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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...H, Fuda NJ, Core LJ, Lis JT. 2013. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339: 950–953. doi:10.1126/science.1229386 ↵Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ Protein A–transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...by bacterial DNA modifications (Rand et al. 2017; Wick et al. 2019). Bacterial DNA methylation can occur frequently in diverse sequence contexts. In nanopore direct RNA sequencing, mismatches in modified RNA molecules can be used to detect modifications (Liu et al. 2019). However, this feature has not been...
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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...for GAPDH-201 in different samples and protocols. Data includes HEK293T and colorectal samples (center1), sequenced with a hexamer-based Ribo-off rRNA depletion protocol, and MCF-7 samples (center2), sequenced with a hexamer-based oligo(dT) mRNA enrichment workflow. Additionally, HEK293T samples were...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (sRNA...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, et al. 2003. Antisense transcripts with rice full-length cDNAs. Genome Biol 5: R5. Ozsolak F, Milos PM. 2011. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12: 87–98. Peisley A, Jo MH, Lin C, Wu B...
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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
...guide RNA or with up to two mismatches and a 2-nt DNA or RNA bulge. Analyzing these locations for sequence reads and mutational signal enabled the identification of 53 sites with strong evidence for off-target activity (Fig. 6C; Supplemental Table S5). These off-target sites were generally concordant...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...on by a specific CRISPR–RNA complex relies on molecular biology protocols that can recognize and isolate the product of the CRISPR–DNA reaction—typically a double-stranded (DSB) or single-stranded break (SSB, or “nick”) in the DNA—using high-throughput sequencing to determine the sequence of those sites and map...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...before (Tan et al. 2022). ONT sequencing relies on detecting alterations in electrical conductance as single-stranded DNA traverses through a protein nanopore. Because the pore accommodates ∼6 nucleotides at a time, the raw signal reflects the joint effects of several bases and must be deconvoluted...
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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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