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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...to a karyotypically normal reference . This needs to be addressed if further progress in understanding the 3D cancer is to be achieved.In conclusion, our findings provide new insights into the complex genomic structural changes that underlie breast cancer metastatic progression. The interplay between subcompartment...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...short, spliced isoforms exist in the Schwann cells because our current data did not have the resolution to resolve alternative splicing. Distinct XIST isoforms have been reported (Johnston et al. 1998; Memili et al. 2001; Yue and Ogawa 2018), but the documented isoforms are not related to the s...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...) exon 22 responds to activity through both SAM68, an RBP splicing regulator, and deposition of the hPTM H3K9me3 in a region- and stimuli-specific manner, and underlies learning and memory (Iijima et al. 2011; Ding et al. 2017). H3K9ac is also associated with alternative splicing outcomes of neuronal...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...by scRNA-seq data (Supplemental Fig. S9B,C), suggests that SF3B1 mutations may not play a significant role in the development of acquired venetoclax resistance in CLL cells.DiscussionCell identity and function could be influenced by the alternative splicing of transcripts which will result...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
..., Denmark; 7Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas 78758, USA Co-corresponding authors: bs674@cornell.edu, ramstein@qgg.au.dkAbstractVariation in protein 3D structures reflects genetic variation and contributes to phenotypic diversity, yet its underlying genetic...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...alternatively spliced fusion isoforms are evident from both long and short reads, and most long reads appear to yield full-length fusion transcript isoforms, whereas the short reads primarily yield fusion isoform breakpoint positions.Fusion transcript detection accuracy using simulated long reads...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...′ UTR of the CD47 gene, significantly impacts gene splicing and is strongly associated with reproductive phenotypes. Additionally, we observe that neuronal cells generally possess longer 3′ UTRs—a pattern conserved across humans, mice, fruit flies, and pigs. Together, these findings enrich the single...
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Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
- Mayank Murali,
- Jamie Saquing,
- Senbao Lu,
- Ziyang Gao,
- Emily F. Watts,
- Ben Jordan,
- Zachary Peters Wakefield,
- Ana Fiszbein,
- David R. Cooper,
- Peter J. Castaldi,
- Dmitry Korkin,
- and Gloria M. Sheynkman
Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
...the functionality of downstream protein products. We introduce Biosurfer, a computational approach for comparing protein isoforms, while systematically tracking the transcriptional, splicing, and translational variations that underlie differences in the sequences of the protein products. Using Biosurfer, we...

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