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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...approach (van der Toorn et al. 2024) could be used to reduce sequencing costs by multiplexing several vectors on a single flow cell. Single-nucleotide polymorphisms (SNPs), however, were difficult to determine from our nanopore direct RNA sequencing due to the relatively higher rate of both random...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
..., a stripe of enriched interactions is detected starting at the CTCF motif and continuing in only one direction. Such directional stripes are hallmarks of blocked loop extrusion and have been reported before (Fudenberg et al. 2016; Vian et al. 2018). Strong evidence for blocked loop extrusion is observed...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...determination. Therefore, integrated analysis of stripes with genomic and epigenomic features at a -wide scale shows vast potential in understanding the cooperation between regulatory elements in 3D nucleome. To this end, we present Quagga, a computational tool for detection and statistical verification...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
..., long-read sequencing-based methods, using single-molecule real-time (SMRT) or nanopore sequencing technology, can directly detect modified bases, eliminating the need for such preprocessing (Moshitch-Moshkovitz et al. 2022; Kong et al. 2023). The SMRT sequencing platform has been adapted for direct RNA...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...CI were carefully chosen because they preserve a 2 large portion of the HIV-1 promoter region of interest in NL4-3-d6-dsGFP reporter virus in the cell line clones. 3 To quantify chromatin interactions, we used the percentage of possible fragments detected (as opposed to 4 direct read numbers) because...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
..., consistent with the conclusions from another independent study (Gohr et al. 2023). These findings suggest that the determinants of splicing order are hardcoded in the .Direct nanopore RNA sequencing (dnRNA-seq) (Garalde et al. 2018) yields long reads that allow for the simultaneous detection of several...
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Method: DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
- Juniper J. Elacqua,
- Navpreet Ranu,
- Sarah E. DiIorio,
- and Paul C. Blainey
Genome Res. January 2021 31: 75-87; Published in Advance December 21, 2020, doi:10.1101/gr.265223.120
...method for nick detection with high resolution, but because it relies on detection via terminal transferase extension, its libraries are not specific to nick sites but represent both double- and single-strand breaks (Cao et al. 2019). Further, owing to the poly(A) tailing at nicks by terminal transferase...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...into the flowcell, the reaction was incubated for 20 min. The remaining steps were identical to the manufacturer's protocol. In our hands, this yielded negligible carryover between runs (0.01%–0.03%).Sample preparation and direct RNA sequencing of independent test data for b96Total RNA was isolated using the All...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...several kilobases in certain contexts. RCA followed by Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) sequencing is a popular protocol adopted in many recent studies, especially for detection of full-length circular RNAs (Liu et al. 2021; Xin et al. 2021; Zhang et al. 2021). A crucial...
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Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
- Gregor Diensthuber,
- Leszek P. Pryszcz,
- Laia Llovera,
- Morghan C. Lucas,
- Anna Delgado-Tejedor,
- Sonia Cruciani,
- Jean-Yves Roignant,
- Oguzhan Begik,
- and Eva Maria Novoa
Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
...contributed equally to this work. Corresponding authors: oguzhan.begik@crg.eu, eva.novoa@crg.euAbstractIn recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, owing to its ability to detect multiple modifications within the same full-length native RNA...

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