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Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
- Gianluca Mattei,
- Marta Baragli,
- Barbara Gega,
- Alessandra Mingrino,
- Martina Chieca,
- Tommaso Ducci,
- Gianmaria Frigè,
- Luca Mazzarella,
- Romina D'Aurizio,
- Francesco De Logu,
- Romina Nassini,
- Pier Giuseppe Pelicci,
- and Alberto Magi
Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
...studies demonstrated that DNA methylation at transcription factor binding sites (TFBSs) can influence gene expression by regulating the ability of TFs to bind to their target DNA sequences (Kaluscha et al. 2022). These findings demonstrate the fundamental importance of studying the colocalization between...
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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
...sequencing by replacing the standard DNA polymerase with a reverse transcriptase (Vilfan et al. 2013), although this approach has not been widely adopted. Nanopore direct RNA sequencing has made it possible to directly sequence full-length native RNA molecules without reverse transcription and amplification...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...RCS. It should be noted that, although NanoRCS enables more accurate SNV detection in cfDNA, native Nanopore sequencing has the advantage of incorporating methylation as an additional modality that can be captured (Simpson et al. 2017; Lau et al. 2023). Future improvements of NanoRCS include encompassing even...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...estimationBefore designing a skimming experiment, it is necessary to determine the minimum level of sequencing depth to obtain sufficient precision for statistical power. A single chimpanzee was sequenced to 11.2× depth using a nanopore PromethION instrument and global DNA methylation assessed at 82...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...for parental DNA to determine the origin of the variant and direction of the skew, and additional genetic testing to ascertain the deleterious variant. A sequencing-based version of this test has recently been proposed (Johansson et al. 2023), directly reading the methylation of the AR and RP2 CpG islands...
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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
...and Chiron and DeepNano for DNA (Boža et al. 2017; Teng et al. 2018; Neumann et al. 2022), among others. However, the effect of using alternative basecalling models on the detection of RNA modifications has so far not been explored.Here we present two novel basecalling models, IVT and SUP (Supplemental Table...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...of repetitive DNA such as the D4Z4 arrays important in FSHD (Nurk et al. 2022). Long-read sequencing technologies, such as nanopore sequencing not only open the door to the full sequencing of the D4Z4 array, but also allow determination of CpG methylation within the array, a critical aspect of genetic analysis...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...this combination of data types has proven effective, it complicates data generation and limits accessibility, especially in developing countries where instrument placement is expensive and limited (Helmy et al. 2016).Nanopore-based DNA sequencing relies on single-stranded molecules passing through a pore embedded...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...for estimating tumor load and identifying the tissue of origin across a wide range of cancer types (Guo et al. 2017; Moss et al. 2018; Liu et al. 2020). Enrichment strategies like cfMeDIP have been used to focus methylation profiling on cfDNA to establish cancer-specific patterns for early detection...
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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...↵Sigurpalsdottir BD, Stefansson OA, Holley G, Beyter D, Zink F, Hardarson MÞ, Sverrisson SÞ, Kristinsdottir N, Magnusdottir DN, Magnusson OÞ, et al. 2024. A comparison of methods for detecting DNA methylation from long-read sequencing of human s. Genome Biol 25: 69. doi:10.1186/s13059-024-03207-9 ↵Sollis E, Mosaku...

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