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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...C, 1). In the fusion-type pattern, HBV integration mediated chromosomal translocations or fusions between different chromosomes, resulting in significant genomic rearrangements (Fig. 1C, 2 and 3). HBV bridges the plus and minus strands of the same chromosome, mediating “fold-back” (head...
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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
...for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan Corresponding authors: akimitsu@ric.u-tokyo.ac.jp, kenzui@ric.u-tokyo.ac.jpAbstractRNA modifications play critical roles in cellular homeostasis and development...
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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
...of the balancers were found to be more intricate than previously described, being composed of complex genomic rearrangements (CGRs) such as chromoanagenesis-like events. Furthermore, srWGS revealed additional structural variants and CGRs not known to be part of the balancer s. Altogether, our study provides...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...al. 2010). More recently, the U.S. Food and Drug Administration (FDA) granted accelerated approval for the treatment of solid tumors harboring NTRK fusions with larotrectinib after showing antitumor activity in three multicenter trials (Drilon et al. 2018). For this reason, a routine task in genomics...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
..., Bethlehem, Pennsylvania 18015, USA Corresponding author: matthew.pollard95@gmail.comAbstractMammalia comprises a great diversity of diet types and associated adaptations. An understanding of the genomic mechanisms underlying these adaptations may offer insights for improving human health. Comparative...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...for the majority of differences between isoforms from the same gene. Random forest classifiers implicated coding sequence (CDS) and untranslated region (UTR) lengths as important determinants of isoform-specific sedimentation profiles, and motif analyses reveal potential cell type–specific and subcellular fraction...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...as a heterogametic sex and the XY system for these species, which was validated for zebra shark by genomic quantitative polymerase chain reaction (PCR) (Fig. 5B). Next, we investigated the origin of the putative X Chromosome of these species—was it derived from the same ancestral chromosomes that were differentiated...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...10 chromosome fusion events in 6 million years of butterfly evolution. G3 (Bethesda) 6: 695–708. doi:10.1534/g3.115.023655 ↵Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20: 238. doi:10.1186/s13059-019-1832-y ↵Fallon TR, Lower SE, Chang C...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...Kingdom ↵6 Present address: Enhanc3D Genomics Ltd., Cambridge CB4 0DS, UK Corresponding author: dimitris.lagos@york.ac.ukAbstractThe use of long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) in clinical oncology remains limited, with no direct comparison between the two methods. We used...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...be converted to cluster 1 in FSHD-hi myotubes via DUX4 and target transcription factor proteins cross-migration through the cytoplasm post-fusion.Corresponding gene expression analyses reveal progressive gene expression changes along the pseudotime trajectory, reflecting cell state alteration (Fig. 4L...
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