005; Ruf et al. 2006) and from transcriptome sequencing of embryos resulting from reciprocal crosses (Babak19These authors contributed equally to this work. Corresponding authors: tlappalainen@ny.org, noah. zaitlen@ucsf.edu Article published online before...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...of microRNA dynamics at the single-cell level.microRNAs (miRNAs) are ∼22 nucleotide (nt) small noncoding RNAs that guide Argonaute effector proteins to target mRNAs in a sequence-specific manner, leading to their translational inhibition and increased degradation through deadenylation and decapping (Bartel...
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