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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...-linked transcription regulators by depleting them in primary cultured neurons. We then define the resulting gene expression disruptions using RNA sequencing and test effects on neuronal firing using multielectrode array recordings. We identify shared gene expression signatures across many ASD risk genes that converge...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...N-increased ATAC-seq peaks found patterns characteristic of basic helix–loop–helix (bHLH) neurogenic TF consensuses (Fig. 4E), corroborating the potential functionality of CrxK88N-increased ATAC-seq peaks in regulating neurogenic programs during normal development. Gene Ontology (GO) analysis...
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Research: A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
- Jesper Eisfeldt,
- Adam Ameur,
- Felix Lenner,
- Esmee Ten Berk de Boer,
- Marlene Ek,
- Josephine Wincent,
- Raquel Vaz,
- Jesper Ottosson,
- Tord Jonson,
- Sofie Ivarsson,
- Sofia Thunström,
- Alexandra Topa,
- Simon Stenberg,
- Anna Rohlin,
- Anna Sandestig,
- Margareta Nordling,
- Pia Palmebäck,
- Magnus Burstedt,
- Frida Nordin,
- Eva-Lena Stattin,
- Maria Sobol,
- Panagiotis Baliakas,
- Marie-Louise Bondeson,
- Ida Höijer,
- Kristine Bilgrav Saether,
- Lovisa Lovmar,
- Hans Ehrencrona,
- Malin Melin,
- Lars Feuk,
- and Anna Lindstrand
Genome Res. November 2024 34: 1774-1784; Published in Advance October 29, 2024, doi:10.1101/gr.279510.124
...50 bp. When SVs involve a repositioning of genetic material either within a chromosome or between chromosomes, they are also referred to as chromosomal rearrangements. These encompass both recurrent and nonrecurrent copy number variations (CNVs, deletions, and duplications) and balanced chromosome...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
..., and four origin recognition complex (ORC) components are all enriched in GSC-like cells compared with CySC-like cells (Table 1).View this table: In this window In a new window Table 1. Composition and function of select DNA replication and chromatin regulation complexesTo control for potential biases...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...structures, methylation patterns, and transcriptional regulation associated with these loci. Our analysis revealed the extent of cis-linked genomic dysregulation resulting from HPV integration, including structural rearrangements and modulation of virus and host gene expression and epigenetic regulation...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...al. 2021). Subtelomeres are often involved in telomere-associated rearrangements owing to their repetitive nature promoting HDR, replication fork stalling and template switching (FoSTeS), and BIR (Corcoran et al. 1988; Louis and Haber 1990; Linardopoulou et al. 2005; Kuo et al. 2006; Rudd et al. 2007...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...of Chromosome 8 and restore euploidy in cells derived from an individual with a complex rearrangement of Chromosome 8p. Transcriptomic analysis revealed 361 differentially expressed genes between the proband and the euploid revertant, highlighting genes both within and outside the 8p region that may contribute...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...driver of divergence. The loss of syntenic regions also contribute to divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus divergence.Genomes from all kingdoms are highly organized but vary...
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